Equivalence class NR_3.0_29795.2 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | #NTs | Date |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 5DH6|1|A+ 5DH6|1|B (rep) | Hammerhead ribozyme (type III) | 5'-R(*GP*GP*GP*CP*GP*U)-D(P*C)-R(P*UP*GP*GP*GP*CP*AP*GP*UP*AP*CP*CP*CP*A)-3', hammerhead ribozyme | synthetic construct | Synthetic | RF00008 | Two divalent metal ions and conformational changes play roles in the hammerhead ribozyme cleavage reaction-G12A mutant in Mg2+ | X-ray diffraction | 2.78 | 68 | 2015-10-07 |
| 2 | 5DI4|1|A+ 5DI4|1|B | Hammerhead ribozyme (type III) | 5'-R(*GP*GP*GP*CP*GP*U)-D(P*C)-R(P*UP*GP*GP*GP*CP*AP*GP*UP*AP*CP*CP*CP*A)-3', RNA (48-MER) | synthetic construct | Synthetic | RF00008 | Two divalent metal ions and conformational changes play roles in the hammerhead ribozyme cleavage reaction-WT ribozyme in Mn2+ at low pH | X-ray diffraction | 2.95 | 68 | 2015-10-07 |
| 3 | 5DQK|1|A+ 5DQK|1|B | Hammerhead ribozyme (type III) | RNA (48-MER), RNA (5'-R(*GP*GP*GP*CP*GP*U)-D(P*C)-R(P*UP*GP*GP*GP*CP*AP*GP*UP*AP*CP*CP*CP*A)-3') | synthetic construct | Synthetic | RF00008 | Two divalent metal ions and conformational changes play roles in the hammerhead ribozyme cleavage reaction-WT ribozyme in Mg2+ | X-ray diffraction | 2.71 | 68 | 2015-10-07 |
| 4 | 5EAO|1|A+ 5EAO|1|B | Hammerhead ribozyme (type III) | RNA (48-MER), RNA (5'-R(*GP*GP*GP*CP*GP*U*(CVC)*UP*GP*GP*GP*CP*AP*GP*UP*AP*CP*CP*CP*A)-3') | synthetic construct | Synthetic | RF00008 | Two active site divalent ion in the crystal structure of the hammerhead ribozyme bound to a transition state analog-Mg2+ | X-ray diffraction | 2.99 | 68 | 2016-02-24 |
| 5 | 5DI2|1|A+ 5DI2|1|B | Hammerhead ribozyme (type III) | 5'-R(*GP*GP*GP*CP*GP*U)-D(P*C)-R(P*UP*GP*GP*GP*CP*AP*GP*UP*AP*CP*CP*CP*A)-3', RNA (48-MER) | synthetic construct | Synthetic | RF00008 | Two divalent metal ions and conformational changes play roles in the hammerhead ribozyme cleavage reaction-WT ribozyme in Mn2+ at high pH | X-ray diffraction | 2.99 | 68 | 2015-10-07 |
Release history
| Release | 3.378 | 3.379 | 3.380 | 3.381 | 3.382 | 3.383 | 3.384 | 3.385 | 3.386 | 3.387 | 3.388 | 3.389 | 3.390 | 3.391 | 3.392 | 3.393 | 3.394 | 3.395 | 3.396 | 3.397 | 3.398 | 3.399 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Date | 2025-03-13 | 2025-03-19 | 2025-03-26 | 2025-04-02 | 2025-04-09 | 2025-04-16 | 2025-04-23 | 2025-04-30 | 2025-05-07 | 2025-05-14 | 2025-05-21 | 2025-05-28 | 2025-06-04 | 2025-06-11 | 2025-06-18 | 2025-06-25 | 2025-07-02 | 2025-07-09 | 2025-07-16 | 2025-07-23 | 2025-07-30 | 2025-08-06 |
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 |
|---|---|---|---|---|---|---|
| 1 | 5DH6|1|A+ 5DH6|1|B | Two divalent metal ions and conformational changes play roles in the hammerhead ribozyme cleavage reaction-G12A mutant in Mg2+ | X-RAY DIFFRACTION | 2.78 | 68 | |
| 2 | 5DI2|1|A+ 5DI2|1|B | Two divalent metal ions and conformational changes play roles in the hammerhead ribozyme cleavage reaction-WT ribozyme in Mn2+ at high pH | X-RAY DIFFRACTION | 2.99 | 68 | |
| 3 | 5DQK|1|A+ 5DQK|1|B | Two divalent metal ions and conformational changes play roles in the hammerhead ribozyme cleavage reaction-WT ribozyme in Mg2+ | X-RAY DIFFRACTION | 2.71 | 68 | |
| 4 | 5DI4|1|A+ 5DI4|1|B | Two divalent metal ions and conformational changes play roles in the hammerhead ribozyme cleavage reaction-WT ribozyme in Mn2+ at low pH | X-RAY DIFFRACTION | 2.95 | 68 | |
| 5 | 5EAO|1|A+ 5EAO|1|B | Two active site divalent ion in the crystal structure of the hammerhead ribozyme bound to a transition state analog-Mg2+ | X-RAY DIFFRACTION | 2.99 | 68 |
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.
Coloring options: