Equivalence class DNA_2.0_57332.2 Current
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | #NTs | Date |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 3FDQ|1|C+ 3FDQ|1|D (rep) | 5'-D(*AP*TP*TP*TP*TP*TP*TP*AP*AP*AP*AP*AP*AP*AP*T)-3', 5'-D(*TP*AP*TP*TP*TP*TP*TP*TP*TP*AP*AP*AP*AP*AP*A)-3' | Recognition of AT-rich DNA binding sites by the MogR Repressor | X-ray diffraction | 1.75 | 30 | 2009-06-02 | ||||
| 2 | 1NKC|1|B+ 1NKC|1|C | DNA PRIMER STRAND, DNA TEMPLATE STRAND | A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A GUANINE-THYMINE MISMATCH AFTER FIVE ROUNDS OF PRIMER EXTENSION, FOLLOWING INCORPORATION OF DCTP, DGTP, DTTP, AND DATP. | X-ray diffraction | 1.8 | 30 | 2004-03-30 | ||||
| 3 | 3MFI|1|T+ 3MFI|1|P | 5'-D(*GP*TP*CP*CP*TP*CP*CP*CP*CP*TP*(DOC))-3', 5'-D(*TP*AP*AP*(TTD)P*GP*AP*GP*GP*GP*GP*AP*GP*GP*AP*C)-3' | DNA Polymerase Eta in Complex With a cis-syn Thymidine Dimer | X-ray diffraction | 1.76 | 24 | 2010-06-23 | ||||
| 4 | 1NK0|1|C+ 1NK0|1|B | DNA PRIMER STRAND, DNA TEMPLATE STRAND | ADENINE-GUANINE MISMATCH AT THE POLYMERASE ACTIVE SITE | X-ray diffraction | 1.7 | 23 | 2004-03-30 | ||||
| 5 | 1RH6|1|C+ 1RH6|1|D | 5'-D(*CP*TP*AP*TP*GP*TP*AP*GP*TP*CP*TP*GP*TP*TP*G)-3', 5'-D(P*CP*AP*AP*CP*AP*GP*AP*CP*TP*AP*CP*AP*TP*AP*G)-3' | Bacteriophage Lambda Excisionase (Xis)-DNA Complex | X-ray diffraction | 1.7 | 28 | 2004-06-29 | ||||
| 6 | 1NK8|1|C+ 1NK8|1|B | DNA PRIMER STRAND, DNA TEMPLATE STRAND | A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A GUANINE-THYMINE MISMATCH AFTER A SINGLE ROUND OF PRIMER EXTENSION, FOLLOWING INCORPORATION OF DCTP. | X-ray diffraction | 1.9 | 23 | 2004-03-30 | ||||
| 7 | 3IAG|1|A+ 3IAG|1|B | 5'-D(*AP*AP*TP*CP*TP*TP*TP*CP*AP*CP*AP*CP*GP*AP*T)-3', 5'-D(*TP*TP*AP*TP*CP*GP*TP*GP*TP*GP*AP*AP*AP*GP*A)-3' | CSL (RBP-Jk) bound to HES-1 nonconsensus site | X-ray diffraction | 2 | 30 | 2009-11-10 | ||||
| 8 | 1NKB|1|C+ 1NKB|1|B | DNA PRIMER STRAND, DNA TEMPLATE STRAND | A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A GUANINE-THYMINE MISMATCH AFTER THREE ROUNDS OF PRIMER EXTENSION, FOLLOWING INCORPORATION OF DCTP, DGTP, AND DTTP. | X-ray diffraction | 2 | 27 | 2004-03-30 | ||||
| 9 | 1U4B|1|C+ 1U4B|1|B | DNA primer strand, DNA template strand with 8-oxoguanine | Extension of an adenine-8oxoguanine mismatch | X-ray diffraction | 1.6 | 23 | 2004-09-14 | ||||
| 10 | 1NK7|1|C+ 1NK7|1|B | DNA PRIMER STRAND, DNA TEMPLATE STRAND | GUANINE-ADENINE MISMATCH AT THE POLYMERASE ACTIVE SITE | X-ray diffraction | 1.9 | 20 | 2004-03-30 | ||||
| 11 | 1NJX|1|C+ 1NJX|1|B | DNA PRIMER STRAND, DNA TEMPLATE STRAND | THYMINE-GUANINE MISMATCH AT THE POLYMERASE ACTIVE SITE | X-ray diffraction | 1.65 | 23 | 2004-03-30 | ||||
| 12 | 1NJW|1|C+ 1NJW|1|B | DNA PRIMER STRAND, DNA TEMPLATE STRAND | GUANINE-THYMINE MISMATCH AT THE POLYMERASE ACTIVE SITE | X-ray diffraction | 1.9 | 23 | 2004-03-30 | ||||
| 13 | 2XHI|1|B+ 2XHI|1|C | 5'-D(*GP*CP*GP*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*AP*CP*GP*C)-3' | Separation-of-function mutants unravel the dual reaction mode of human 8-oxoguanine DNA glycosylase | X-ray diffraction | 1.55 | 28 | 2011-01-26 | ||||
