Equivalence class DNA_3.0_20780.2 Current
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | #NTs | Date |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 2VBL|1|C+ 2VBL|1|E+ 2VBL|1|S+ 2VBL|1|T (rep) | 5'-D(*DA*DA*DA*DA*DG*DG*DC*DA*DG*DAP)-3', 5'-D(*DA*DG*DG*DA*DT*DC*DC*DT*DA*DAP)-3', 5'-D(*DT*DC*DT*DG*DC*DC*DT*DT*DT*DT*DT*DT *DGP*DAP)-3', 5'-D(*DT*DT*DA*DG*DG*DA*DT*DC*DC*DT*DT*DC *DAP*DAP)-3' | Molecular basis of human XPC gene recognition and cleavage by engineered homing endonuclease heterodimers | X-ray diffraction | 1.8 | 48 | 2008-10-28 | ||||
| 2 | 3MXA|1|C+ 3MXA|1|E+ 3MXA|1|D+ 3MXA|1|F | DNA (5'-D(*TP*CP*TP*GP*GP*CP*TP*GP*AP*GP*GP*TP*AP*C)-3'), DNA (5'-D(*TP*TP*GP*TP*TP*CP*TP*CP*AP*GP*GP*TP*AP*C)-3'), DNA (5'-D(P*CP*TP*CP*AP*GP*CP*CP*AP*GP*A)-3'), DNA (5'-D(P*CP*TP*GP*AP*GP*AP*AP*CP*AP*A)-3') | Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus | X-ray diffraction | 2.3 | 48 | 2010-10-06 | ||||
| 3 | 2VBN|1|C+ 2VBN|1|E+ 2VBN|1|S+ 2VBN|1|T | 5'-D(*AP*AP*AP*AP*GP*GP*CP*AP*GP*AP)-3', 5'-D(*AP*GP*GP*AP*TP*CP*CP*TP*AP*AP)-3', 5'-D(*TP*CP*TP*GP*CP*CP*TP*TP*TP*TP *TP*TP*GP*AP)-3', 5'-D(*TP*TP*AP*GP*GP*AP*TP*CP*CP*TP *TP*CP*AP*AP)-3' | Molecular basis of human XPC gene recognition and cleavage by engineered homing endonuclease heterodimers | X-ray diffraction | 1.9 | 48 | 2008-10-28 | ||||
| 4 | 1N3F|1|C+ 1N3F|1|E+ 1N3F|1|D+ 1N3F|1|F | 5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*GP*A)-3', 5'-D(P*GP*AP*CP*AP*GP*TP*TP*TP*CP*G-3') | Crystal structure of I-CreI bound to a palindromic DNA sequence II (palindrome of right side of wildtype DNA target sequence) | X-ray diffraction | 2 | 48 | 2003-06-03 | ||||
| 5 | 1N3F|1|I+ 1N3F|1|K+ 1N3F|1|J+ 1N3F|1|L | 5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*GP*A)-3', 5'-D(P*GP*AP*CP*AP*GP*TP*TP*TP*CP*G-3') | Crystal structure of I-CreI bound to a palindromic DNA sequence II (palindrome of right side of wildtype DNA target sequence) | X-ray diffraction | 2 | 48 | 2003-06-03 | ||||
| 6 | 1N3E|1|C+ 1N3E|1|E+ 1N3E|1|D+ 1N3E|1|F | 5'-D(*CP*GP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*C)-3', 5'-D(P*GP*AP*CP*GP*TP*TP*TP*TP*CP*G)-3' | Crystal structure of I-CreI bound to a palindromic DNA sequence I (palindrome of left side of wildtype DNA target sequence) | X-ray diffraction | 2.5 | 48 | 2003-06-03 | ||||
| 7 | 1N3E|1|I+ 1N3E|1|K+ 1N3E|1|J+ 1N3E|1|L | 5'-D(*CP*GP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*C)-3', 5'-D(P*GP*AP*CP*GP*TP*TP*TP*TP*CP*G)-3' | Crystal structure of I-CreI bound to a palindromic DNA sequence I (palindrome of left side of wildtype DNA target sequence) | X-ray diffraction | 2.5 | 48 | 2003-06-03 | ||||
| 8 | 2GIG|1|E+ 2GIG|1|F | 5'-D(*GP*CP*CP*GP*GP*TP*CP*GP*AP*CP*CP*GP*GP*C)-3' | Alteration of sequence specificity of the type II restriction endonuclease HINCII through an indirect readout mechanism | X-ray diffraction | 1.83 | 28 | 2006-07-18 | ||||
| 9 | 3C58|1|B+ 3C58|1|C | DNA (5'-D(*DCP*DTP*DCP*DTP*DTP*DTP*(SOS)P*DTP*DTP*DTP*DCP*DTP*DCP*DG)-3'), DNA (5'-D(*DGP*DCP*DGP*DAP*DGP*DAP*DAP*DAP*DCP*DAP*DAP*DAP*DGP*DA)-3') | Crystal structure of a complex between the wild-type lactococcus lactis Fpg (MutM) and a N7-Benzyl-Fapy-dG containing DNA | X-ray diffraction | 1.9 | 28 | 2008-12-16 | ||||
| 10 | 3E40|1|E+ 3E40|1|F | 5'-D(*DGP*DCP*DCP*DGP*DGP*DTP*DP*DAP*DAP*DCP*DCP*DGP*DGP*DC)-3') | Q138F HincII bound to GTTAAC and cocrystallized with 5 mM Ca2+ | X-ray diffraction | 2.1 | 28 | 2008-08-26 | ||||
| 11 | 3E3Y|1|E+ 3E3Y|1|F | 5'-D(*DGP*DCP*DCP*DGP*DGP*DTP*DTP*DAP*DAP*DCP*DCP*DGP*DGP*DC)-3' | Q138F HincII bound to GTTAAC and cocrystallized with 5 mM Ca2+ | X-ray diffraction | 2.13 | 28 | 2008-08-26 | ||||
| 12 | 1TDZ|1|B+ 1TDZ|1|C | 5'-D(*CP*TP*CP*TP*TP*TP*(FOX)P*TP*TP*TP*CP*TP*CP*G)-3', 5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3' | Crystal Structure Complex Between the Lactococcus Lactis FPG (Mutm) and a FAPY-dG Containing DNA | X-ray diffraction | 1.8 | 28 | 2004-09-07 | ||||
| 13 | 1PJJ|1|D+ 1PJJ|1|E | DNA (5'-D(*CP*TP*CP*TP*TP*TP*(3DR)P*TP*TP*TP*CP*TP*CP*G)-3'), DNA (5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3') | Complex between the Lactococcus lactis Fpg and an abasic site containing DNA. | X-ray diffraction | 1.9 | 28 | 2004-06-08 | ||||
| 14 | 1PJI|1|D+ 1PJI|1|E | DNA (5'-D(*CP*TP*CP*TP*TP*TP*(PDI)P*TP*TP*TP*CP*TP*CP*G)-3'), DNA (5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3') | Crystal structure of wild type Lactococcus lactis FPG complexed to a 1,3 propanediol containing DNA | X-ray diffraction | 1.9 | 27 | 2004-08-03 | ||||
