Equivalence class DNA_all_20780.1 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | #NTs | Date |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 1MNN|1|B+ 1MNN|1|C (rep) | 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 | ||||
| 2 | 2VBL|1|C+ 2VBL|1|E+ 2VBL|1|S+ 2VBL|1|T | 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 | ||||
| 3 | 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 | ||||
| 4 | 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 | ||||
| 5 | 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 | ||||
| 6 | 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 | ||||
| 7 | 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 | ||||
| 8 | 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 | ||||
| 9 | 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 | ||||
| 10 | 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 | ||||
| 11 | 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 | ||||
| 12 | 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 | ||||
| 13 | 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 | ||||
| 14 | 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 | ||||
| 15 | 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 | ||||
| 16 | 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 | ||||
| 17 | 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 | ||||
| 18 | 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 | ||||
| 19 | 2VS8|1|G+ 2VS8|1|J | 5'-D(*CP*CP*GP*GP*CP*AP*AP* GP*GP*CP)-3', 5'-D(*GP*CP*CP*TP*TP*GP*CP*CP*GP*GP *GP*TP*AP*A)-3' | Desulfurococcus mucosus | The crystal structure of I-DmoI in complex with DNA and Mn | X-ray diffraction | 2.1 | 0 | 2008-11-11 | |||
| 20 | 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 | ||||
| 21 | 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 | ||||
| 22 | 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 | ||||
| 23 | 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 | ||||
| 24 | 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 | ||||
| 25 | 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 | ||||
| 26 | 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 | ||||
| 27 | 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 | ||||
| 28 | 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 | ||||
| 29 | 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 | ||||
| 30 | 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 | ||||
| 31 | 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 | ||||
| 32 | 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 | ||||
| 33 | 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 | ||||
| 34 | 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 | ||||
| 35 | 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 | ||||
| 36 | 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 | ||||
| 37 | 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 | ||||
| 38 | 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 | ||||
| 39 | 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 | ||||
| 40 | 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 | ||||
| 41 | 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 | ||||
| 42 | 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 | ||||
| 43 | 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 | ||||
| 44 | 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 | ||||
| 45 | 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 | ||||
| 46 | 1N6J|1|C+ 1N6J|1|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 | 0 | 2003-11-11 | ||||
| 47 | 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 | ||||
| 48 | 1PZU|1|T+ 1PZU|1|W | 5'-D(*AP*AP*TP*GP*GP*AP*AP*AP*TP*TP*CP*CP*TP*C)-3', 5'-D(*TP*TP*GP*AP*GP*GP*AP*AP*TP*TP*TP*CP*CP*A)-3' | An asymmetric NFAT1-RHR homodimer on a pseudo-palindromic, Kappa-B site | X-ray diffraction | 3.1 | 28 | 2003-09-09 | ||||
| 49 | 1PZU|1|V+ 1PZU|1|Z | 5'-D(*AP*AP*TP*GP*GP*AP*AP*AP*TP*TP*CP*CP*TP*C)-3', 5'-D(*TP*TP*GP*AP*GP*GP*AP*AP*TP*TP*TP*CP*CP*A)-3' | An asymmetric NFAT1-RHR homodimer on a pseudo-palindromic, Kappa-B site | X-ray diffraction | 3.1 | 28 | 2003-09-09 | ||||
| 50 | 1PZU|1|X+ 1PZU|1|Y | 5'-D(*AP*AP*TP*GP*GP*AP*AP*AP*TP*TP*CP*CP*TP*C)-3', 5'-D(*TP*TP*GP*AP*GP*GP*AP*AP*TP*TP*TP*CP*CP*A)-3' | An asymmetric NFAT1-RHR homodimer on a pseudo-palindromic, Kappa-B site | X-ray diffraction | 3.1 | 28 | 2003-09-09 | ||||
| 51 | 1PYI|1|D+ 1PYI|1|E | DNA (5'-D(*TP*CP*GP*GP*CP*AP*AP*TP*TP*GP*CP*CP*GP*A)-3') | CRYSTAL STRUCTURE OF A PPR1-DNA COMPLEX: DNA RECOGNITION BY PROTEINS CONTAINING A ZN2CYS6 BINUCLEAR CLUSTER | X-ray diffraction | 3.2 | 28 | 1995-02-27 | ||||
