Equivalence class DNA_2.0_86977.1 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | #NTs | Date |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 3O1M|1|B+ 3O1M|1|C (rep) | DNA (5'-D(*AP*AP*CP*GP*GP*TP*AP*TP*TP*AP*CP*CP*T)-3'), DNA (5'-D(*T*AP*GP*GP*TP*AP*AP*(ME6)P*AP*CP*CP*GP*T)-3') | Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase | X-ray diffraction | 1.75 | 25 | 2010-11-17 | ||||
| 2 | 3MR2|1|T+ 3MR2|1|P | DNA (5'-D(*T*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3'), DNA (5'-D(*TP*AP*GP*CP*GP*TP*CP*AP*T)-3') | Human DNA polymerase eta in complex with normal DNA and incoming nucleotide (Nrm) | X-ray diffraction | 1.83 | 21 | 2010-06-30 | ||||
| 3 | 3O1P|1|B+ 3O1P|1|C | DNA (5'-D(*AP*AP*CP*GP*GP*TP*AP*TP*TP*AP*CP*CP*T)-3'), DNA (5'-D(*T*AP*GP*GP*TP*AP*AP*(EDA)P*AP*CP*CP*GP*T)-3') | Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase | X-ray diffraction | 1.51 | 25 | 2010-11-17 | ||||
| 4 | 3BKZ|1|B+ 3BKZ|1|C | DNA (5'-D(*DAP*DAP*DCP*DGP*DAP*DTP*DAP*DTP*DTP*DAP*DCP*DCP*DT)-3'), DNA (5'-D(*DTP*DAP*DGP*DGP*DTP*DAP*DAP*DCP*DAP*DTP*DCP*DGP*DT)-3') | X-ray structure of E coli AlkB crosslinked to dsDNA in the active site | X-ray diffraction | 1.65 | 26 | 2008-04-22 | ||||
| 5 | 3BIE|1|C+ 3BIE|1|B | DNA (5'-D(*DAP*DAP*DCP*DGP*DGP*DTP*DTP*DTP*DTP*DAP*DCP*DCP*DT)-3'), DNA (5'-D(P*DAP*DGP*DGP*DTP*DAP*DAP*(MA7)P*DAP*DCP*DCP*DGP*DT)-3') | X-ray structure of E coli AlkB bound to dsDNA containing 1meA/T with Mn and 2KG | X-ray diffraction | 1.68 | 25 | 2008-04-22 | ||||
| 6 | 1SXQ|1|C+ 1SXQ|1|E | 5'-D(*AP*AP*AP*AP*AP*AP*CP*TP*TP*TP*TP*TP*T)-3', 5'-D(*AP*AP*AP*AP*AP*AP*GP*TP*TP*TP*TP*TP*T)-3' | BGT in complex with a 13mer DNA containing a central C:G base pair and UDP | X-ray diffraction | 1.8 | 26 | 2004-06-22 | ||||
| 7 | 1SXQ|1|D+ 1SXQ|1|F | 5'-D(*AP*AP*AP*AP*AP*AP*CP*TP*TP*TP*TP*TP*T)-3', 5'-D(*AP*AP*AP*AP*AP*AP*GP*TP*TP*TP*TP*TP*T)-3' | BGT in complex with a 13mer DNA containing a central C:G base pair and UDP | X-ray diffraction | 1.8 | 26 | 2004-06-22 | ||||
| 8 | 3O1T|1|C+ 3O1T|1|B | DNA (5'-D(*AP*AP*CP*GP*GP*TP*AP*TP*TP*AP*CP*CP*T)-3'), DNA (5'-D(*AP*GP*GP*TP*AP*AP*(MDU)P*AP*CP*CP*GP*T)-3') | Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase | X-ray diffraction | 1.48 | 25 | 2010-11-17 | ||||
| 9 | 3I0X|1|C+ 3I0X|1|D | 5'-D(*AP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3', 5'-D(*GP*GP*TP*AP*GP*AP*CP*AP*TP*GP*GP*A)-3' | Crystal structure of Clostridium acetobutylicum 8-oxoguanine glycosylase/lyase in complex with dsDNA containing adenine opposite to 8-oxoG | X-ray diffraction | 1.8 | 25 | 2009-09-29 | ||||
| 10 | 3I0W|1|B+ 3I0W|1|C | 5'-D(*AP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3', 5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*A)-3' | Crystal structure of Clostridium acetobutylicum 8-oxoguanine glycosylase/lyase in complex with dsDNA containing cytosine opposite to 8-oxoG | X-ray diffraction | 1.73 | 25 | 2009-09-29 | ||||
| 11 | 3O1U|1|C+ 3O1U|1|B | DNA (5'-D(*AP*AP*CP*GP*GP*TP*AP*TP*TP*AP*CP*CP*T)-3'), DNA (5'-D(*AP*GP*GP*TP*AP*AP*(MDV)P*AP*CP*CP*GP*T)-3') | Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase | X-ray diffraction | 1.54 | 25 | 2010-11-17 | ||||
| 12 | 1M5R|1|C+ 1M5R|1|E | 5'-D(*CP*TP*AP*TP*CP*TP*GP*AP*GP*TP*AP*TP*C)-3', 5'-D(*GP*AP*TP*AP*CP*TP*3DRP*AP*GP*AP*TP*AP*G)-3' | Ternary complex of T4 phage BGT with UDP and a 13 mer DNA duplex | X-ray diffraction | 1.8 | 26 | 2002-12-11 | ||||
| 13 | 1M5R|1|D+ 1M5R|1|F | 5'-D(*CP*TP*AP*TP*CP*TP*GP*AP*GP*TP*AP*TP*C)-3', 5'-D(*GP*AP*TP*AP*CP*TP*3DRP*AP*GP*AP*TP*AP*G)-3' | Ternary complex of T4 phage BGT with UDP and a 13 mer DNA duplex | X-ray diffraction | 1.8 | 26 | 2002-12-11 | ||||
| 14 | 3O1R|1|C+ 3O1R|1|B | DNA (5'-D(*AP*AP*CP*GP*GP*TP*AP*TP*TP*AP*CP*CP*T)-3'), DNA (5'-D(*AP*GP*GP*TP*AP*AP*(MDK)P*AP*CP*CP*GP*T)-3') | Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase | X-ray diffraction | 1.77 | 25 | 2010-11-17 | ||||
| 15 | 2HHW|1|C+ 2HHW|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*(DDG))-3' | ddTTP:O6-methyl-guanine pair in the polymerase active site, in the closed conformation | X-ray diffraction | 1.88 | 20 | 2006-12-12 | ||||
| 16 | 2HHW|1|F+ 2HHW|1|E | 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*(DDG))-3' | ddTTP:O6-methyl-guanine pair in the polymerase active site, in the closed conformation | X-ray diffraction | 1.88 | 20 | 2006-12-12 | ||||
| 17 | 3O1O|1|B+ 3O1O|1|C | DNA (5'-D(*AP*AP*CP*GP*GP*TP*AP*TP*TP*AP*CP*CP*T)-3'), DNA (5'-D(*T*AP*GP*GP*TP*AP*AP*(MFT)P*AP*CP*CP*GP*T)-3') | Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase | X-ray diffraction | 1.92 | 25 | 2010-11-17 | ||||
| 18 | 2UYC|1|C+ 2UYC|1|D | 5'-D(*GP*TP*CP*AP*GP*CP*GP*CP*AP*TP *CP*C)-3', 5'-D(*TP*GP*GP*AP*TP*GP*5CMP*GP*CP*TP *GP*AP*C)-3' | synthetic construct | HhaI DNA methyltransferase R163N mutant complex with 13mer GCGC-GMGC oligonucleotide and SAH | X-ray diffraction | 2 | 25 | 2008-05-27 | |||
| 19 | 3H8R|1|B+ 3H8R|1|C | 5'-D(*CP*TP*GP*TP*AP*TP*(2YR)P*AP*TP*(6MA)P*GP*CP*G)-3', 5'-D(*TP*CP*GP*CP*TP*AP*TP*AP*AP*TP*AP*CP*A)-3' | synthetic construct | Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked host-guest system | X-ray diffraction | 1.77 | 26 | 2010-03-31 | |||
| 20 | 3L2C|1|B+ 3L2C|1|C | FOXO consensus binding sequence, minus strand, FOXO consensus binding sequence, plus strand | Crystal Structure of the DNA Binding Domain of FOXO4 Bound to DNA | X-ray diffraction | 1.868 | 26 | 2009-12-29 | ||||
| 21 | 3OHA|1|T+ 3OHA|1|P | 5'-D(*GP*TP*CP*CP*TP*CP*CP*CP*CP*TP*(DOC))-3', 5'-D(P*TP*(8OG)P*GP*AP*GP*GP*GP*GP*AP*GP*GP*AP*C)-3' | Yeast DNA polymerase eta inserting dCTP opposite an 8oxoG lesion | X-ray diffraction | 2 | 24 | 2010-12-22 | ||||
| 22 | 3O1S|1|C+ 3O1S|1|B | DNA (5'-D(*AP*AP*CP*GP*GP*TP*AP*TP*TP*AP*CP*CP*T)-3'), DNA (5'-D(*AP*GP*GP*TP*AP*AP*(MDQ)P*AP*CP*CP*GP*T)-3') | Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase | X-ray diffraction | 1.58 | 25 | 2010-11-17 | ||||
| 23 | 3BTX|1|B+ 3BTX|1|C | DNA (5'-D(*CP*TP*GP*TP*AP*TP*(2YR)P*AP*TP*TP*GP*CP*G)-3'), DNA (5'-D(*DTP*DCP*DGP*DCP*DAP*DAP*DTP*DAP*DAP*DTP*DAP*DCP*DA)-3') | X-ray structure of human ABH2 bound to dsDNA through active site cross-linking | X-ray diffraction | 2 | 26 | 2008-04-22 | ||||
| 24 | 2HVI|1|C+ 2HVI|1|B | 5'-D(*C*AP*TP*GP*CP*GP*AP*GP*TP*CP*AP*GP*G)-3', 5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DDG))-3' | ddCTP:G pair in the polymerase active site (0 position) | X-ray diffraction | 1.98 | 21 | 2006-12-12 | ||||
| 25 | 2HVI|1|F+ 2HVI|1|E | 5'-D(*C*AP*TP*GP*CP*GP*AP*GP*TP*CP*AP*GP*G)-3', 5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DDG))-3' | ddCTP:G pair in the polymerase active site (0 position) | X-ray diffraction | 1.98 | 21 | 2006-12-12 | ||||
| 26 | 3H8X|1|B+ 3H8X|1|C | 5'-D(*CP*TP*GP*TP*(ME6)P*TP*(2YR)P*AP*TP*TP*GP*CP*G)-3', 5'-D(*TP*CP*GP*CP*AP*AP*TP*AP*AP*GP*AP*CP*A)-3' | synthetic construct | Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked host-guest system | X-ray diffraction | 1.95 | 26 | 2010-03-31 | |||
| 27 | 3O1V|1|C+ 3O1V|1|B | DNA (5'-D(*AP*AP*CP*GP*GP*TP*AP*TP*TP*AP*CP*CP*T)-3'), DNA (5'-D(*AP*GP*GP*TP*AP*AP*(MDJ)P*AP*CP*CP*GP*T)-3') | Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase | X-ray diffraction | 1.9 | 25 | 2010-11-17 | ||||
| 28 | 3H8O|1|B+ 3H8O|1|C | 5'-D(*CP*TP*GP*TP*AP*TP*(2YR)P*AP*TP*(MA7)P*GP*CP*G)-3', 5'-D(*TP*CP*GP*CP*TP*AP*TP*AP*AP*TP*AP*CP*A)-3' | synthetic construct | Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked host-guest system | X-ray diffraction | 2 | 26 | 2010-03-31 | |||
| 29 | 2ZO1|1|D+ 2ZO1|1|E | DNA (5'-D(*DGP*DTP*DCP*DAP*DGP*(5CM)P*DGP*DCP*DAP*DAP*DTP*DGP*DG)-3'), DNA (5'-D(*DTP*DCP*DCP*DAP*DTP*DGP*DCP*DGP*DCP*DTP*DGP*DAP*DC)-3') | Mouse NP95 SRA domain DNA specific complex 2 | X-ray diffraction | 1.96 | 21 | 2008-09-09 | ||||
| 30 | 3BI3|1|B+ 3BI3|1|C | DNA (5'-D(*DAP*DAP*DCP*DGP*DGP*DTP*DAP*DTP*DTP*DAP*DCP*DCP*DT)-3'), DNA (5'-D(*TP*AP*GP*GP*TP*AP*AP*(MA7)P*AP*(2YR)P*CP*GP*T)-3') | X-ray structure of AlkB protein bound to dsDNA containing 1meA/A with cofactors | X-ray diffraction | 1.9 | 25 | 2008-04-22 | ||||
| 31 | 1PUY|1|A | 5'-D(*GP*TP*TP*TP*TP*GP*(S02)P*CP*AP*AP*AP*AP*C)-3' | 1.5 A resolution structure of a synthetic DNA hairpin with a stilbenediether linker | X-ray diffraction | 1.5 | 12 | 2003-10-14 | ||||
| 32 | 1PUY|1|B | 5'-D(*GP*TP*TP*TP*TP*GP*(S02)P*CP*AP*AP*AP*AP*C)-3' | 1.5 A resolution structure of a synthetic DNA hairpin with a stilbenediether linker | X-ray diffraction | 1.5 | 12 | 2003-10-14 | ||||
| 33 | 3E6C|1|A+ 3E6C|1|B | DNA (5'-D(P*DGP*DCP*DAP*DTP*DTP*DAP*DAP*DCP*DAP*DTP*DGP*DCP*DC)-3'), DNA (5'-D(P*DGP*DGP*DCP*DAP*DTP*DGP*DTP*DTP*DAP*DAP*DTP*DGP*DC)-3') | CprK OCPA DNA Complex | X-ray diffraction | 1.8 | 26 | 2008-09-30 | ||||
| 34 | 1YO5|1|A+ 1YO5|1|B | Enhancer site of Prostate Specific Antigen Promoter Region | Analysis of the 2.0A crystal structure of the protein-DNA complex of human PDEF Ets domain bound to the prostate specific antigen regulatory site | X-ray diffraction | 2 | 26 | 2005-05-17 | ||||
| 35 | 4BDP|1|T+ 4BDP|1|P | DNA (5'-D(*GP*CP*AP*TP*CP*AP*TP*GP*CP*AP*A)-3'), DNA (5'-D(*TP*AP*TP*TP*GP*CP*AP*TP*GP*AP*TP*GP*C)-3') | CRYSTAL STRUCTURE OF BACILLUS DNA POLYMERASE I FRAGMENT COMPLEXED TO 11 BASE PAIRS OF DUPLEX DNA AFTER ADDITION OF TWO DATP RESIDUES | X-ray diffraction | 1.8 | 24 | 1999-01-13 | ||||
| 36 | 1Y8Z|1|C+ 1Y8Z|1|D | 5'-D(*CP*TP*AP*TP*CP*TP*GP*AP*G)-3', 5'-D(*GP*AP*TP*AP*CP*TP*(5HU)P*AP*GP*AP*TP*AP*G)-3' | alpha-glucosyltransferase in complex with UDP and a 13-mer DNA containing a HMU base at 1.9 A resolution | X-ray diffraction | 1.9 | 22 | 2005-08-30 | ||||