| 15 | 1MNN|1|B+ 1MNN|1|C | 5'-D(*AP*GP*TP*TP*TP*TP*TP*GP*TP*GP*TP*CP*GP*C)-3', 5'-D(*TP*GP*CP*GP*AP*CP*AP*CP*AP*AP*AP*AP*AP*C)-3' | Structure of the sporulation specific transcription factor Ndt80 bound to DNA | X-ray diffraction | 1.4 | 28 | 2002-11-20 | ||||
| 16 | 1XC8|1|B+ 1XC8|1|C | 5'-D(*CP*TP*CP*TP*TP*TP*(FOX)P*TP*TP*TP*CP*TP*CP*G)-3', 5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3' | CRYSTAL STRUCTURE COMPLEX BETWEEN THE WILD-TYPE LACTOCOCCUS LACTIS FPG (MUTM) AND A FAPY-DG CONTAINING DNA | X-ray diffraction | 1.95 | 28 | 2005-09-06 | ||||
| 17 | 1PM5|1|D+ 1PM5|1|E | DNA (5'-D(*CP*TP*CP*TP*TP*TP*(3DR)P*TP*TP*TP*CP*TP*CP*G)-3'), DNA (5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3') | Crystal structure of wild type Lactococcus lactis Fpg complexed to a tetrahydrofuran containing DNA | X-ray diffraction | 1.95 | 28 | 2004-07-27 | ||||
| 18 | 1NNJ|1|D+ 1NNJ|1|E | 5'-D(*CP*TP*CP*TP*TP*TP*(PDI)P*TP*TP*TP*CP*TP*CP*G)-3', 5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3' | Crystal structure Complex between the Lactococcus lactis Fpg and an abasic site containing DNA | X-ray diffraction | 1.9 | 27 | 2003-02-11 | ||||
| 19 | 2GIJ|1|E+ 2GIJ|1|F | 5'-D(*GP*CP*CP*GP*GP*TP*TP*AP*AP*CP*CP*GP*GP*C)-3' | Q138F HincII bound to cognate DNA GTTAAC and Ca2+ | X-ray diffraction | 1.93 | 28 | 2006-07-18 | ||||
| 20 | 2EVF|1|B+ 2EVF|1|C | 5'-D(*AP*GP*TP*TP*TP*TP*AP*GP*TP*GP*TP*CP*GP*C)-3', 5'-D(*TP*GP*CP*GP*AP*CP*AP*CP*TP*AP*AP*AP*AP*C)-3' | Structure of a Ndt80-DNA complex (MSE mutant mA6T) | X-ray diffraction | 1.56 | 27 | 2006-03-21 | ||||
| 21 | 2EUX|1|B+ 2EUX|1|C | 5'-D(*AP*GP*TP*TP*TP*TP*TP*GP*CP*GP*TP*CP*GP*C)-3', 5'-D(*TP*GP*CP*GP*AP*CP*GP*CP*AP*AP*AP*AP*AP*C)-3' | Structure of a Ndt80-DNA complex (MSE VARIANT vA4G) | X-ray diffraction | 1.57 | 28 | 2006-03-21 | ||||
| 22 | 3LNQ|1|B+ 3LNQ|1|C | 5'-D(*CP*CP*CP*TP*AP*AP*TP*TP*AP*AP*AP*CP*CP*C)-3', 5'-D(*GP*GP*GP*TP*TP*TP*AP*AP*TP*TP*AP*GP*GP*G)-3' | Structure of Aristaless homeodomain in complex with DNA | X-ray diffraction | 2.25 | 28 | 2010-04-28 | ||||
| 23 | 2EVG|1|B+ 2EVG|1|C | 5'-D(*AP*GP*TP*TP*TP*AP*TP*GP*TP*GP*TP*CP*GP*C)-3', 5'-D(*TP*GP*CP*GP*AP*CP*AP*CP*AP*TP*AP*AP*AP*C)-3' | Structure of a Ndt80-DNA complex (MSE mutant mA7T) | X-ray diffraction | 1.55 | 27 | 2006-03-21 | ||||
| 24 | 2EUZ|1|B+ 2EUZ|1|C | 5'-D(*AP*GP*TP*TP*TP*TP*TP*AP*TP*GP*TP*CP*GP*C)-3', 5'-D(*TP*GP*CP*GP*AP*CP*AP*TP*AP*AP*AP*AP*AP*C)-3' | Structure of a Ndt80-DNA complex (MSE mutant mC5T) | X-ray diffraction | 1.56 | 27 | 2006-03-21 | ||||
| 25 | 1LV5|1|F+ 1LV5|1|E | 5'-D(*AP*CP*GP*TP*CP*GP*CP*TP*GP*AP*TP*CP*CP*G)-3', 5'-D(*GP*GP*AP*TP*CP*AP*GP*CP*GP*A)-3' | Crystal Structure of the Closed Conformation of Bacillus DNA Polymerase I Fragment Bound to DNA and dCTP | X-ray diffraction | 1.95 | 24 | 2003-03-25 | ||||
| 26 | 2EUW|1|B+ 2EUW|1|C | 5'-D(*AP*GP*TP*TP*TP*TP*TP*GP*AP*GP*TP*CP*GP*C)-3', 5'-D(*TP*GP*CP*GP*AP*CP*TP*CP*AP*AP*AP*AP*AP*C)-3' | Structure of a Ndt80-DNA complex (MSE mutant mA4T) | X-ray diffraction | 1.68 | 27 | 2006-03-21 | ||||
| 27 | 2YVH|1|E+ 2YVH|1|F | 5'-D(*DGP*DGP*DTP*DCP*DGP*DGP*DTP*DAP*DCP*DAP*DGP*DTP*DTP*DA)-3', 5'-D(*DTP*DAP*DAP*DCP*DTP*DGP*DTP*DAP*DCP*DCP*DGP*DAP*DCP*DC)-3' | Crystal structure of the operator-binding form of the multi-drug binding transcriptional repressor CgmR | X-ray diffraction | 2.5 | 28 | 2008-04-15 | ||||
| 28 | 1LV5|1|D+ 1LV5|1|C | 5'-D(*AP*CP*GP*TP*CP*GP*CP*TP*GP*AP*TP*CP*CP*G)-3', 5'-D(*GP*GP*AP*TP*CP*AP*GP*CP*GP*A)-3' | Crystal Structure of the Closed Conformation of Bacillus DNA Polymerase I Fragment Bound to DNA and dCTP | X-ray diffraction | 1.95 | 24 | 2003-03-25 | ||||
| 29 | 2EVH|1|B+ 2EVH|1|C | 5'-D(*AP*GP*TP*TP*TP*CP*TP*GP*TP*GP*TP*CP*GP*C)-3', 5'-D(*TP*GP*CP*GP*AP*CP*AP*CP*AP*GP*AP*AP*AP*C)-3' | Structure of a Ndt80-DNA complex (MSE mutant mA7G) | X-ray diffraction | 1.989 | 27 | 2006-03-21 | ||||
| 30 | 3D1N|1|E+ 3D1N|1|F | 5'-D(*DAP*DGP*DCP*DAP*DTP*DAP*DAP*DAP*DTP*DAP*DAP*DTP*DAP*DA)-3', 5'-D(*DTP*DTP*DAP*DTP*DTP*DAP*DTP*DTP*DTP*DAP*DTP*DGP*DCP*DT)-3' | Structure of human Brn-5 transcription factor in complex with corticotrophin-releasing hormone gene promoter | X-ray diffraction | 2.51 | 28 | 2009-05-26 | ||||
| 31 | 2GIH|1|E+ 2GIH|1|F | 5'-D(*GP*CP*CP*GP*GP*TP*CP*GP*AP*CP*CP*GP*GP*C)-3' | Q138F HincII bound to cognate DNA GTCGAC and Ca2+ | X-ray diffraction | 2.5 | 28 | 2006-07-18 | ||||
| 32 | 3D1N|1|A+ 3D1N|1|B | 5'-D(*DAP*DGP*DCP*DAP*DTP*DAP*DAP*DAP*DTP*DAP*DAP*DTP*DAP*DA)-3', 5'-D(*DTP*DTP*DAP*DTP*DTP*DAP*DTP*DTP*DTP*DAP*DTP*DGP*DCP*DT)-3' | Structure of human Brn-5 transcription factor in complex with corticotrophin-releasing hormone gene promoter | X-ray diffraction | 2.51 | 28 | 2009-05-26 | ||||