| 14 | 1NK9|1|C+ 1NK9|1|B | DNA PRIMER STRAND, DNA TEMPLATE STRAND | A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A GUANINE-THYMINE MISMATCH AFTER TWO ROUNDS OF PRIMER EXTENSION, FOLLOWING INCORPORATION OF DCTP AND DGTP. | X-ray diffraction | 1.9 | 24 | 2004-03-30 | ||||
| 15 | 2HHQ|1|C+ 2HHQ|1|B | 5'-D(*CP*AP*TP*(6OG)P*CP*GP*AP*GP*TP*CP*AP*GP*G)-3', 5'-D(*GP*CP*CP*TP*GP*AP*CP*TP*CP*GP*TP*AP*TP*GP*A)-3' | O6-methyl-guanine:T pair in the polymerase-10 basepair position | X-ray diffraction | 1.8 | 28 | 2006-12-12 | ||||
| 16 | 1XC9|1|C+ 1XC9|1|B | DNA primer strand, DNA template strand with benzo[a]pyrene adduct | Structure of a high-fidelity polymerase bound to a benzo[a]pyrene adduct that blocks replication | X-ray diffraction | 1.9 | 22 | 2004-12-14 | ||||
| 17 | 1M3Q|1|B+ 1M3Q|1|C | 5'-D(*GP*CP*GP*TP*CP*CP*AP*(DRZ)P*GP*TP*CP*TP*AP*CP*C)-3', 5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3' | Crystal Structure of hogg1 D268E Mutant with Base-Excised DNA and 8-aminoguanine | X-ray diffraction | 1.9 | 30 | 2004-02-17 | ||||
| 18 | 1U47|1|C+ 1U47|1|B | DNA primer strand, DNA template strand with 8-oxoguanine | cytosine-8-Oxoguanine base pair at the polymerase active site | X-ray diffraction | 2 | 22 | 2004-09-14 | ||||
| 19 | 1DSZ|1|C+ 1DSZ|1|D | DNA (5'-D(*CP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*AP*G)-3'), DNA (5'-D(*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*G)-3') | STRUCTURE OF THE RXR/RAR DNA-BINDING DOMAIN HETERODIMER IN COMPLEX WITH THE RETINOIC ACID RESPONSE ELEMENT DR1 | X-ray diffraction | 1.7 | 30 | 2000-07-10 |
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 | 1NKC|1|B+ 1NKC|1|C | A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A GUANINE-THYMINE MISMATCH AFTER FIVE ROUNDS OF PRIMER EXTENSION, FOLLOWING INCORPORATION OF DCTP, DGTP, DTTP, AND DATP. | X-RAY DIFFRACTION | 1.8 | 30 | B-form double helix,double helix,feature,mispair,structure | enzyme,polymerase,transferase | |
| 2 | 1DSZ|1|C+ 1DSZ|1|D | STRUCTURE OF THE RXR/RAR DNA-BINDING DOMAIN HETERODIMER IN COMPLEX WITH THE RETINOIC ACID RESPONSE ELEMENT DR1 | X-RAY DIFFRACTION | 1.7 | 30 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),Zinc-coordinating,nuclear receptor ZnC4,regulatory,transcription | |
| 3 | 3IAG|1|A+ 3IAG|1|B | CSL (RBP-Jk) bound to HES-1 nonconsensus site | X-RAY DIFFRACTION | 2 | 30 | B-form double helix,double helix,structure | DNA-binding transcription factor (TF),immunoglobulin (Ig) fold,regulatory,rel homology,transcription | |
| 4 | 1U4B|1|C+ 1U4B|1|B | Extension of an adenine-8oxoguanine mismatch | X-RAY DIFFRACTION | 1.6 | 23 | enzyme,polymerase,transferase | ||
| 5 | 1NKB|1|C+ 1NKB|1|B | A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A GUANINE-THYMINE MISMATCH AFTER THREE ROUNDS OF PRIMER EXTENSION, FOLLOWING INCORPORATION OF DCTP, DGTP, AND DTTP. | X-RAY DIFFRACTION | 2 | 27 | B-form double helix,double helix,feature,mispair,structure | enzyme,polymerase,transferase | |