| 37 | 2OXV|1|C | DNA (5'-D(*TP*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3') | Structure of the A138T promiscuous mutant of the EcoRI restriction endonuclease bound to its cognate recognition site. | X-ray diffraction | 1.95 | 13 | 2007-10-23 | ||||
| 38 | 1GD2|1|A+ 1GD2|1|B | DNA (5'-D(*AP*GP*GP*TP*TP*AP*CP*GP*TP*AP*AP*CP*C)-3') | CRYSTAL STRUCTURE OF BZIP TRANSCRIPTION FACTOR PAP1 BOUND TO DNA | X-ray diffraction | 2 | 26 | 2000-10-02 | ||||
| 39 | 1GD2|1|C+ 1GD2|1|D | DNA (5'-D(*AP*GP*GP*TP*TP*AP*CP*GP*TP*AP*AP*CP*C)-3') | CRYSTAL STRUCTURE OF BZIP TRANSCRIPTION FACTOR PAP1 BOUND TO DNA | X-ray diffraction | 2 | 26 | 2000-10-02 | ||||
| 40 | 1WTE|1|X+ 1WTE|1|Y | 5'-D(*AP*CP*CP*GP*GP*GP*CP*CP*CP*TP*GP*CP*C)-3', 5'-D(*GP*GP*CP*AP*GP*GP*GP*CP*CP*CP*GP*GP*T)-3' | Crystal structure of type II restrcition endonuclease, EcoO109I complexed with cognate DNA | X-ray diffraction | 1.9 | 26 | 2004-12-14 | ||||
| 41 | 3GV5|1|F+ 3GV5|1|E | 5'-D(*GP*TP*GP*GP*AP*TP*GP*AP*G)-3', 5'-D(P*CP*AP*TP*TP*CP*TP*CP*AP*TP*CP*CP*AP*C)-3' | Human DNA polymerase iota in complex with T template DNA and incoming ddADP | X-ray diffraction | 2 | 22 | 2009-06-02 | ||||
| 42 | 3GV5|1|T+ 3GV5|1|P | 5'-D(*GP*TP*GP*GP*AP*TP*GP*AP*G)-3', 5'-D(P*CP*AP*TP*TP*CP*TP*CP*AP*TP*CP*CP*AP*C)-3' | Human DNA polymerase iota in complex with T template DNA and incoming ddADP | X-ray diffraction | 2 | 22 | 2009-06-02 | ||||
| 43 | 1K3X|1|B+ 1K3X|1|C | 5'-D(*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3', 5'-D(*GP*GP*CP*(BRU)P*(BRU)P*CP*AP*(BRU)P*CP*CP*(BRU)P*GP*G)-3' | Crystal structure of a trapped reaction intermediate of the DNA repair enzyme Endonuclease VIII with Brominated-DNA | X-ray diffraction | 1.25 | 19 | 2002-10-04 | ||||
| 44 | 1K3W|1|B+ 1K3W|1|C | 5'-D(*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3', 5'-D(*GP*GP*CP*TP*TP*CP*AP*TP*CP*CP*TP*GP*G)-3' | Crystal structure of a trapped reaction intermediate of the DNA Repair Enzyme Endonuclease VIII with DNA | X-ray diffraction | 1.42 | 18 | 2002-10-04 | ||||
| 45 | 1LLM|1|A+ 1LLM|1|B | 5'-D(*TP*CP*CP*CP*AP*CP*GP*CP*GP*TP*GP*GP*G)-3' | Crystal Structure of a Zif23-GCN4 Chimera Bound to DNA | X-ray diffraction | 1.5 | 26 | 2003-09-30 | ||||
| 46 | 1QUM|1|D+ 1QUM|1|C+ 1QUM|1|B | 5'-D(*(3DR)P*CP*GP*AP*CP*GP*A)-3', 5'-D(*CP*GP*TP*CP*C)-3', 5'-D(*TP*CP*GP*TP*CP*GP*GP*GP*GP*AP*CP*G)-3' | CRYSTAL STRUCTURE OF ESCHERICHIA COLI ENDONUCLEASE IV IN COMPLEX WITH DAMAGED DNA | X-ray diffraction | 1.55 | 26 | 1999-08-31 | ||||
| 47 | 3PVI|1|C+ 3PVI|1|D | DNA (5'-D(*TP*GP*AP*CP*CP*AP*GP*CP*TP*GP*GP*TP*C)-3') | D34G MUTANT OF PVUII ENDONUCLEASE COMPLEXED WITH COGNATE DNA SHOWS THAT ASP34 IS DIRECTLY INVOLVED IN DNA RECOGNITION AND INDIRECTLY INVOLVED IN CATALYSIS | X-ray diffraction | 1.59 | 26 | 1998-10-14 | ||||
| 48 | 1DC1|1|C+ 1DC1|1|W | DNA (5'-D(*T*AP*TP*AP*CP*TP*CP*GP*AP*GP*TP*AP*T)-3') | RESTRICTION ENZYME BSOBI/DNA COMPLEX STRUCTURE: ENCIRCLEMENT OF THE DNA AND HISTIDINE-CATALYZED HYDROLYSIS WITHIN A CANONICAL RESTRICTION ENZYME FOLD | X-ray diffraction | 1.7 | 25 | 2001-02-21 | ||||
| 49 | 2PVI|1|C+ 2PVI|1|D | DNA (5'-D(*TP*GP*AP*CP*CP*AP*GP*(C38)P*TP*GP*GP*TP*C)-3') | PVUII ENDONUCLEASE COMPLEXED TO AN IODINATED COGNATE DNA | X-ray diffraction | 1.76 | 26 | 1999-12-20 | ||||