| 33 | 2EVI|1|B+ 2EVI|1|C | 5'-D(*AP*GP*TP*TP*AP*TP*TP*GP*TP*GP*TP*CP*GP*C)-3', 5'-D(*TP*GP*CP*GP*AP*CP*AP*CP*AP*AP*TP*AP*AP*C)-3' | Structure of a Ndt80-DNA complex (MSE mutant mA8T) | X-ray diffraction | 1.8 | 27 | 2006-03-21 | ||||
| 34 | 2GII|1|E+ 2GII|1|F | 5'-D(*GP*CP*CP*GP*GP*TP*TP*AP*AP*CP*CP*GP*GP*C)-3' | Q138F HincII bound to cognate DNA GTTAAC | X-ray diffraction | 2.3 | 28 | 2006-07-18 | ||||
| 35 | 2ETW|1|B+ 2ETW|1|C | 5'-D(*AP*GP*TP*TP*TP*TP*TP*GP*TP*GP*TP*GP*GP*C)-3', 5'-D(*TP*GP*CP*CP*AP*CP*AP*CP*AP*AP*AP*AP*AP*C)-3' | Principles of protein-DNA recognition revealed in the structural analysis of Ndt80-MSE DNA complexes | X-ray diffraction | 1.67 | 27 | 2006-03-21 | ||||
| 36 | 3D1N|1|C+ 3D1N|1|D | 5'-D(*DAP*DGP*DCP*DAP*DTP*DAP*DAP*DAP*DTP*DAP*DAP*DTP*DAP*DA)-3', 5'-D(*DTP*DTP*DAP*DTP*DTP*DAP*DTP*DTP*DTP*DAP*DTP*DGP*DCP*DT)-3' | Structure of human Brn-5 transcription factor in complex with corticotrophin-releasing hormone gene promoter | X-ray diffraction | 2.51 | 28 | 2009-05-26 | ||||
| 37 | 2EVJ|1|B+ 2EVJ|1|C | 5'-D(*AP*GP*TP*GP*TP*TP*TP*GP*TP*GP*TP*CP*GP*C)-3', 5'-D(*TP*GP*CP*GP*AP*CP*AP*CP*AP*AP*AP*CP*AP*C)-3' | Structure of an Ndt80-DNA complex (MSE mutant mA9C) | X-ray diffraction | 1.89 | 27 | 2006-03-21 | ||||
| 38 | 2D5V|1|C+ 2D5V|1|D | 5'-D(*AP*TP*TP*AP*TP*TP*GP*AP*CP*TP*TP*AP*GP*A)-3', 5'-D(*TP*CP*TP*AP*AP*GP*TP*CP*AP*AP*TP*AP*AP*T)-3' | Crystal structure of HNF-6alpha DNA-binding domain in complex with the TTR promoter | X-ray diffraction | 2 | 27 | 2006-12-05 | ||||
| 39 | 2EUV|1|B+ 2EUV|1|C | 5'-D(*AP*GP*TP*AP*TP*TP*TP*GP*TP*GP*TP*TP*GP*C)-3', 5'-D(*TP*GP*CP*AP*AP*CP*AP*CP*AP*AP*AP*TP*AP*C)-3' | Principles of protein-DNA recognition revealed in the structural analysis of Ndt80-MSE DNA complexes | X-ray diffraction | 1.94 | 25 | 2006-03-21 | ||||
| 40 | 2YVH|1|G+ 2YVH|1|H | 5'-D(*DGP*DGP*DTP*DCP*DGP*DGP*DTP*DAP*DCP*DAP*DGP*DTP*DTP*DA)-3', 5'-D(*DTP*DAP*DAP*DCP*DTP*DGP*DTP*DAP*DCP*DCP*DGP*DAP*DCP*DC)-3' | Crystal structure of the operator-binding form of the multi-drug binding transcriptional repressor CgmR | X-ray diffraction | 2.5 | 28 | 2008-04-15 | ||||
| 41 | 3D1N|1|G+ 3D1N|1|H | 5'-D(*DAP*DGP*DCP*DAP*DTP*DAP*DAP*DAP*DTP*DAP*DAP*DTP*DAP*DA)-3', 5'-D(*DTP*DTP*DAP*DTP*DTP*DAP*DTP*DTP*DTP*DAP*DTP*DGP*DCP*DT)-3' | Structure of human Brn-5 transcription factor in complex with corticotrophin-releasing hormone gene promoter | X-ray diffraction | 2.51 | 28 | 2009-05-26 | ||||
| 42 | 1JJ8|1|A+ 1JJ8|1|B | 5'-D(*AP*TP*CP*TP*TP*AP*TP*CP*AP*AP*AP*AP*AP*C)-3', 5'-D(*TP*GP*(5IT)P*TP*TP*TP*TP*GP*AP*TP*AP*AP*GP*A)-3' | Testing the Water-Mediated HIN Recombinase DNA Recognition by Systematic Mutations | X-ray diffraction | 2.75 | 28 | 2002-02-22 | ||||
| 43 | 3E43|1|E+ 3E43|1|F | 5'-D(*DGP*DCP*DCP*DGP*DGP*DTP*DTP*DAP*DAP*DCP*DCP*DGP*DGP*DC)-3' | Q138F HincII bound to GTTAAC and cocrystallized with 2.5 mM MgCl2 | X-ray diffraction | 2.73 | 28 | 2008-08-26 | ||||
| 44 | 3EBC|1|E+ 3EBC|1|F | 5'-D(*DGP*DCP*DCP*DCP*DGP*DTP*DCP*DGP*DAP*DCP*DCP*DGP*DGP*DC)-3', 5'-D(*DGP*DCP*DCP*DGP*DGP*DTP*DCP*DGP*DAP*DCP*DGP*DGP*DGP*DC)-3' | Structure of N141A HincII with Cognate DNA | X-ray diffraction | 2.55 | 28 | 2008-12-23 | ||||
| 45 | 1UA0|1|C+ 1UA0|1|B | DNA primer strand, DNA template strand with aminofluorene adduct | Aminofluorene DNA adduct at the pre-insertion site of a DNA polymerase | X-ray diffraction | 2.1 | 21 | 2004-09-28 | ||||
| 46 | 3E41|1|E+ 3E41|1|F | 5'-D(*DGP*DCP*DCP*DGP*DGP*DTP*DCP*DGP*DAP*DCP*DCP*DGP*DGP*DC)-3' | Q138F HincII bound to GTCGAC and 5 mM Ca2+ | X-ray diffraction | 2.73 | 28 | 2008-08-26 | ||||
| 47 | 3E45|1|E+ 3E45|1|F | 5'-D(*DGP*DCP*DCP*DGP*DGP*DTP*DGP*DCP*DAP*DCP*DCP*DGP*DGP*DC)-3' | Q138F HincII bound to Noncognate DNA (GTGCAC) and Ca2+ | X-ray diffraction | 2.78 | 28 | 2008-08-26 | ||||
| 48 | 2H7F|1|Z+ 2H7F|1|Y | 5'-D(*TP*AP*AP*TP*AP*AP*GP*GP*GP*CP*GP*AP*CP*A)-3', 5'-D(*TP*TP*GP*TP*CP*GP*CP*CP*CP*TP*T)-3' | Structure of variola topoisomerase covalently bound to DNA | X-ray diffraction | 2.7 | 25 | 2006-08-15 | ||||
| 49 | 1UA1|1|C+ 1UA1|1|B | DNA primer strand, DNA template strand with aminofluorene adduct | Structure of aminofluorene adduct paired opposite cytosine at the polymerase active site. | X-ray diffraction | 2 | 23 | 2004-09-28 | ||||
| 50 | 1VRR|1|C+ 1VRR|1|D | 5'-D(*TP*TP*AP*TP*AP*GP*AP*TP*CP*TP*AP*TP*AP*A)-3' | Crystal structure of the restriction endonuclease BstYI complex with DNA | X-ray diffraction | 2.7 | 28 | 2005-06-07 | ||||