| 6 | 1NK9|1|C+ 1NK9|1|B | A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A GUANINE-THYMINE MISMATCH AFTER TWO ROUNDS OF PRIMER EXTENSION, FOLLOWING INCORPORATION OF DCTP AND DGTP. | X-RAY DIFFRACTION | 1.9 | 24 | double helix,feature,mispair,structure | enzyme,polymerase,transferase | |
| 7 | 3FDQ|1|C+ 3FDQ|1|D | Recognition of AT-rich DNA binding sites by the MogR Repressor | X-RAY DIFFRACTION | 1.75 | 30 | B-form double helix,double helix,structure | regulatory,transcription | |
| 8 | 1RH6|1|C+ 1RH6|1|D | Bacteriophage Lambda Excisionase (Xis)-DNA Complex | X-RAY DIFFRACTION | 1.7 | 28 | B-form double helix,double helix,structure | enzyme,recombinase | |
| 9 | 1U47|1|C+ 1U47|1|B | cytosine-8-Oxoguanine base pair at the polymerase active site | X-RAY DIFFRACTION | 2 | 22 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 10 | 1NJX|1|C+ 1NJX|1|B | THYMINE-GUANINE MISMATCH AT THE POLYMERASE ACTIVE SITE | X-RAY DIFFRACTION | 1.65 | 23 | B-form double helix,double helix,feature,mispair,structure | enzyme,polymerase,transferase | |
| 11 | 1NJW|1|C+ 1NJW|1|B | GUANINE-THYMINE MISMATCH AT THE POLYMERASE ACTIVE SITE | X-RAY DIFFRACTION | 1.9 | 23 | B-form double helix,double helix,feature,mispair,structure | enzyme,polymerase,transferase | |
| 12 | 2HHQ|1|C+ 2HHQ|1|B | O6-methyl-guanine:T pair in the polymerase-10 basepair position | X-RAY DIFFRACTION | 1.8 | 28 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 13 | 1XC9|1|C+ 1XC9|1|B | Structure of a high-fidelity polymerase bound to a benzo[a]pyrene adduct that blocks replication | X-RAY DIFFRACTION | 1.9 | 22 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 14 | 3MFI|1|T+ 3MFI|1|P | DNA Polymerase Eta in Complex With a cis-syn Thymidine Dimer | X-RAY DIFFRACTION | 1.76 | 24 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 15 | 1NK7|1|C+ 1NK7|1|B | GUANINE-ADENINE MISMATCH AT THE POLYMERASE ACTIVE SITE | X-RAY DIFFRACTION | 1.9 | 20 | B-form double helix,double helix,structure | enzyme,polymerase,transferase | |
| 16 | 1NK0|1|C+ 1NK0|1|B | ADENINE-GUANINE MISMATCH AT THE POLYMERASE ACTIVE SITE | X-RAY DIFFRACTION | 1.7 | 23 | B-form double helix,double helix,feature,mispair,structure | enzyme,polymerase,transferase | |
| 17 | 1NK8|1|C+ 1NK8|1|B | A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A GUANINE-THYMINE MISMATCH AFTER A SINGLE ROUND OF PRIMER EXTENSION, FOLLOWING INCORPORATION OF DCTP. | X-RAY DIFFRACTION | 1.9 | 23 | B-form double helix,double helix,feature,mispair,structure | enzyme,polymerase,transferase | |
| 18 | 1M3Q|1|B+ 1M3Q|1|C | Crystal Structure of hogg1 D268E Mutant with Base-Excised DNA and 8-aminoguanine | X-RAY DIFFRACTION | 1.9 | 30 | B-form double helix,double helix,structure | enzyme,hydrolase | |
| 19 | 2XHI|1|B+ 2XHI|1|C | Separation-of-function mutants unravel the dual reaction mode of human 8-oxoguanine DNA glycosylase | X-RAY DIFFRACTION | 1.55 | 28 | B-form double helix,double helix,structure | enzyme,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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