| 50 | 1EYU|1|C+ 1EYU|1|D | DNA (5'-D(*TP*GP*AP*CP*CP*AP*GP*CP*TP*GP*GP*TP*C)-3') | HIGH RESOLUTION STRUCTURE OF THE PVUII ENDONCULEASE/COGNATE DNA COMPLEX AT PH 4.6 | X-ray diffraction | 1.78 | 26 | 2000-07-21 | ||||
| 51 | 1CL8|1|B | DNA (5'-D(*TP*CP*GP*CP*GP*AP*(PRN)P*TP*TP*CP*GP*CP*G)-3') | A PRE-TRANSITION STATE ECO RI ENDONUCLEASE/COGNATE DNA (TCGCGAPTTCGCG) COMPLEX WITH DNA BASE ANALOG PURINE (P) | X-ray diffraction | 1.8 | 13 | 1999-05-19 | ||||
| 52 | 1A73|1|C+ 1A73|1|E+ 1A73|1|D+ 1A73|1|F | DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*A)-3'), DNA (5'-D(P*GP*AP*GP*AP*GP*TP*CP*A)-3') | INTRON-ENCODED ENDONUCLEASE I-PPOI COMPLEXED WITH DNA | X-ray diffraction | 1.8 | 42 | 1998-10-14 | ||||
| 53 | 1CKQ|1|B | DNA (5'-D(*TP*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3') | PRE-TRANSITION STATE ECO RI ENDONUCLEASE/COGNATE DNA (TCGCGAATTCGCG) COMPLEX | X-ray diffraction | 1.85 | 13 | 1999-04-26 | ||||
| 54 | 2C7Q|1|C+ 2C7Q|1|D | 5'-D(*T*GP*GP*(2PR)*GP*GP*(5CM)*GP*CP*TP*GP* AP*C)-3', 5'-D(*T*GP*TP*CP*AP*GP*CP*GP*CP*CP*GP*CP*C)-3' | synthetic construct | HhaI DNA methyltransferase complex with oligonucleotide containing 2- aminopurine outside the recognition sequence (paired with G) and SAH | X-ray diffraction | 1.85 | 25 | 2005-12-14 | |||
| 55 | 2C7O|1|C+ 2C7O|1|D | 5'-D(*T*GP*GP*AP*TP*GP*(5CM)*GP*CP*TP*GP*AP *C)-3', 5'-D(*T*GP*TP*CP*AP*(2PR)*CP*GP*CP*AP*TP*CP *C)-3' | synthetic construct | HhaI DNA methyltransferase complex with 13mer oligonucleotide containing 2-aminopurine adjacent to the target base (PCGC:GMGC) and SAH | X-ray diffraction | 1.9 | 25 | 2005-12-14 | |||
| 56 | 2HR1|1|D+ 2HR1|1|C | 5'-D(*GP*AP*TP*AP*GP*CP*GP*CP*TP*AP*TP*C)-3', 5'-D(*TP*GP*AP*TP*AP*GP*CP*GP*CP*TP*AP*TP*C)-3' | Ternary structure of WT M.HhaI C5-Cytosine DNA methyltransferase with unmodified DNA and AdoHcy | X-ray diffraction | 1.96 | 25 | 2006-09-19 |
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 | 1Y8Z|1|C+ 1Y8Z|1|D | alpha-glucosyltransferase in complex with UDP and a 13-mer DNA containing a HMU base at 1.9 A resolution | X-RAY DIFFRACTION | 1.9 | 22 | enzyme,transferase | ||
| 2 | 1QUM|1|D+ 1QUM|1|C+ 1QUM|1|B | CRYSTAL STRUCTURE OF ESCHERICHIA COLI ENDONUCLEASE IV IN COMPLEX WITH DAMAGED DNA | X-RAY DIFFRACTION | 1.55 | 26 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 3 | 3I0X|1|C+ 3I0X|1|D | Crystal structure of Clostridium acetobutylicum 8-oxoguanine glycosylase/lyase in complex with dsDNA containing adenine opposite to 8-oxoG | X-RAY DIFFRACTION | 1.8 | 25 | B-form double helix,double helix,structure | enzyme,hydrolase | |
| 4 | 3I0W|1|B+ 3I0W|1|C | Crystal structure of Clostridium acetobutylicum 8-oxoguanine glycosylase/lyase in complex with dsDNA containing cytosine opposite to 8-oxoG | X-RAY DIFFRACTION | 1.73 | 25 | B-form double helix,double helix,structure | enzyme,hydrolase | |
| 5 | 3GV5|1|F+ 3GV5|1|E | Human DNA polymerase iota in complex with T template DNA and incoming ddADP | X-RAY DIFFRACTION | 2 | 22 | enzyme,polymerase,transferase | ||
| 6 | 3GV5|1|T+ 3GV5|1|P | Human DNA polymerase iota in complex with T template DNA and incoming ddADP | X-RAY DIFFRACTION | 2 | 22 | enzyme,polymerase,transferase | ||