| 51 | 3E42|1|E+ 3E42|1|F | 5'-D(*DGP*DCP*DCP*DGP*DGP*DTP*DCP*DGP*DAP*DCP*DCP*DGP*DGP*DC)-3' | Q138F HincII bound to GTCGAC and Ca2+ (cocrystallized) | X-ray diffraction | 2.68 | 28 | 2008-08-26 | ||||
| 52 | 2D5V|1|E+ 2D5V|1|F | 5'-D(*AP*TP*TP*AP*TP*TP*GP*AP*CP*TP*TP*AP*GP*A)-3', 5'-D(*TP*CP*TP*AP*AP*GP*TP*CP*AP*AP*TP*AP*AP*T)-3' | Crystal structure of HNF-6alpha DNA-binding domain in complex with the TTR promoter | X-ray diffraction | 2 | 26 | 2006-12-05 | ||||
| 53 | 3CMY|1|B+ 3CMY|1|C | 5'-D(*DAP*DCP*DAP*DTP*DAP*DAP*DP*DCP*DGP*DAP*DTP*DTP*DAP*DC)-3', 5'-D(*DTP*DGP*DTP*DAP*DAP*DTP*DCP*DGP*DAP*DTP*DTP*DAP*DTP*DG)-3' | Structure of a homeodomain in complex with DNA | X-ray diffraction | 1.95 | 15 | 2009-02-17 | ||||
| 54 | 2HHS|1|C+ 2HHS|1|B | 5'-D(*CP*AP*TP*(6OG)P*CP*GP*AP*GP*TP*CP*AP*GP*G)-3', 5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*GP*CP*AP*TP*GP*A)-3' | O6-methyl:C pair in the polymerase-10 basepair position | X-ray diffraction | 1.8 | 27 | 2006-12-12 | ||||
| 55 | 2PYL|1|Y+ 2PYL|1|X | 5'-d(CTGACGAATGTACA)-3', 5'-d(GACTGCTTAC(2DA))-3' | Phi29 DNA polymerase complexed with primer-template DNA and incoming nucleotide substrates (ternary complex) | X-ray diffraction | 2.2 | 25 | 2007-07-17 | ||||
| 56 | 1YQR|1|B+ 1YQR|1|C | 5'-D(P*CP*GP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3', 5'-D(P*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3' | Catalytically inactive human 8-oxoguanine glycosylase crosslinked to oxoG containing DNA | X-ray diffraction | 2.43 | 28 | 2005-04-05 | ||||
| 57 | 3EI1|1|G+ 3EI1|1|H | 5'-D(*DAP*DCP*DGP*DCP*DGP*DAP*(64T)P*(5PY)P*DGP*DCP*DGP*DCP*DCP*DC)-3', 5'-D(*DTP*DGP*DGP*DGP*DCP*DGP*DCP*DAP*DAP*DTP*DCP*DGP*DCP*DG)-3' | Structure of hsDDB1-drDDB2 bound to a 14 bp 6-4 photoproduct containing DNA-duplex | X-ray diffraction | 2.8 | 28 | 2009-01-20 | ||||
| 58 | 1T3N|1|T+ 1T3N|1|P | Primer DNA strand, Template DNA strand | Structure of the catalytic core of DNA polymerase Iota in complex with DNA and dTTP | X-ray diffraction | 2.3 | 27 | 2004-07-20 | ||||
| 59 | 3GP8|1|X | 5'-D(*TP*TP*TP*TP*TP*T*TP*TP*TP*TP*TP*TP*TP*T)-3' | Crystal structure of the binary complex of RecD2 with DNA | X-ray diffraction | 2.5 | 8 | 2009-06-16 | ||||
| 60 | 1ZET|1|T+ 1ZET|1|P | 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*CP*(DOC))-3', 5'-D(P*AP*GP*GP*GP*(BRU)P*CP*CP*(BRU)P*(BRU)P*CP*CP*CP*CP*C)-3' | X-ray data do not support hoogsteen base-pairing during replication by human polymerase iota | X-ray diffraction | 2.3 | 27 | 2005-07-19 | ||||
| 61 | 1N6J|2|C+ 1N6J|2|D | 5'-D(*AP*GP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*GP*C)-3', 5'-D(*GP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*CP*T)-3' | Structural basis of sequence-specific recruitment of histone deacetylases by Myocyte Enhancer Factor-2 | X-ray diffraction | 2.2 | 28 | 2003-11-11 | ||||
| 62 | 3QK4|1|A+ 3QK4|1|B | DNA (5'-D(*CP*GP*CP*GP*GP*GP*TP*AP*CP*CP*CP*GP*CP*G)-3') | Crystal structure of d(CGCGGGTACCCGCG)2 as A-DNA duplex | X-ray diffraction | 2.6 | 28 | 2011-03-02 | ||||
| 63 | 3K4X|1|C+ 3K4X|1|B | DNA (5'-D(*CP*CP*CP*AP*TP*CP*GP*TP*AP*T)-3'), DNA (5'-D(*TP*TP*TP*TP*AP*TP*AP*CP*GP*AP*TP*GP*GP*G)-3') | Eukaryotic Sliding Clamp PCNA Bound to DNA | X-ray diffraction | 2.98 | 20 | 2010-02-16 | ||||
| 64 | 1FJL|1|D+ 1FJL|1|E | DNA (5'-D(*AP*AP*TP*AP*AP*TP*CP*TP*GP*AP*TP*TP*AP*C)-3'), DNA (5'-D(*TP*GP*TP*AP*AP*TP*CP*AP*GP*AP*TP*TP*AP*T)-3') | HOMEODOMAIN FROM THE DROSOPHILA PAIRED PROTEIN BOUND TO A DNA OLIGONUCLEOTIDE | X-ray diffraction | 2 | 28 | 1996-06-20 | ||||
| 65 | 1HCR|1|B+ 1HCR|1|C | DNA (5'-D(*TP*CP*TP*TP*AP*TP*CP*AP*AP*AP*AP*AP*C)-3'), DNA (5'-D(*TP*GP*TP*TP*TP*TP*TP*GP*AP*TP*AP*AP*GP*A)-3') | HIN RECOMBINASE BOUND TO DNA: THE ORIGIN OF SPECIFICITY IN MAJOR AND MINOR GROOVE INTERACTIONS | X-ray diffraction | 2.3 | 27 | 1994-04-30 | ||||
| 66 | 3GNA|1|D+ 3GNA|1|E | 5'-D(*AP*CP*TP*TP*AP*AP*CP*AP*AP*AP*AP*AP*CP*C)-3', 5'-D(*TP*GP*GP*TP*TP*TP*TP*TP*GP*TP*TP*AP*AP*G)-3' | Crystal structure of the RAG1 nonamer-binding domain with DNA | X-ray diffraction | 2.4 | 28 | 2009-04-28 | ||||
| 67 | 1FJL|1|F | DNA (5'-D(*TP*GP*TP*AP*AP*TP*CP*TP*GP*AP*TP*TP*AP*C)-3') | HOMEODOMAIN FROM THE DROSOPHILA PAIRED PROTEIN BOUND TO A DNA OLIGONUCLEOTIDE | X-ray diffraction | 2 | 14 | 1996-06-20 | ||||
| 68 | 3GNB|1|D+ 3GNB|1|E | 5'-D(*AP*AP*TP*TP*TP*TP*CP*AP*GP*AP*AP*AP*CP*C)-3', 5'-D(*AP*GP*GP*TP*TP*TP*CP*TP*GP*AP*AP*AP*AP*C)-3' | Crystal structure of the RAG1 nonamer-binding domain with DNA | X-ray diffraction | 3 | 28 | 2009-04-28 | ||||
