Equivalence class DNA_all_08274.1 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | #NTs | Date |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 2VBO|1|C+ 2VBO|1|E (rep) | 5'-D(*TP*CP*TP*GP*CP*CP*TP*TP*TP*TP *TP*TP*GP*AP*AP*GP*GP*AP*TP*CP*CP*TP*AP*A)-3', 5'-D(*TP*TP*AP*GP*GP*AP*TP*CP*CP*TP *TP*CP*AP*AP*AP*AP*AP*AP*GP*GP*CP*AP*GP*A)-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 | 2VBJ|1|C+ 2VBJ|1|E | 5'-D(*TP*CP*TP*GP*CP*CP*TP*TP*TP*TP *TP*TP*GP*AP*AP*GP*GP*AP*TP*CP*CP*TP*AP*A)-3', 5'-D(*TP*TP*AP*GP*GP*AP*TP*CP*CP*TP *TP*CP*AP*AP*AP*AP*AP*AP*GP*GP*CP*AP*GP*A)-3' | synthetic construct | Molecular basis of human XPC gene recognition and cleavage by engineered homing endonuclease heterodimers | X-ray diffraction | 1.95 | 48 | 2008-10-28 | |||
| 3 | 3MXB|1|C+ 3MXB|1|E | DNA (5'-D(*TP*CP*TP*GP*GP*CP*TP*GP*AP*GP*GP*TP*AP*CP*CP*TP*GP*AP*GP*AP*AP*CP*AP*A)-3'), DNA (5'-D(*TP*TP*GP*TP*TP*CP*TP*CP*AP*GP*GP*TP*AP*CP*CP*TP*CP*AP*GP*CP*CP*AP*GP*A)-3') | Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus | X-ray diffraction | 2.3 | 48 | 2010-10-06 | ||||
| 4 | 3MXB|1|T+ 3MXB|1|V | DNA (5'-D(*TP*CP*TP*GP*GP*CP*TP*GP*AP*GP*GP*TP*AP*CP*CP*TP*GP*AP*GP*AP*AP*CP*AP*A)-3'), DNA (5'-D(*TP*TP*GP*TP*TP*CP*TP*CP*AP*GP*GP*TP*AP*CP*CP*TP*CP*AP*GP*CP*CP*AP*GP*A)-3') | Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus | X-ray diffraction | 2.3 | 48 | 2010-10-06 | ||||
| 5 | 2XE0|1|C+ 2XE0|1|D | 24MER DNA | Homo sapiens | Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus | X-ray diffraction | 2.31 | 48 | 2010-09-29 | |||
| 6 | 1M5X|1|C+ 1M5X|1|D | 5'-D(*CP*GP*GP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*CP*TP*GP*C)-3', 5'-D(*GP*CP*AP*GP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*CP*CP*G)-3' | Crystal structure of the homing endonuclease I-MsoI bound to its DNA substrate | X-ray diffraction | 2.25 | 48 | 2003-06-03 | ||||
| 7 | 2FLD|1|C+ 2FLD|1|D | 5'-D(*CP*GP*GP*AP*AP*CP*GP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*CP*TP*TP*CP*TP*GP*C)-3', 5'-D(*GP*CP*AP*GP*AP*AP*GP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*CP*GP*TP*TP*CP*CP*G)-3' | I-MsoI Re-Designed for Altered DNA Cleavage Specificity | X-ray diffraction | 2 | 48 | 2006-06-06 | ||||
| 8 | 3MX9|1|C+ 3MX9|1|D | DNA (5'-D(*TP*CP*TP*GP*GP*CP*TP*GP*AP*GP*GP*TP*AP*CP*CP*TP*GP*AP*GP*AP*AP*CP*AP*A)-3'), DNA (5'-D(*TP*TP*GP*TP*TP*CP*TP*CP*AP*GP*GP*TP*AP*CP*CP*TP*CP*AP*GP*CP*CP*AP*GP*A)-3') | Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus | X-ray diffraction | 2.6 | 48 | 2010-10-06 | ||||
| 9 | 2I3Q|1|C+ 2I3Q|1|D | 5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*AP*CP*TP*CP*AP*CP*GP*TP*CP*GP*TP*TP*TP*TP*GP*C)-3', 5'-D(*GP*CP*AP*AP*AP*AP*CP*GP*AP*CP*GP*TP*GP*AP*GP*TP*CP*AP*GP*TP*TP*TP*CP*G)-3' | Q44V mutant of Homing Endonuclease I-CreI | X-ray diffraction | 2.3 | 48 | 2006-09-05 | ||||
| 10 | 3MIP|1|C+ 3MIP|1|D | DNA (5'-D(*CP*GP*GP*AP*GP*CP*GP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*CP*GP*CP*CP*TP*GP*C)-3'), DNA (5'-D(*GP*CP*AP*GP*GP*CP*GP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*CP*GP*CP*TP*CP*CP*G)-3') | I-MsoI re-designed for altered DNA cleavage specificity (-8GCG) | X-ray diffraction | 2.4 | 48 | 2010-05-19 | ||||
| 11 | 3MIS|1|C+ 3MIS|1|D | DNA (5'-D(*CP*GP*GP*AP*GP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*CP*CP*TP*GP*C)-3'), DNA (5'-D(*GP*CP*AP*GP*GP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*CP*TP*CP*CP*G)-3') | I-MsoI re-designed for altered DNA cleavage specificity (-8G) | X-ray diffraction | 2.3 | 48 | 2010-05-19 | ||||