| 7 | 4BDP|1|T+ 4BDP|1|P | CRYSTAL STRUCTURE OF BACILLUS DNA POLYMERASE I FRAGMENT COMPLEXED TO 11 BASE PAIRS OF DUPLEX DNA AFTER ADDITION OF TWO DATP RESIDUES | X-RAY DIFFRACTION | 1.8 | 24 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 8 | 2C7O|1|C+ 2C7O|1|D | HhaI DNA methyltransferase complex with 13mer oligonucleotide containing 2-aminopurine adjacent to the target base (PCGC:GMGC) and SAH | X-RAY DIFFRACTION | 1.9 | 25 | B-form double helix,double helix,structure | enzyme,methylase,transferase | |
| 9 | 2UYC|1|C+ 2UYC|1|D | HhaI DNA methyltransferase R163N mutant complex with 13mer GCGC-GMGC oligonucleotide and SAH | X-RAY DIFFRACTION | 2 | 25 | double helix,structure | enzyme,methylase,transferase | |
| 10 | 2C7Q|1|C+ 2C7Q|1|D | HhaI DNA methyltransferase complex with oligonucleotide containing 2- aminopurine outside the recognition sequence (paired with G) and SAH | X-RAY DIFFRACTION | 1.85 | 25 | enzyme,methylase,transferase | ||
| 11 | 1K3W|1|B+ 1K3W|1|C | Crystal structure of a trapped reaction intermediate of the DNA Repair Enzyme Endonuclease VIII with DNA | X-RAY DIFFRACTION | 1.42 | 18 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 12 | 1K3X|1|B+ 1K3X|1|C | Crystal structure of a trapped reaction intermediate of the DNA repair enzyme Endonuclease VIII with Brominated-DNA | X-RAY DIFFRACTION | 1.25 | 19 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 13 | 1SXQ|1|C+ 1SXQ|1|E | BGT in complex with a 13mer DNA containing a central C:G base pair and UDP | X-RAY DIFFRACTION | 1.8 | 26 | B-form double helix,double helix,structure | enzyme,transferase | |
| 14 | 1SXQ|1|D+ 1SXQ|1|F | BGT in complex with a 13mer DNA containing a central C:G base pair and UDP | X-RAY DIFFRACTION | 1.8 | 26 | B-form double helix,double helix,structure | enzyme,transferase | |
| 15 | 1YO5|1|A+ 1YO5|1|B | Analysis of the 2.0A crystal structure of the protein-DNA complex of human PDEF Ets domain bound to the prostate specific antigen regulatory site | X-RAY DIFFRACTION | 2 | 26 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead | |
| 16 | 2ZO1|1|D+ 2ZO1|1|E | Mouse NP95 SRA domain DNA specific complex 2 | X-RAY DIFFRACTION | 1.96 | 21 | B-form double helix,double helix,structure | enzyme,ligase | |
| 17 | 3L2C|1|B+ 3L2C|1|C | Crystal Structure of the DNA Binding Domain of FOXO4 Bound to DNA | X-RAY DIFFRACTION | 1.868 | 26 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead | |
| 18 | 1GD2|1|C+ 1GD2|1|D | CRYSTAL STRUCTURE OF BZIP TRANSCRIPTION FACTOR PAP1 BOUND TO DNA | X-RAY DIFFRACTION | 2 | 26 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),basic transcription factor,leucine zipper (bZIP),regulatory,transcription | |
| 19 | 1GD2|1|A+ 1GD2|1|B | CRYSTAL STRUCTURE OF BZIP TRANSCRIPTION FACTOR PAP1 BOUND TO DNA | X-RAY DIFFRACTION | 2 | 26 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),basic transcription factor,leucine zipper (bZIP),regulatory,transcription | |
| 20 | 3OHA|1|T+ 3OHA|1|P | Yeast DNA polymerase eta inserting dCTP opposite an 8oxoG lesion | X-RAY DIFFRACTION | 2 | 24 | double helix,structure | enzyme,polymerase,transferase | |
| 21 | 1LLM|1|A+ 1LLM|1|B | Crystal Structure of a Zif23-GCN4 Chimera Bound to DNA | X-RAY DIFFRACTION | 1.5 | 26 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc finger C2H2,Zinc-coordinating,regulatory,transcription | |