| 69 | 3BEP|1|D+ 3BEP|1|C | DNA (5'-D(*DTP*DTP*DTP*DTP*DAP*DTP*DAP*DCP*DGP*DAP*DTP*DGP*DGP*DG)-3'), DNA (5'-D(P*DCP*DCP*DCP*DAP*DTP*DCP*DGP*DTP*DAP*DT)-3') | Structure of a sliding clamp on DNA | X-ray diffraction | 1.92 | 24 | 2008-01-29 | ||||
| 70 | 3AAF|1|C+ 3AAF|1|D | DNA (5'-D(*AP*CP*CP*CP*TP*AP*AP*TP*TP*AP*GP*GP*GP*T)-3') | Structure of WRN RQC domain bound to double-stranded DNA | X-ray diffraction | 1.9 | 28 | 2010-02-16 | ||||
| 71 | 2PYJ|1|K+ 2PYJ|1|J | 5'-d(ACACGTAAGCAGTC)-3', 5'-d(GACTGCTTA(DOC)-3' | Phi29 DNA polymerase complexed with primer-template DNA and incoming nucleotide substrates (ternary complex) | X-ray diffraction | 2.03 | 24 | 2007-07-17 | ||||
| 72 | 2PYJ|1|Y+ 2PYJ|1|X | 5'-d(ACACGTAAGCAGTC)-3', 5'-d(GACTGCTTA(DOC)-3' | Phi29 DNA polymerase complexed with primer-template DNA and incoming nucleotide substrates (ternary complex) | X-ray diffraction | 2.03 | 24 | 2007-07-17 | ||||
| 73 | 2H7G|1|Z+ 2H7G|1|Y | 5'-D(*TP*AP*AP*TP*AP*AP*GP*GP*GP*CP*GP*AP*CP*A)-3', 5'-D(*TP*TP*GP*TP*CP*GP*CP*CP*CP*TP*TP*A)-3' | Structure of variola topoisomerase non-covalently bound to DNA | X-ray diffraction | 1.9 | 26 | 2006-08-15 | ||||
| 74 | 2PYJ|1|R+ 2PYJ|1|Q | 5'-d(ACACGTAAGCAGTC)-3', 5'-d(GACTGCTTA(DOC)-3' | Phi29 DNA polymerase complexed with primer-template DNA and incoming nucleotide substrates (ternary complex) | X-ray diffraction | 2.03 | 23 | 2007-07-17 | ||||
| 75 | 1G9Z|1|C+ 1G9Z|1|E+ 1G9Z|1|D+ 1G9Z|1|F | 5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*C)-3', 5'-D(*GP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*A)-3', 5'-D(P*GP*AP*CP*AP*GP*TP*TP*TP*CP*G)-3', 5'-D(P*GP*AP*CP*GP*TP*TP*TP*TP*GP*C)-3' | LAGLIDADG HOMING ENDONUCLEASE I-CREI / DNA PRODUCT COMPLEX WITH MAGNESIUM | X-ray diffraction | 1.8 | 48 | 2001-04-02 | ||||
| 76 | 1F2I|1|A+ 1F2I|1|B | 5'-D(*AP*TP*GP*GP*GP*CP*GP*CP*GP*CP*CP*CP*AP*T)-3' | COCRYSTAL STRUCTURE OF SELECTED ZINC FINGER DIMER BOUND TO DNA | X-ray diffraction | 2.35 | 28 | 2001-09-14 | ||||
| 77 | 1F2I|1|C+ 1F2I|1|D | 5'-D(*AP*TP*GP*GP*GP*CP*GP*CP*GP*CP*CP*CP*AP*T)-3' | COCRYSTAL STRUCTURE OF SELECTED ZINC FINGER DIMER BOUND TO DNA | X-ray diffraction | 2.35 | 28 | 2001-09-14 | ||||
| 78 | 1F2I|1|E+ 1F2I|1|F | 5'-D(*AP*TP*GP*GP*GP*CP*GP*CP*GP*CP*CP*CP*AP*T)-3' | COCRYSTAL STRUCTURE OF SELECTED ZINC FINGER DIMER BOUND TO DNA | X-ray diffraction | 2.35 | 28 | 2001-09-14 | ||||
| 79 | 1QSS|1|C+ 1QSS|1|B | 5'-D(*AP*CP*CP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3', 5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DDG))-3' | DDGTP-TRAPPED CLOSED TERNARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS | X-ray diffraction | 2.3 | 26 | 1999-08-16 | ||||
| 80 | 1QSY|1|C+ 1QSY|1|B | 5'-D(*AP*TP*TP*GP*CP*GP*CP*CP*TP*P*GP*GP*TP*C)-3', 5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(2DA))-3' | DDATP-Trapped closed ternary complex of the large fragment of DNA Polymerase I from thermus aquaticus | X-ray diffraction | 2.3 | 26 | 1999-08-16 | ||||
| 81 | 1QTM|1|C+ 1QTM|1|B | 5'-D(*AP*AP*AP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3', 5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(2DT))-3' | DDTTP-TRAPPED CLOSED TERNARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS | X-ray diffraction | 2.3 | 26 | 1999-08-16 | ||||
| 82 | 3KTQ|1|C+ 3KTQ|1|B | DNA (5'-D(*AP*GP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3'), DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*DOC)-3') | CRYSTAL STRUCTURE OF AN ACTIVE TERNARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS | X-ray diffraction | 2.3 | 26 | 1999-01-13 | ||||
| 83 | 1MDY|1|E+ 1MDY|1|F | DNA (5'-D(*TP*CP*AP*AP*CP*AP*GP*CP*TP*GP*TP*TP*GP*A)-3') | CRYSTAL STRUCTURE OF MYOD BHLH DOMAIN BOUND TO DNA: PERSPECTIVES ON DNA RECOGNITION AND IMPLICATIONS FOR TRANSCRIPTIONAL ACTIVATION | X-ray diffraction | 2.8 | 28 | 1994-08-31 | ||||
| 84 | 1MDY|1|G+ 1MDY|1|H | DNA (5'-D(*TP*CP*AP*AP*CP*AP*GP*CP*TP*GP*TP*TP*GP*A)-3') | CRYSTAL STRUCTURE OF MYOD BHLH DOMAIN BOUND TO DNA: PERSPECTIVES ON DNA RECOGNITION AND IMPLICATIONS FOR TRANSCRIPTIONAL ACTIVATION | X-ray diffraction | 2.8 | 28 | 1994-08-31 | ||||
| 85 | 1MHD|1|D+ 1MHD|1|C | DNA | CRYSTAL STRUCTURE OF A SMAD MH1 DOMAIN BOUND TO DNA | X-ray diffraction | 2.8 | 27 | 1999-08-18 |
Release history
| Release | 0.6 |
|---|---|
| Date | 2011-03-05 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|
Instances are ordered to put similar structures near each other. Select one instance to see its 3D structure. Selecting two or more instances will show their superposition, but only chains with identical numbers of observed nucleotides will superpose well. Large structures are slow to display; this tool is not designed for that.