| 52 | 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 | ||||
| 53 | 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 | ||||
| 54 | 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 | ||||
| 55 | 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 | ||||
| 56 | 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 | ||||
| 57 | 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 | ||||
| 58 | 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 | ||||
| 59 | 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 | ||||
| 60 | 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 | ||||
| 61 | 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 | ||||
| 62 | 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 | ||||
| 63 | 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 | ||||
| 64 | 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 | ||||
| 65 | 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 | ||||
| 66 | 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 | ||||
| 67 | 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 | ||||
| 68 | 2PRT|1|B+ 2PRT|1|C | DNA (5'-D(*CP*AP*GP*AP*CP*GP*CP*CP*CP*CP*CP*GP*CP*G)-3'), DNA (5'-D(*CP*GP*CP*GP*GP*GP*GP*GP*CP*GP*TP*CP*TP*G)-3') | Structure of the Wilms Tumor Suppressor Protein Zinc Finger Domain Bound to DNA | X-ray diffraction | 3.15 | 26 | 2008-03-04 | ||||
| 69 | 1K8J|1|A+ 1K8J|1|B | FIRST STRAND OF CK14 DNA DUPLEX, SECOND STRAND OF CK14 DNA DUPLEX | NMR STRUCTURE OF THE CK14 DNA DUPLEX: A PORTION OF THE KNOWN NF-kB SEQUENCE CK1 | Solution NMR | 28 | 2003-04-15 | |||||
| 70 | 1BWG|1|A+ 1BWG|1|B | DNA (5'-D(*GP*AP*CP*TP*GP*AP*GP*AP*GP*AP*CP*GP*TP*A)-3'), DNA (5'-D(*TP*AP*CP*GP*TP*CP*TP*CP*TP*CP*AP*GP*TP*C)-3') | DNA TRIPLEX WITH 5' AND 3' JUNCTIONS, NMR, 10 STRUCTURES | Solution NMR | 28 | 1999-03-23 | |||||
| 71 | 1K9L|1|A+ 1K9L|1|B | 5'-D(*TP*AP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*TP*A)-3' | Solution Structure of DNA TATGAGCGCTCATA | Solution NMR | 28 | 2001-11-07 | |||||
| 72 | 1KXS|1|A+ 1KXS|1|B | 5'-D(*CP*GP*TP*TP*TP*TP*AP*GP*AP*CP*TP*TP*GP*C)-3', 5'-D(*GP*CP*AP*AP*GP*TP*CP*(HEU)P*AP*AP*AP*AP*CP*G)-3' | NMR STUDY OF B-DNA CONTAINING A MODIFIED BASE PAIR: THE 2'-DEOXYADENOSINE 3-(2-HYDROXYETHYL-2'-DEOXYURIDINE) | Solution NMR | 28 | 2002-03-06 | |||||
| 73 | 1K9H|1|A+ 1K9H|1|B | 5'-D(*TP*GP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*CP*A)-3' | NMR structure of DNA TGTGAGCGCTCACA | Solution NMR | 28 | 2001-11-07 | |||||
| 74 | 2L2U|1|A+ 2L2U|1|B | DNA (5'-D(*CP*AP*GP*CP*GP*(3DR)P*GP*TP*AP*TP*AP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*TP*AP*(3DR)P*AP*CP*AP*CP*GP*CP*TP*G)-3') | NMR Solution Structures of +3 (5' staggered) Bistranded Abasic Site Lesions in DNA | Solution NMR | 28 | 2010-11-03 | |||||
| 75 | 1LFU|1|A+ 1LFU|1|B | 5'-D(*GP*CP*GP*CP*AP*TP*GP*AP*TP*TP*GP*CP*CP*C)-3', 5'-D(*GP*GP*GP*CP*AP*AP*TP*CP*AP*TP*GP*CP*GP*C)-3' | NMR Solution Structure of the Extended PBX Homeodomain Bound to DNA | Solution NMR | 28 | 2003-01-14 | |||||
| 76 | 1K8L|1|A+ 1K8L|1|B | FIRST STRAND OF CK14 DNA DUPLEX, SECOND STRAND OF CK14 DNA DUPLEX | XBY6: An analog of CK14 containing 6 dithiophosphate groups | Solution NMR | 28 | 2003-04-15 | |||||
| 77 | 1AHD|1|A+ 1AHD|1|B | DNA (5'-D(*CP*TP*CP*TP*AP*AP*TP*GP*GP*CP*TP*TP*TP*C)-3'), DNA (5'-D(*GP*AP*AP*AP*GP*CP*CP*AP*TP*TP*AP*GP*AP*G)-3') | DETERMINATION OF THE NMR SOLUTION STRUCTURE OF AN ANTENNAPEDIA HOMEODOMAIN-DNA COMPLEX | Solution NMR | 0 | 1993-10-31 | |||||
| 78 | 2K7F|1|B+ 2K7F|1|C | 5'-D(P*DCP*DGP*DAP*DCP*DCP*DTP*DCP*DGP*DAP*DGP*DAP*DTP*DCP*DA)-3', 5'-D(P*DCP*DTP*DCP*DGP*DAP*DGP*DGP*DTP*DCP*DG)-3' | HADDOCK calculated model of the complex between the BRCT region of RFC p140 and dsDNA | Solution NMR | 0 | 2009-09-08 | |||||
| 79 | 2JPA|1|B+ 2JPA|1|C | DNA (5'-D(P*DCP*DAP*DGP*DAP*DCP*DGP*DCP*DCP*DCP*DCP*DCP*DGP*DCP*DG)-3'), DNA (5'-D(P*DCP*DGP*DCP*DGP*DGP*DGP*DGP*DGP*DCP*DGP*DTP*DCP*DTP*DG)-3') | synthetic construct | Structure of the Wilms Tumor Suppressor Protein Zinc Finger Domain Bound to DNA | Solution NMR | 28 | 2007-10-30 | ||||
| 80 | 2O8K|1|B+ 2O8K|1|C | 5'-D(*GP*AP*AP*AP*CP*GP*TP*GP*CP*CP*AP*AP*AP*A)-3', 5'-D(*TP*TP*TP*TP*GP*GP*CP*AP*CP*GP*TP*TP*TP*C)-3' | NMR Structure of the Sigma-54 RpoN Domain Bound to the-24 Promoter Element | Solution NMR | 28 | 2007-07-17 | |||||
| 81 | 2O9L|1|B+ 2O9L|1|C | 5'-D(*GP*AP*AP*AP*CP*GP*TP*GP*CP*CP*AP*AP*AP*A)-3', 5'-D(*TP*TP*TP*TP*GP*GP*CP*AP*CP*GP*TP*TP*TP*C)-3' | AMBER refined NMR Structure of the Sigma-54 RpoN Domain Bound to the-24 Promoter Element | Solution NMR | 28 | 2007-07-17 | |||||