| 22 | 3E6C|1|A+ 3E6C|1|B | CprK OCPA DNA Complex | X-RAY DIFFRACTION | 1.8 | 26 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),helix-turn-helix (HTH),regulatory,transcription,winged helix/forkhead | |
| 23 | 1EYU|1|C+ 1EYU|1|D | HIGH RESOLUTION STRUCTURE OF THE PVUII ENDONCULEASE/COGNATE DNA COMPLEX AT PH 4.6 | X-RAY DIFFRACTION | 1.78 | 26 | double helix,structure | enzyme,hydrolase,nuclease | |
| 24 | 2PVI|1|C+ 2PVI|1|D | PVUII ENDONUCLEASE COMPLEXED TO AN IODINATED COGNATE DNA | X-RAY DIFFRACTION | 1.76 | 26 | double helix,structure | enzyme,hydrolase,nuclease | |
| 25 | 3PVI|1|C+ 3PVI|1|D | D34G MUTANT OF PVUII ENDONUCLEASE COMPLEXED WITH COGNATE DNA SHOWS THAT ASP34 IS DIRECTLY INVOLVED IN DNA RECOGNITION AND INDIRECTLY INVOLVED IN CATALYSIS | X-RAY DIFFRACTION | 1.59 | 26 | double helix,structure | enzyme,hydrolase,nuclease | |
| 26 | 1WTE|1|X+ 1WTE|1|Y | Crystal structure of type II restrcition endonuclease, EcoO109I complexed with cognate DNA | X-RAY DIFFRACTION | 1.9 | 26 | double helix,structure | enzyme,hydrolase,nuclease | |
| 27 | 1A73|1|C+ 1A73|1|E+ 1A73|1|D+ 1A73|1|F | INTRON-ENCODED ENDONUCLEASE I-PPOI COMPLEXED WITH DNA | X-RAY DIFFRACTION | 1.8 | 42 | double helix,structure | enzyme,hydrolase,nuclease | |
| 28 | 1CKQ|1|B | PRE-TRANSITION STATE ECO RI ENDONUCLEASE/COGNATE DNA (TCGCGAATTCGCG) COMPLEX | X-RAY DIFFRACTION | 1.85 | 13 | double helix,structure | enzyme,hydrolase,nuclease | |
| 29 | 1CL8|1|B | A PRE-TRANSITION STATE ECO RI ENDONUCLEASE/COGNATE DNA (TCGCGAPTTCGCG) COMPLEX WITH DNA BASE ANALOG PURINE (P) | X-RAY DIFFRACTION | 1.8 | 13 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 30 | 2OXV|1|C | Structure of the A138T promiscuous mutant of the EcoRI restriction endonuclease bound to its cognate recognition site. | X-RAY DIFFRACTION | 1.95 | 13 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 31 | 1DC1|1|C+ 1DC1|1|W | RESTRICTION ENZYME BSOBI/DNA COMPLEX STRUCTURE: ENCIRCLEMENT OF THE DNA AND HISTIDINE-CATALYZED HYDROLYSIS WITHIN A CANONICAL RESTRICTION ENZYME FOLD | X-RAY DIFFRACTION | 1.7 | 25 | double helix,structure | enzyme,hydrolase,nuclease | |
| 32 | 2HR1|1|D+ 2HR1|1|C | Ternary structure of WT M.HhaI C5-Cytosine DNA methyltransferase with unmodified DNA and AdoHcy | X-RAY DIFFRACTION | 1.96 | 25 | B-form double helix,double helix,structure | enzyme,methylase,transferase | |
| 33 | 1M5R|1|D+ 1M5R|1|F | Ternary complex of T4 phage BGT with UDP and a 13 mer DNA duplex | X-RAY DIFFRACTION | 1.8 | 26 | enzyme,transferase | ||
| 34 | 1M5R|1|C+ 1M5R|1|E | Ternary complex of T4 phage BGT with UDP and a 13 mer DNA duplex | X-RAY DIFFRACTION | 1.8 | 26 | enzyme,transferase | ||
| 35 | 3BTX|1|B+ 3BTX|1|C | X-ray structure of human ABH2 bound to dsDNA through active site cross-linking | X-RAY DIFFRACTION | 2 | 26 | enzyme,oxidoreductase | ||
| 36 | 3H8R|1|B+ 3H8R|1|C | Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked host-guest system | X-RAY DIFFRACTION | 1.77 | 26 | enzyme,oxidoreductase | ||
| 37 | 3H8O|1|B+ 3H8O|1|C | Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked host-guest system | X-RAY DIFFRACTION | 2 | 26 | enzyme,oxidoreductase | ||