| #S | View | PDB | Title | Method | Resolution | #NTs | NAKB NA annotation | NAKB protein annotation |
|---|---|---|---|---|---|---|---|---|
| 1 | 3QK4|1|A+ 3QK4|1|B | Crystal structure of d(CGCGGGTACCCGCG)2 as A-DNA duplex | X-RAY DIFFRACTION | 2.6 | 28 | NAKB_NA_annotation | NAKB_protein_annotation | |
| 2 | 2PYJ|1|K+ 2PYJ|1|J | Phi29 DNA polymerase complexed with primer-template DNA and incoming nucleotide substrates (ternary complex) | X-RAY DIFFRACTION | 2.03 | 24 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 3 | 1N6J|2|C+ 1N6J|2|D | Structural basis of sequence-specific recruitment of histone deacetylases by Myocyte Enhancer Factor-2 | X-RAY DIFFRACTION | 2.2 | 28 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),MADS box,other α-helix,regulatory,transcription | |
| 4 | 3BEP|1|D+ 3BEP|1|C | Structure of a sliding clamp on DNA | X-RAY DIFFRACTION | 1.92 | 24 | double helix,feature,mispair,structure | enzyme,polymerase,transferase | |
| 5 | 1UA1|1|C+ 1UA1|1|B | Structure of aminofluorene adduct paired opposite cytosine at the polymerase active site. | X-RAY DIFFRACTION | 2 | 23 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 6 | 2H7G|1|Z+ 2H7G|1|Y | Structure of variola topoisomerase non-covalently bound to DNA | X-RAY DIFFRACTION | 1.9 | 26 | B-form double helix,double helix,structure | enzyme,isomerase | |
| 7 | 2H7F|1|Z+ 2H7F|1|Y | Structure of variola topoisomerase covalently bound to DNA | X-RAY DIFFRACTION | 2.7 | 25 | B-form double helix,double helix,structure | enzyme,isomerase | |
| 8 | 2GII|1|E+ 2GII|1|F | Q138F HincII bound to cognate DNA GTTAAC | X-RAY DIFFRACTION | 2.3 | 28 | double helix,structure | enzyme,hydrolase,nuclease | |
| 9 | 3E43|1|E+ 3E43|1|F | Q138F HincII bound to GTTAAC and cocrystallized with 2.5 mM MgCl2 | X-RAY DIFFRACTION | 2.73 | 28 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 10 | 2GIJ|1|E+ 2GIJ|1|F | Q138F HincII bound to cognate DNA GTTAAC and Ca2+ | X-RAY DIFFRACTION | 1.93 | 28 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 11 | 3E3Y|1|E+ 3E3Y|1|F | Q138F HincII bound to GTTAAC and cocrystallized with 5 mM Ca2+ | X-RAY DIFFRACTION | 2.13 | 28 | double helix,structure | enzyme,hydrolase,nuclease | |
| 12 | 3E40|1|E+ 3E40|1|F | Q138F HincII bound to GTTAAC and cocrystallized with 5 mM Ca2+ | X-RAY DIFFRACTION | 2.1 | 28 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 13 | 3E45|1|E+ 3E45|1|F | Q138F HincII bound to Noncognate DNA (GTGCAC) and Ca2+ | X-RAY DIFFRACTION | 2.78 | 28 | double helix,structure | enzyme,hydrolase,nuclease | |
| 14 | 3E41|1|E+ 3E41|1|F | Q138F HincII bound to GTCGAC and 5 mM Ca2+ | X-RAY DIFFRACTION | 2.73 | 28 | double helix,structure | enzyme,hydrolase,nuclease | |
| 15 | 3E42|1|E+ 3E42|1|F | Q138F HincII bound to GTCGAC and Ca2+ (cocrystallized) | X-RAY DIFFRACTION | 2.68 | 28 | double helix,structure | enzyme,hydrolase,nuclease | |
| 16 | 2GIG|1|E+ 2GIG|1|F | Alteration of sequence specificity of the type II restriction endonuclease HINCII through an indirect readout mechanism | X-RAY DIFFRACTION | 1.83 | 28 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 17 | 2GIH|1|E+ 2GIH|1|F | Q138F HincII bound to cognate DNA GTCGAC and Ca2+ | X-RAY DIFFRACTION | 2.5 | 28 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 18 | 1YQR|1|B+ 1YQR|1|C | Catalytically inactive human 8-oxoguanine glycosylase crosslinked to oxoG containing DNA | X-RAY DIFFRACTION | 2.43 | 28 | B-form double helix,double helix,structure | enzyme,hydrolase | |
| 19 | 3EI1|1|G+ 3EI1|1|H | Structure of hsDDB1-drDDB2 bound to a 14 bp 6-4 photoproduct containing DNA-duplex | X-RAY DIFFRACTION | 2.8 | 28 | DNA replication/repair,regulatory | ||
| 20 | 2HHS|1|C+ 2HHS|1|B | O6-methyl:C pair in the polymerase-10 basepair position | X-RAY DIFFRACTION | 1.8 | 27 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 21 | 3EBC|1|E+ 3EBC|1|F | Structure of N141A HincII with Cognate DNA | X-RAY DIFFRACTION | 2.55 | 28 | double helix,structure | enzyme,hydrolase,nuclease | |
| 22 | 2YVH|1|G+ 2YVH|1|H | Crystal structure of the operator-binding form of the multi-drug binding transcriptional repressor CgmR | X-RAY DIFFRACTION | 2.5 | 28 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,tetR family,transcription | |
| 23 | 2YVH|1|E+ 2YVH|1|F | Crystal structure of the operator-binding form of the multi-drug binding transcriptional repressor CgmR | X-RAY DIFFRACTION | 2.5 | 28 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,tetR family,transcription | |
| 24 | 3MXA|1|C+ 3MXA|1|E+ 3MXA|1|D+ 3MXA|1|F | Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus | X-RAY DIFFRACTION | 2.3 | 48 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 25 | 1G9Z|1|C+ 1G9Z|1|E+ 1G9Z|1|D+ 1G9Z|1|F | LAGLIDADG HOMING ENDONUCLEASE I-CREI / DNA PRODUCT COMPLEX WITH MAGNESIUM | X-RAY DIFFRACTION | 1.8 | 48 | double helix,structure | enzyme,hydrolase,nuclease | |
| 26 | 2VBL|1|C+ 2VBL|1|E+ 2VBL|1|S+ 2VBL|1|T | Molecular basis of human XPC gene recognition and cleavage by engineered homing endonuclease heterodimers | X-RAY DIFFRACTION | 1.8 | 48 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 27 | 2VBN|1|C+ 2VBN|1|E+ 2VBN|1|S+ 2VBN|1|T | Molecular basis of human XPC gene recognition and cleavage by engineered homing endonuclease heterodimers | X-RAY DIFFRACTION | 1.9 | 48 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 28 | 1N3E|1|C+ 1N3E|1|E+ 1N3E|1|D+ 1N3E|1|F | Crystal structure of I-CreI bound to a palindromic DNA sequence I (palindrome of left side of wildtype DNA target sequence) | X-RAY DIFFRACTION | 2.5 | 48 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 29 | 1N3E|1|I+ 1N3E|1|K+ 1N3E|1|J+ 1N3E|1|L | Crystal structure of I-CreI bound to a palindromic DNA sequence I (palindrome of left side of wildtype DNA target sequence) | X-RAY DIFFRACTION | 2.5 | 48 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 30 | 1N3F|1|I+ 1N3F|1|K+ 1N3F|1|J+ 1N3F|1|L | Crystal structure of I-CreI bound to a palindromic DNA sequence II (palindrome of right side of wildtype DNA target sequence) | X-RAY DIFFRACTION | 2 | 48 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 31 | 1N3F|1|C+ 1N3F|1|E+ 1N3F|1|D+ 1N3F|1|F | Crystal structure of I-CreI bound to a palindromic DNA sequence II (palindrome of right side of wildtype DNA target sequence) | X-RAY DIFFRACTION | 2 | 48 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 32 | 3CMY|1|B+ 3CMY|1|C | Structure of a homeodomain in complex with DNA | X-RAY DIFFRACTION | 1.95 | 15 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription | |
| 33 | 1MDY|1|G+ 1MDY|1|H | CRYSTAL STRUCTURE OF MYOD BHLH DOMAIN BOUND TO DNA: PERSPECTIVES ON DNA RECOGNITION AND IMPLICATIONS FOR TRANSCRIPTIONAL ACTIVATION | X-RAY DIFFRACTION | 2.8 | 28 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),basic transcription factor,helix-loop-helix (bHLH),regulatory,transcription | |
| 34 | 1MDY|1|E+ 1MDY|1|F | CRYSTAL STRUCTURE OF MYOD BHLH DOMAIN BOUND TO DNA: PERSPECTIVES ON DNA RECOGNITION AND IMPLICATIONS FOR TRANSCRIPTIONAL ACTIVATION | X-RAY DIFFRACTION | 2.8 | 28 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),basic transcription factor,helix-loop-helix (bHLH),regulatory,transcription | |
| 35 | 2EUV|1|B+ 2EUV|1|C | Principles of protein-DNA recognition revealed in the structural analysis of Ndt80-MSE DNA complexes | X-RAY DIFFRACTION | 1.94 | 25 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),P53 like,immunoglobulin (Ig) fold,regulatory,transcription | |
| 36 | 2ETW|1|B+ 2ETW|1|C | Principles of protein-DNA recognition revealed in the structural analysis of Ndt80-MSE DNA complexes | X-RAY DIFFRACTION | 1.67 | 27 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),P53 like,immunoglobulin (Ig) fold,regulatory,transcription | |
| 37 | 2EUX|1|B+ 2EUX|1|C | Structure of a Ndt80-DNA complex (MSE VARIANT vA4G) | X-RAY DIFFRACTION | 1.57 | 28 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),P53 like,immunoglobulin (Ig) fold,regulatory,transcription | |
| 38 | 2EUW|1|B+ 2EUW|1|C | Structure of a Ndt80-DNA complex (MSE mutant mA4T) | X-RAY DIFFRACTION | 1.68 | 27 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),P53 like,immunoglobulin (Ig) fold,regulatory,transcription | |
| 39 | 2EVH|1|B+ 2EVH|1|C | Structure of a Ndt80-DNA complex (MSE mutant mA7G) | X-RAY DIFFRACTION | 1.989 | 27 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),P53 like,immunoglobulin (Ig) fold,regulatory,transcription | |
| 40 | 2EVG|1|B+ 2EVG|1|C | Structure of a Ndt80-DNA complex (MSE mutant mA7T) | X-RAY DIFFRACTION | 1.55 | 27 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),P53 like,immunoglobulin (Ig) fold,regulatory,transcription | |
| 41 | 2EVJ|1|B+ 2EVJ|1|C | Structure of an Ndt80-DNA complex (MSE mutant mA9C) | X-RAY DIFFRACTION | 1.89 | 27 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),P53 like,immunoglobulin (Ig) fold,regulatory,transcription | |
| 42 | 2EUZ|1|B+ 2EUZ|1|C | Structure of a Ndt80-DNA complex (MSE mutant mC5T) | X-RAY DIFFRACTION | 1.56 | 27 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),P53 like,immunoglobulin (Ig) fold,regulatory,transcription | |
| 43 | 1MNN|1|B+ 1MNN|1|C | Structure of the sporulation specific transcription factor Ndt80 bound to DNA | X-RAY DIFFRACTION | 1.4 | 28 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),P53 like,immunoglobulin (Ig) fold,regulatory,transcription | |
| 44 | 2EVI|1|B+ 2EVI|1|C | Structure of a Ndt80-DNA complex (MSE mutant mA8T) | X-RAY DIFFRACTION | 1.8 | 27 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),P53 like,immunoglobulin (Ig) fold,regulatory,transcription | |
| 45 | 2EVF|1|B+ 2EVF|1|C | Structure of a Ndt80-DNA complex (MSE mutant mA6T) | X-RAY DIFFRACTION | 1.56 | 27 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),P53 like,immunoglobulin (Ig) fold,regulatory,transcription | |
| 46 | 2D5V|1|C+ 2D5V|1|D | Crystal structure of HNF-6alpha DNA-binding domain in complex with the TTR promoter | X-RAY DIFFRACTION | 2 | 27 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription | |
| 47 | 2D5V|1|E+ 2D5V|1|F | Crystal structure of HNF-6alpha DNA-binding domain in complex with the TTR promoter | X-RAY DIFFRACTION | 2 | 26 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription | |
| 48 | 1ZET|1|T+ 1ZET|1|P | X-ray data do not support hoogsteen base-pairing during replication by human polymerase iota | X-RAY DIFFRACTION | 2.3 | 27 | double helix,structure | enzyme,polymerase,transferase | |
| 49 | 1T3N|1|T+ 1T3N|1|P | Structure of the catalytic core of DNA polymerase Iota in complex with DNA and dTTP | X-RAY DIFFRACTION | 2.3 | 27 | double helix,structure | enzyme,polymerase,transferase | |
| 50 | 1FJL|1|D+ 1FJL|1|E | HOMEODOMAIN FROM THE DROSOPHILA PAIRED PROTEIN BOUND TO A DNA OLIGONUCLEOTIDE | X-RAY DIFFRACTION | 2 | 28 | B-form double helix,double helix,feature,mispair,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription | |
| 51 | 1FJL|1|F | HOMEODOMAIN FROM THE DROSOPHILA PAIRED PROTEIN BOUND TO A DNA OLIGONUCLEOTIDE | X-RAY DIFFRACTION | 2 | 14 | B-form double helix,double helix,feature,mispair,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription | |
| 52 | 3AAF|1|C+ 3AAF|1|D | Structure of WRN RQC domain bound to double-stranded DNA | X-RAY DIFFRACTION | 1.9 | 28 | double helix,structure | enzyme,helicase,hydrolase | |
| 53 | 1JJ8|1|A+ 1JJ8|1|B | Testing the Water-Mediated HIN Recombinase DNA Recognition by Systematic Mutations | X-RAY DIFFRACTION | 2.75 | 28 | B-form double helix,double helix,structure | enzyme,recombinase | |
| 54 | 3K4X|1|C+ 3K4X|1|B | Eukaryotic Sliding Clamp PCNA Bound to DNA | X-RAY DIFFRACTION | 2.98 | 20 | B-form double helix,double helix,structure | DNA replication/repair,regulatory | |
| 55 | 3D1N|1|C+ 3D1N|1|D | Structure of human Brn-5 transcription factor in complex with corticotrophin-releasing hormone gene promoter | X-RAY DIFFRACTION | 2.51 | 28 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription | |
| 56 | 3D1N|1|E+ 3D1N|1|F | Structure of human Brn-5 transcription factor in complex with corticotrophin-releasing hormone gene promoter | X-RAY DIFFRACTION | 2.51 | 28 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription | |
| 57 | 3D1N|1|G+ 3D1N|1|H | Structure of human Brn-5 transcription factor in complex with corticotrophin-releasing hormone gene promoter | X-RAY DIFFRACTION | 2.51 | 28 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription | |
| 58 | 3D1N|1|A+ 3D1N|1|B | Structure of human Brn-5 transcription factor in complex with corticotrophin-releasing hormone gene promoter | X-RAY DIFFRACTION | 2.51 | 28 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription | |
| 59 | 3LNQ|1|B+ 3LNQ|1|C | Structure of Aristaless homeodomain in complex with DNA | X-RAY DIFFRACTION | 2.25 | 28 | double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription | |
| 60 | 1VRR|1|C+ 1VRR|1|D | Crystal structure of the restriction endonuclease BstYI complex with DNA | X-RAY DIFFRACTION | 2.7 | 28 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 61 | 1F2I|1|E+ 1F2I|1|F | COCRYSTAL STRUCTURE OF SELECTED ZINC FINGER DIMER BOUND TO DNA | X-RAY DIFFRACTION | 2.35 | 28 | DNA-binding transcription factor (TF),Zinc finger C2H2,Zinc-coordinating,regulatory,transcription | ||
| 62 | 1F2I|1|A+ 1F2I|1|B | COCRYSTAL STRUCTURE OF SELECTED ZINC FINGER DIMER BOUND TO DNA | X-RAY DIFFRACTION | 2.35 | 28 | DNA-binding transcription factor (TF),Zinc finger C2H2,Zinc-coordinating,regulatory,transcription | ||
| 63 | 1F2I|1|C+ 1F2I|1|D | COCRYSTAL STRUCTURE OF SELECTED ZINC FINGER DIMER BOUND TO DNA | X-RAY DIFFRACTION | 2.35 | 28 | DNA-binding transcription factor (TF),Zinc finger C2H2,Zinc-coordinating,regulatory,transcription | ||
| 64 | 1MHD|1|D+ 1MHD|1|C | CRYSTAL STRUCTURE OF A SMAD MH1 DOMAIN BOUND TO DNA | X-RAY DIFFRACTION | 2.8 | 27 | B-form double helix,double helix,structure | β-sheet,DNA-binding transcription factor (TF),SMAD-like,regulatory,transcription | |
| 65 | 1HCR|1|B+ 1HCR|1|C | HIN RECOMBINASE BOUND TO DNA: THE ORIGIN OF SPECIFICITY IN MAJOR AND MINOR GROOVE INTERACTIONS | X-RAY DIFFRACTION | 2.3 | 27 | enzyme,recombinase | ||
| 66 | 3GNA|1|D+ 3GNA|1|E | Crystal structure of the RAG1 nonamer-binding domain with DNA | X-RAY DIFFRACTION | 2.4 | 28 | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription | ||
| 67 | 3GNB|1|D+ 3GNB|1|E | Crystal structure of the RAG1 nonamer-binding domain with DNA | X-RAY DIFFRACTION | 3 | 28 | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription | ||
| 68 | 1QTM|1|C+ 1QTM|1|B | DDTTP-TRAPPED CLOSED TERNARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS | X-RAY DIFFRACTION | 2.3 | 26 | double helix,structure | enzyme,polymerase,transferase | |
| 69 | 1QSS|1|C+ 1QSS|1|B | DDGTP-TRAPPED CLOSED TERNARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS | X-RAY DIFFRACTION | 2.3 | 26 | double helix,structure | enzyme,polymerase,transferase | |
| 70 | 1QSY|1|C+ 1QSY|1|B | DDATP-Trapped closed ternary complex of the large fragment of DNA Polymerase I from thermus aquaticus | X-RAY DIFFRACTION | 2.3 | 26 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 71 | 3KTQ|1|C+ 3KTQ|1|B | CRYSTAL STRUCTURE OF AN ACTIVE TERNARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS | X-RAY DIFFRACTION | 2.3 | 26 | double helix,structure | enzyme,polymerase,transferase | |
| 72 | 2PYL|1|Y+ 2PYL|1|X | Phi29 DNA polymerase complexed with primer-template DNA and incoming nucleotide substrates (ternary complex) | X-RAY DIFFRACTION | 2.2 | 25 | double helix,structure | enzyme,polymerase,transferase | |
| 73 | 1LV5|1|D+ 1LV5|1|C | Crystal Structure of the Closed Conformation of Bacillus DNA Polymerase I Fragment Bound to DNA and dCTP | X-RAY DIFFRACTION | 1.95 | 24 | double helix,structure | enzyme,polymerase,transferase | |
| 74 | 1LV5|1|F+ 1LV5|1|E | Crystal Structure of the Closed Conformation of Bacillus DNA Polymerase I Fragment Bound to DNA and dCTP | X-RAY DIFFRACTION | 1.95 | 24 | double helix,structure | enzyme,polymerase,transferase | |
| 75 | 1UA0|1|C+ 1UA0|1|B | Aminofluorene DNA adduct at the pre-insertion site of a DNA polymerase | X-RAY DIFFRACTION | 2.1 | 21 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 76 | 2PYJ|1|Y+ 2PYJ|1|X | Phi29 DNA polymerase complexed with primer-template DNA and incoming nucleotide substrates (ternary complex) | X-RAY DIFFRACTION | 2.03 | 24 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 77 | 2PYJ|1|R+ 2PYJ|1|Q | Phi29 DNA polymerase complexed with primer-template DNA and incoming nucleotide substrates (ternary complex) | X-RAY DIFFRACTION | 2.03 | 23 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 78 | 1PJI|1|D+ 1PJI|1|E | Crystal structure of wild type Lactococcus lactis FPG complexed to a 1,3 propanediol containing DNA | X-RAY DIFFRACTION | 1.9 | 27 | B-form double helix,double helix,structure | enzyme,hydrolase | |
| 79 | 1PM5|1|D+ 1PM5|1|E | Crystal structure of wild type Lactococcus lactis Fpg complexed to a tetrahydrofuran containing DNA | X-RAY DIFFRACTION | 1.95 | 28 | B-form double helix,double helix,structure | enzyme,hydrolase | |
| 80 | 1PJJ|1|D+ 1PJJ|1|E | Complex between the Lactococcus lactis Fpg and an abasic site containing DNA. | X-RAY DIFFRACTION | 1.9 | 28 | B-form double helix,double helix,structure | enzyme,hydrolase | |
| 81 | 1NNJ|1|D+ 1NNJ|1|E | Crystal structure Complex between the Lactococcus lactis Fpg and an abasic site containing DNA | X-RAY DIFFRACTION | 1.9 | 27 | B-form double helix,double helix,structure | enzyme,hydrolase | |
| 82 | 1TDZ|1|B+ 1TDZ|1|C | Crystal Structure Complex Between the Lactococcus Lactis FPG (Mutm) and a FAPY-dG Containing DNA | X-RAY DIFFRACTION | 1.8 | 28 | B-form double helix,double helix,structure | enzyme,hydrolase | |
| 83 | 1XC8|1|B+ 1XC8|1|C | CRYSTAL STRUCTURE COMPLEX BETWEEN THE WILD-TYPE LACTOCOCCUS LACTIS FPG (MUTM) AND A FAPY-DG CONTAINING DNA | X-RAY DIFFRACTION | 1.95 | 28 | B-form double helix,double helix,structure | enzyme,hydrolase | |
| 84 | 3C58|1|B+ 3C58|1|C | Crystal structure of a complex between the wild-type lactococcus lactis Fpg (MutM) and a N7-Benzyl-Fapy-dG containing DNA | X-RAY DIFFRACTION | 1.9 | 28 | enzyme,hydrolase | ||
| 85 | 3GP8|1|X | Crystal structure of the binary complex of RecD2 with DNA | X-RAY DIFFRACTION | 2.5 | 8 | enzyme,helicase,hydrolase |
Heat map of mutual geometric discrepancy, in Angstroms per nucleotide. The ordering in the heat map is the same as in the table. The colorbar ranges from 0 to the maximum observed discrepancy. Click above the diagonal to select a range of structures, below the diagonal to select two structures.
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