Equivalence class DNA_2.0_77675.1 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | #NTs | Date |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 1ENN|1|A+ 1ENN|1|B (rep) | DNA (5'-D(*GP*CP*GP*AP*AP*TP*TP*CP*G)-3') | SOLVENT ORGANIZATION IN AN OLIGONUCLEOTIDE CRYSTAL: THE STRUCTURE OF D(GCGAATTCG)2 AT ATOMIC RESOLUTION | X-ray diffraction | 0.89 | 18 | 2000-05-03 | ||||
| 2 | 1XJY|1|A+ 1XJY|1|B | 5'-D(*TP*CP*TP*GP*CP*GP*GP*TP*C)-3', 5'-D(*TP*GP*AP*CP*CP*GP*CP*AP*G)-3' | The crystal structures of the DNA binding sites of the RUNX1 transcription factor | X-ray diffraction | 2 | 18 | 2005-03-15 | ||||
| 3 | 3OQG|1|C+ 3OQG|1|D | DNA 5'-D(*GP*AP*TP*CP*TP*GP*AP*AP*C)-3', DNA 5'-D(*GP*TP*TP*CP*AP*GP*AP*TP*C)-3' | Restriction endonuclease HPY188I in complex with substrate DNA | X-ray diffraction | 1.75 | 18 | 2010-10-20 | ||||
| 4 | 3G00|1|H+ 3G00|1|I | 5'-D(*CP*GP*TP*AP*TP*TP*AP*CP*G)-3', 5'-D(*CP*GP*TP*AP*UP*TP*AP*CP*G)-3' | Mth0212 in complex with a 9bp blunt end dsDNA at 1.7 Angstrom | X-ray diffraction | 1.74 | 18 | 2010-03-09 | ||||
| 5 | 1XJX|1|A+ 1XJX|1|B | 5'-D(*TP*CP*TP*GP*CP*GP*GP*TP*C)-3', 5'-D(*TP*GP*AP*CP*CP*GP*CP*AP*G)-3' | The crystal structures of the DNA binding sites of the RUNX1 transcription factor | X-ray diffraction | 1.7 | 18 | 2005-03-15 | ||||
| 6 | 1UE2|1|A | 5'-D(*GP*(C38)P*GP*AP*AP*AP*GP*CP*T)-3' | Crystal structure of d(GC38GAAAGCT) | X-ray diffraction | 1.4 | 9 | 2004-01-13 | ||||
| 7 | 2GB7|1|E+ 2GB7|1|F | DNA STRAND 1, DNA STRAND 2 | Metal-depleted Ecl18kI in complex with uncleaved, modified DNA | X-ray diffraction | 1.7 | 18 | 2006-06-20 | ||||
| 8 | 2GB7|1|G+ 2GB7|1|H | DNA STRAND 1, DNA STRAND 2 | Metal-depleted Ecl18kI in complex with uncleaved, modified DNA | X-ray diffraction | 1.7 | 18 | 2006-06-20 | ||||
| 9 | 3GV8|1|T+ 3GV8|1|P | 5'-D(*AP*GP*GP*AP*CP*CP*C)-3', 5'-D(*AP*TP*GP*GP*GP*TP*CP*CP*T)-3' | Human DNA polymerase iota in complex with T template DNA and incoming dGTP | X-ray diffraction | 2 | 16 | 2009-06-02 | ||||
| 10 | 3IMB|1|E+ 3IMB|1|F | 5'-D(*CP*GP*CP*CP*CP*GP*GP*AP*C)-3', 5'-D(*GP*TP*CP*CP*GP*GP*GP*CP*G)-3' | Alternative binding mode of restriction endonuclease BcnI to cognate DNA | X-ray diffraction | 1.89 | 18 | 2010-08-11 | ||||
| 11 | 3IMB|1|G+ 3IMB|1|H | 5'-D(*CP*GP*CP*CP*CP*GP*GP*AP*C)-3', 5'-D(*GP*TP*CP*CP*GP*GP*GP*CP*G)-3' | Alternative binding mode of restriction endonuclease BcnI to cognate DNA | X-ray diffraction | 1.89 | 18 | 2010-08-11 | ||||
| 12 | 3IMB|1|I+ 3IMB|1|J | 5'-D(*CP*GP*CP*CP*CP*GP*GP*AP*C)-3', 5'-D(*GP*TP*CP*CP*GP*GP*GP*CP*G)-3' | Alternative binding mode of restriction endonuclease BcnI to cognate DNA | X-ray diffraction | 1.89 | 18 | 2010-08-11 | ||||
| 13 | 3IMB|1|K+ 3IMB|1|L | 5'-D(*CP*GP*CP*CP*CP*GP*GP*AP*C)-3', 5'-D(*GP*TP*CP*CP*GP*GP*GP*CP*G)-3' | Alternative binding mode of restriction endonuclease BcnI to cognate DNA | X-ray diffraction | 1.89 | 18 | 2010-08-11 | ||||
| 14 | 2FQZ|1|E+ 2FQZ|1|F | DNA STRAND 1, DNA STRAND 2 | Metal-depleted Ecl18kI in complex with uncleaved DNA | X-ray diffraction | 2 | 18 | 2006-06-20 | ||||
| 15 | 2FQZ|1|G+ 2FQZ|1|H | DNA STRAND 1, DNA STRAND 2 | Metal-depleted Ecl18kI in complex with uncleaved DNA | X-ray diffraction | 2 | 18 | 2006-06-20 | ||||
| 16 | 3HR3|1|A | 5'-D(*GP*CP*GP*(US4)P*(OMU))P*AP*CP*GP*C)-3' | synthetic construct | Interplay of Structure, Hydration and Thermal Stability in Formacetal Modified Oligonucleotides: RNA May Tolerate Hydrophobic Modifications Better than DNA | X-ray diffraction | 1.75 | 9 | 2009-10-27 | |||