| 12 | 2I3P|1|C+ 2I3P|1|D | 5'-D(*CP*GP*AP*AP*AP*TP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*AP*TP*TP*TP*GP*C)-3', 5'-D(*GP*CP*AP*AP*AP*TP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*AP*TP*TP*TP*CP*G)-3' | K28R mutant of Homing Endonuclease I-CreI | X-ray diffraction | 2.3 | 48 | 2006-09-05 | ||||
| 13 | 3FD2|1|B+ 3FD2|1|C | 5'-D(*CP*GP*GP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*CP*TP*GP*C)-3', 5'-D(*GP*CP*AP*GP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*CP*CP*G)-3' | synthetic construct | Crystal structure of mMsoI/DNA complex with calcium | X-ray diffraction | 2.69 | 48 | 2009-06-30 | |||
| 14 | 3KO2|1|C+ 3KO2|1|D | 5'-D(*CP*GP*GP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*GP*TP*CP*TP*GP*C)-3', 5'-D(*GP*CP*AP*GP*AP*CP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*CP*CP*G)-3' | I-MsoI re-designed for altered DNA cleavage specificity (-7C) | X-ray diffraction | 2.9 | 48 | 2010-05-19 | ||||
| 15 | 3KO2|1|H+ 3KO2|1|I | 5'-D(*CP*GP*GP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*GP*TP*CP*TP*GP*C)-3', 5'-D(*GP*CP*AP*GP*AP*CP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*CP*CP*G)-3' | I-MsoI re-designed for altered DNA cleavage specificity (-7C) | X-ray diffraction | 2.9 | 48 | 2010-05-19 | ||||
| 16 | 1U0D|1|C+ 1U0D|1|D | 5'-D(*CP*GP*GP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*TP*CP*GP*C)-3', 5'-D(*GP*CP*GP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*CP*CP*G)-3' | Y33H Mutant of Homing endonuclease I-CreI | X-ray diffraction | 2.9 | 48 | 2004-11-02 | ||||
| 17 | 1T9I|1|C+ 1T9I|1|D | 5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*TP*TP*GP*C)-3', 5'-D(*GP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*TP*CP*G)-3' | I-CreI(D20N)/DNA complex | X-ray diffraction | 1.6 | 48 | 2004-11-16 | ||||
| 18 | 1T9J|1|C+ 1T9J|1|D | 5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*TP*TP*GP*C)-3', 5'-D(*GP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*TP*CP*G)-3' | I-CreI(Q47E)/DNA complex | X-ray diffraction | 2 | 48 | 2004-11-16 | ||||
| 19 | 1G9Y|1|C+ 1G9Y|1|D | 5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*TP*TP*GP*C)-3', 5'-D(*GP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*TP*CP*G)-3' | HOMING ENDONUCLEASE I-CREI / DNA SUBSTRATE COMPLEX WITH CALCIUM | X-ray diffraction | 2.05 | 48 | 2001-04-02 | ||||
| 20 | 1U0C|1|C+ 1U0C|1|D | 5'-D(*CP*GP*TP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*TP*AP*GP*C)-3', 5'-D(*GP*CP*TP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*AP*CP*G)-3' | Y33C Mutant of Homing endonuclease I-CreI | X-ray diffraction | 2.5 | 0 | 2004-11-02 | ||||
| 21 | 1BP7|1|1+ 1BP7|1|2 | DNA (5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*TP*TP* GP*C)-3'), DNA (5'-D(*GP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*TP* CP*G)-3') | GROUP I MOBILE INTRON ENDONUCLEASE I-CREI COMPLEXED WITH HOMING SITE DNA | X-ray diffraction | 3 | 48 | 1999-01-06 | ||||
| 22 | 1BP7|1|3+ 1BP7|1|4 | DNA (5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*TP*TP* GP*C)-3'), DNA (5'-D(*GP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*TP* CP*G)-3') | GROUP I MOBILE INTRON ENDONUCLEASE I-CREI COMPLEXED WITH HOMING SITE DNA | X-ray diffraction | 3 | 48 | 1999-01-06 |