| 38 | 3MR2|1|T+ 3MR2|1|P | Human DNA polymerase eta in complex with normal DNA and incoming nucleotide (Nrm) | X-RAY DIFFRACTION | 1.83 | 21 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 39 | 2HHW|1|F+ 2HHW|1|E | ddTTP:O6-methyl-guanine pair in the polymerase active site, in the closed conformation | X-RAY DIFFRACTION | 1.88 | 20 | double helix,structure | enzyme,polymerase,transferase | |
| 40 | 2HHW|1|C+ 2HHW|1|B | ddTTP:O6-methyl-guanine pair in the polymerase active site, in the closed conformation | X-RAY DIFFRACTION | 1.88 | 20 | double helix,structure | enzyme,polymerase,transferase | |
| 41 | 2HVI|1|F+ 2HVI|1|E | ddCTP:G pair in the polymerase active site (0 position) | X-RAY DIFFRACTION | 1.98 | 21 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 42 | 2HVI|1|C+ 2HVI|1|B | ddCTP:G pair in the polymerase active site (0 position) | X-RAY DIFFRACTION | 1.98 | 21 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 43 | 3H8X|1|B+ 3H8X|1|C | Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked host-guest system | X-RAY DIFFRACTION | 1.95 | 26 | enzyme,oxidoreductase | ||
| 44 | 3BIE|1|C+ 3BIE|1|B | X-ray structure of E coli AlkB bound to dsDNA containing 1meA/T with Mn and 2KG | X-RAY DIFFRACTION | 1.68 | 25 | enzyme,oxidoreductase | ||
| 45 | 3O1S|1|C+ 3O1S|1|B | Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase | X-RAY DIFFRACTION | 1.58 | 25 | enzyme,oxidoreductase | ||
| 46 | 3O1R|1|C+ 3O1R|1|B | Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase | X-RAY DIFFRACTION | 1.77 | 25 | enzyme,oxidoreductase | ||
| 47 | 3O1U|1|C+ 3O1U|1|B | Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase | X-RAY DIFFRACTION | 1.54 | 25 | enzyme,oxidoreductase | ||
| 48 | 3O1T|1|C+ 3O1T|1|B | Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase | X-RAY DIFFRACTION | 1.48 | 25 | enzyme,oxidoreductase | ||
| 49 | 3O1V|1|C+ 3O1V|1|B | Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase | X-RAY DIFFRACTION | 1.9 | 25 | enzyme,oxidoreductase | ||
| 50 | 3BI3|1|B+ 3BI3|1|C | X-ray structure of AlkB protein bound to dsDNA containing 1meA/A with cofactors | X-RAY DIFFRACTION | 1.9 | 25 | enzyme,oxidoreductase | ||
| 51 | 3O1P|1|B+ 3O1P|1|C | Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase | X-RAY DIFFRACTION | 1.51 | 25 | enzyme,oxidoreductase | ||
| 52 | 3O1M|1|B+ 3O1M|1|C | Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase | X-RAY DIFFRACTION | 1.75 | 25 | enzyme,oxidoreductase | ||
| 53 | 3O1O|1|B+ 3O1O|1|C | Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase | X-RAY DIFFRACTION | 1.92 | 25 | enzyme,oxidoreductase | ||
| 54 | 3BKZ|1|B+ 3BKZ|1|C | X-ray structure of E coli AlkB crosslinked to dsDNA in the active site | X-RAY DIFFRACTION | 1.65 | 26 | B-form double helix,double helix,feature,mispair,structure | enzyme,oxidoreductase | |
| 55 | 1PUY|1|A | 1.5 A resolution structure of a synthetic DNA hairpin with a stilbenediether linker | X-RAY DIFFRACTION | 1.5 | 12 | B-form double helix,double helix,structure | ||
| 56 | 1PUY|1|B | 1.5 A resolution structure of a synthetic DNA hairpin with a stilbenediether linker | X-RAY DIFFRACTION | 1.5 | 12 | B-form double helix,double helix,structure |
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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