| 82 | 2JXI|1|C+ 2JXI|1|D | DNA (5'-D(*DAP*DAP*DAP*DGP*DGP*DTP*DGP*DCP*DAP*DAP*DCP*DCP*DGP*DC)-3'), DNA (5'-D(*DGP*DCP*DGP*DGP*DTP*DTP*DGP*DCP*DAP*DCP*DCP*DTP*DTP*DT)-3') | synthetic construct | Solution structure of the DNA-binding domain of Pseudomonas putida Proline utilization A (putA) bound to GTTGCA DNA sequence | Solution NMR | 28 | 2008-10-21 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
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Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
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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 | 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 | |
| 2 | 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 | |
| 3 | 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 | |
| 4 | 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 | |
| 5 | 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 | |
| 6 | 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 | |
| 7 | 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 | |
| 8 | 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 | ||
| 9 | 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 | ||
| 10 | 1K8J|1|A+ 1K8J|1|B | NMR STRUCTURE OF THE CK14 DNA DUPLEX: A PORTION OF THE KNOWN NF-kB SEQUENCE CK1 | SOLUTION NMR | 28 | B-form double helix,double helix,structure | |||
| 11 | 1BWG|1|A+ 1BWG|1|B | DNA TRIPLEX WITH 5' AND 3' JUNCTIONS, NMR, 10 STRUCTURES | SOLUTION NMR | 28 | structure,triple helix | |||
| 12 | 1PZU|1|X+ 1PZU|1|Y | An asymmetric NFAT1-RHR homodimer on a pseudo-palindromic, Kappa-B site | X-RAY DIFFRACTION | 3.1 | 28 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),immunoglobulin (Ig) fold,regulatory,rel homology,transcription | |
| 13 | 1PZU|1|V+ 1PZU|1|Z | An asymmetric NFAT1-RHR homodimer on a pseudo-palindromic, Kappa-B site | X-RAY DIFFRACTION | 3.1 | 28 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),immunoglobulin (Ig) fold,regulatory,rel homology,transcription | |
| 14 | 1PZU|1|T+ 1PZU|1|W | An asymmetric NFAT1-RHR homodimer on a pseudo-palindromic, Kappa-B site | X-RAY DIFFRACTION | 3.1 | 28 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),immunoglobulin (Ig) fold,regulatory,rel homology,transcription | |
| 15 | 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 | |
| 16 | 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 | |
| 17 | 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 | |
| 18 | 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 | |
| 19 | 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 | |
| 20 | 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 | |
| 21 | 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 | |
| 22 | 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 | |
| 23 | 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 | |
| 24 | 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 | |
| 25 | 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 | |
| 26 | 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 | |
| 27 | 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 | |
| 28 | 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 | |
| 29 | 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 | |
| 30 | 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 | |
| 31 | 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 | |
| 32 | 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 | |
| 33 | 1K9H|1|A+ 1K9H|1|B | NMR structure of DNA TGTGAGCGCTCACA | SOLUTION NMR | 28 | B-form double helix,double helix,structure | |||
| 34 | 2L2U|1|A+ 2L2U|1|B | NMR Solution Structures of +3 (5' staggered) Bistranded Abasic Site Lesions in DNA | SOLUTION NMR | 28 | double helix,structure | |||
| 35 | 1K9L|1|A+ 1K9L|1|B | Solution Structure of DNA TATGAGCGCTCATA | SOLUTION NMR | 28 | B-form double helix,double helix,structure | |||
| 36 | 1K8L|1|A+ 1K8L|1|B | XBY6: An analog of CK14 containing 6 dithiophosphate groups | SOLUTION NMR | 28 | B-form double helix,double helix,structure | |||
| 37 | 1AHD|1|A+ 1AHD|1|B | DETERMINATION OF THE NMR SOLUTION STRUCTURE OF AN ANTENNAPEDIA HOMEODOMAIN-DNA COMPLEX | SOLUTION NMR | 0 | double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription | ||
| 38 | 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 | |
| 39 | 2JPA|1|B+ 2JPA|1|C | Structure of the Wilms Tumor Suppressor Protein Zinc Finger Domain Bound to DNA | SOLUTION NMR | 28 | double helix,structure | DNA-binding transcription factor (TF),Zinc finger C2H2,Zinc-coordinating,regulatory,transcription | ||