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 | 2VBJ|1|C+ 2VBJ|1|E | Molecular basis of human XPC gene recognition and cleavage by engineered homing endonuclease heterodimers | X-RAY DIFFRACTION | 1.95 | 48 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 2 | 2VBO|1|C+ 2VBO|1|E | 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 | |
| 3 | 2XE0|1|C+ 2XE0|1|D | Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus | X-RAY DIFFRACTION | 2.31 | 48 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 4 | 3MX9|1|C+ 3MX9|1|D | Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus | X-RAY DIFFRACTION | 2.6 | 48 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 5 | 3MXB|1|C+ 3MXB|1|E | 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 | |
| 6 | 3MXB|1|T+ 3MXB|1|V | 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 | |
| 7 | 1BP7|1|3+ 1BP7|1|4 | GROUP I MOBILE INTRON ENDONUCLEASE I-CREI COMPLEXED WITH HOMING SITE DNA | X-RAY DIFFRACTION | 3 | 48 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 8 | 1BP7|1|1+ 1BP7|1|2 | GROUP I MOBILE INTRON ENDONUCLEASE I-CREI COMPLEXED WITH HOMING SITE DNA | X-RAY DIFFRACTION | 3 | 48 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 9 | 1G9Y|1|C+ 1G9Y|1|D | HOMING ENDONUCLEASE I-CREI / DNA SUBSTRATE COMPLEX WITH CALCIUM | X-RAY DIFFRACTION | 2.05 | 48 | double helix,structure | enzyme,hydrolase,nuclease | |
| 10 | 2I3P|1|C+ 2I3P|1|D | K28R mutant of Homing Endonuclease I-CreI | X-RAY DIFFRACTION | 2.3 | 48 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 11 | 2I3Q|1|C+ 2I3Q|1|D | Q44V mutant of Homing Endonuclease I-CreI | X-RAY DIFFRACTION | 2.3 | 48 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 12 | 1T9J|1|C+ 1T9J|1|D | I-CreI(Q47E)/DNA complex | X-RAY DIFFRACTION | 2 | 48 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 13 | 1T9I|1|C+ 1T9I|1|D | I-CreI(D20N)/DNA complex | X-RAY DIFFRACTION | 1.6 | 48 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 14 | 1U0C|1|C+ 1U0C|1|D | Y33C Mutant of Homing endonuclease I-CreI | X-RAY DIFFRACTION | 2.5 | 0 | double helix,structure | enzyme,hydrolase,nuclease | |
| 15 | 3MIP|1|C+ 3MIP|1|D | I-MsoI re-designed for altered DNA cleavage specificity (-8GCG) | X-RAY DIFFRACTION | 2.4 | 48 | double helix,structure | enzyme,hydrolase,nuclease | |
| 16 | 2FLD|1|C+ 2FLD|1|D | I-MsoI Re-Designed for Altered DNA Cleavage Specificity | X-RAY DIFFRACTION | 2 | 48 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 17 | 1M5X|1|C+ 1M5X|1|D | Crystal structure of the homing endonuclease I-MsoI bound to its DNA substrate | X-RAY DIFFRACTION | 2.25 | 48 | B-form double helix,double helix,structure | enzyme,hydrolase,nuclease | |
| 18 | 3FD2|1|B+ 3FD2|1|C | Crystal structure of mMsoI/DNA complex with calcium | X-RAY DIFFRACTION | 2.69 | 48 | double helix,structure | enzyme,hydrolase,nuclease | |
| 19 | 3MIS|1|C+ 3MIS|1|D | I-MsoI re-designed for altered DNA cleavage specificity (-8G) | X-RAY DIFFRACTION | 2.3 | 48 | double helix,structure | enzyme,hydrolase,nuclease | |
| 20 | 3KO2|1|H+ 3KO2|1|I | I-MsoI re-designed for altered DNA cleavage specificity (-7C) | X-RAY DIFFRACTION | 2.9 | 48 | double helix,structure | enzyme,hydrolase,nuclease | |
| 21 | 3KO2|1|C+ 3KO2|1|D | I-MsoI re-designed for altered DNA cleavage specificity (-7C) | X-RAY DIFFRACTION | 2.9 | 48 | double helix,structure | enzyme,hydrolase,nuclease | |
| 22 | 1U0D|1|C+ 1U0D|1|D | Y33H Mutant of Homing endonuclease I-CreI | X-RAY DIFFRACTION | 2.9 | 48 | double helix,structure | enzyme,hydrolase,nuclease |
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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