| 17 | 1RXW|1|C+ 1RXW|1|B | 5'-d(*C*pG*pA*pT*pG*pC*pT*pA)-3', 5'-d(*T*pA*pG*pC*pA*pT*pC*pG*pG)-3' | Crystal structure of A. fulgidus FEN-1 bound to DNA | X-ray diffraction | 2 | 15 | 2004-01-27 |
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 | 2FQZ|1|E+ 2FQZ|1|F | Metal-depleted Ecl18kI in complex with uncleaved DNA | X-RAY DIFFRACTION | 2 | 18 | B-form double helix,double helix,structure | enzyme,hydrolase | |
| 2 | 2GB7|1|E+ 2GB7|1|F | Metal-depleted Ecl18kI in complex with uncleaved, modified DNA | X-RAY DIFFRACTION | 1.7 | 18 | B-form double helix,double helix,structure | enzyme,hydrolase | |
| 3 | 2FQZ|1|G+ 2FQZ|1|H | Metal-depleted Ecl18kI in complex with uncleaved DNA | X-RAY DIFFRACTION | 2 | 18 | B-form double helix,double helix,structure | enzyme,hydrolase | |
| 4 | 2GB7|1|G+ 2GB7|1|H | Metal-depleted Ecl18kI in complex with uncleaved, modified DNA | X-RAY DIFFRACTION | 1.7 | 18 | B-form double helix,double helix,structure | enzyme,hydrolase | |
| 5 | 3HR3|1|A | Interplay of Structure, Hydration and Thermal Stability in Formacetal Modified Oligonucleotides: RNA May Tolerate Hydrophobic Modifications Better than DNA | X-RAY DIFFRACTION | 1.75 | 9 | A-form double helix,double helix,structure | ||
| 6 | 3G00|1|H+ 3G00|1|I | Mth0212 in complex with a 9bp blunt end dsDNA at 1.7 Angstrom | X-RAY DIFFRACTION | 1.74 | 18 | B-form double helix,double helix,feature,mispair,structure | enzyme,hydrolase,nuclease | |
| 7 | 1XJX|1|A+ 1XJX|1|B | The crystal structures of the DNA binding sites of the RUNX1 transcription factor | X-RAY DIFFRACTION | 1.7 | 18 | A-form double helix,double helix,structure | ||
| 8 | 1XJY|1|A+ 1XJY|1|B | The crystal structures of the DNA binding sites of the RUNX1 transcription factor | X-RAY DIFFRACTION | 2 | 18 | A-form double helix,double helix,structure | ||
| 9 | 3GV8|1|T+ 3GV8|1|P | Human DNA polymerase iota in complex with T template DNA and incoming dGTP | X-RAY DIFFRACTION | 2 | 16 | double helix,structure | enzyme,polymerase,transferase | |
| 10 | 1ENN|1|A+ 1ENN|1|B | SOLVENT ORGANIZATION IN AN OLIGONUCLEOTIDE CRYSTAL: THE STRUCTURE OF D(GCGAATTCG)2 AT ATOMIC RESOLUTION | X-RAY DIFFRACTION | 0.89 | 18 | B-form double helix,double helix,structure | ||
| 11 | 3OQG|1|C+ 3OQG|1|D | Restriction endonuclease HPY188I in complex with substrate DNA | X-RAY DIFFRACTION | 1.75 | 18 | double helix,structure | enzyme,hydrolase,nuclease | |
| 12 | 1RXW|1|C+ 1RXW|1|B | Crystal structure of A. fulgidus FEN-1 bound to DNA | X-RAY DIFFRACTION | 2 | 15 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease,regulatory,transcription | |
| 13 | 3IMB|1|K+ 3IMB|1|L | Alternative binding mode of restriction endonuclease BcnI to cognate DNA | X-RAY DIFFRACTION | 1.89 | 18 | double helix,structure | enzyme,hydrolase,nuclease | |
| 14 | 3IMB|1|G+ 3IMB|1|H | Alternative binding mode of restriction endonuclease BcnI to cognate DNA | X-RAY DIFFRACTION | 1.89 | 18 | double helix,structure | enzyme,hydrolase,nuclease | |
| 15 | 3IMB|1|I+ 3IMB|1|J | Alternative binding mode of restriction endonuclease BcnI to cognate DNA | X-RAY DIFFRACTION | 1.89 | 18 | double helix,structure | enzyme,hydrolase,nuclease | |
| 16 | 3IMB|1|E+ 3IMB|1|F | Alternative binding mode of restriction endonuclease BcnI to cognate DNA | X-RAY DIFFRACTION | 1.89 | 18 | double helix,structure | enzyme,hydrolase,nuclease | |
| 17 | 1UE2|1|A | Crystal structure of d(GC38GAAAGCT) | X-RAY DIFFRACTION | 1.4 | 9 | NAKB_NA_annotation | NAKB_protein_annotation |
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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