| 40 | 2PRT|1|B+ 2PRT|1|C | Structure of the Wilms Tumor Suppressor Protein Zinc Finger Domain Bound to DNA | X-RAY DIFFRACTION | 3.15 | 26 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc finger C2H2,Zinc-coordinating,regulatory,transcription | |
| 41 | 2VS8|1|G+ 2VS8|1|J | The crystal structure of I-DmoI in complex with DNA and Mn | X-RAY DIFFRACTION | 2.1 | 0 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 42 | 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 | |
| 43 | 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 | |
| 44 | 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 | |
| 45 | 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 | |
| 46 | 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 | |
| 47 | 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 | |
| 48 | 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 | |
| 49 | 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 | |
| 50 | 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 | |
| 51 | 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 | |
| 52 | 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 | |
| 53 | 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 | |
| 54 | 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 | |
| 55 | 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 | |
| 56 | 2JXI|1|C+ 2JXI|1|D | Solution structure of the DNA-binding domain of Pseudomonas putida Proline utilization A (putA) bound to GTTGCA DNA sequence | SOLUTION NMR | 28 | double helix,structure | enzyme,oxidoreductase,regulatory,transcription | ||
| 57 | 1KXS|1|A+ 1KXS|1|B | NMR STUDY OF B-DNA CONTAINING A MODIFIED BASE PAIR: THE 2'-DEOXYADENOSINE 3-(2-HYDROXYETHYL-2'-DEOXYURIDINE) | SOLUTION NMR | 28 | B-form double helix,double helix,structure | |||
| 58 | 1PYI|1|D+ 1PYI|1|E | CRYSTAL STRUCTURE OF A PPR1-DNA COMPLEX: DNA RECOGNITION BY PROTEINS CONTAINING A ZN2CYS6 BINUCLEAR CLUSTER | X-RAY DIFFRACTION | 3.2 | 28 | double helix,structure | DNA-binding transcription factor (TF),Zinc-coordinating,regulatory,transcription | |
| 59 | 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 | |
| 60 | 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 | |
| 61 | 1LFU|1|A+ 1LFU|1|B | NMR Solution Structure of the Extended PBX Homeodomain Bound to DNA | SOLUTION NMR | 28 | double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),homeodomain,regulatory,transcription | ||
| 62 | 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 | |
| 63 | 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 | |
| 64 | 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 | |
| 65 | 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 | |
| 66 | 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 | |
| 67 | 1N6J|1|C+ 1N6J|1|D | Structural basis of sequence-specific recruitment of histone deacetylases by Myocyte Enhancer Factor-2 | X-RAY DIFFRACTION | 2.2 | 0 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),MADS box,other α-helix,regulatory,transcription | |
| 68 | 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 | ||
| 69 | 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 | ||
| 70 | 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 | ||
| 71 | 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 | ||
| 72 | 2O9L|1|B+ 2O9L|1|C | AMBER refined NMR Structure of the Sigma-54 RpoN Domain Bound to the-24 Promoter Element | SOLUTION NMR | 28 | double helix,structure | regulatory,transcription | ||
| 73 | 2K7F|1|B+ 2K7F|1|C | HADDOCK calculated model of the complex between the BRCT region of RFC p140 and dsDNA | SOLUTION NMR | 0 | double helix,structure | DNA replication/repair,regulatory | ||
| 74 | 2O8K|1|B+ 2O8K|1|C | NMR Structure of the Sigma-54 RpoN Domain Bound to the-24 Promoter Element | SOLUTION NMR | 28 | double helix,structure | regulatory,transcription | ||
| 75 | 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 | |
| 76 | 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 | |
| 77 | 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 | |
| 78 | 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 | |
| 79 | 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 | |
| 80 | 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 | |
| 81 | 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 | |
| 82 | 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 |
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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