Equivalence class NR_4.0_27812.1 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 2P7E|1|D+ 2P7E|1|C+ 2P7E|1|P (rep) | Ribozyme strand III, Ribozyme strand II, 3' substrate strand, octameric fragment | Vanadate at the Active Site of a Small Ribozyme Suggests a Role for Water in Transition-State Stabilization | X-ray diffraction | 2.05 | 2007-05-22 | ||||
| 2 | 2NPY|1|D+ 2NPY|1|C+ 2NPY|1|A+ 2NPY|1|B | 5'-R(*UP*CP*CP*CP*(U2N)P*GP*UP*CP*CP*AP*CP*CP*G)-3', 5'-R(*CP*GP*GP*UP*GP*AP*GP*AP*AP*GP*GP*G)-3', 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3', 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3' | Crystal Structure of a junctioned hairpin ribozyme incorporating 9atom linker and 2'-deoxy 2'-amino U at A-1 | X-ray diffraction | 2.65 | 2007-08-14 | ||||
| 3 | 1ZFT|1|D+ 1ZFT|1|C+ 1ZFT|1|A+ 1ZFT|1|B | 5'-R(*UP*CP*CP*CP*(A2M)P*GP*UP*CP*CP*AP*CP*CP*G)-3', 5'-R(*CP*GP*GP*UP*GP*AP*IP*AP*AP*GP*GP*G)-3', 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3', 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3' | The crystal structure of an all-RNA minimal Hairpin Ribozyme with mutant G8I at the cleavage site | X-ray diffraction | 2.33 | 2006-02-14 | ||||
| 4 | 2P7F|1|D+ 2P7F|1|C+ 2P7F|1|A+ 2P7F|1|B | substrate strand, Loop A ribozyme strand, Loop B ribozyme strand, Loop B S-turn strand | The Novel Use of a 2',5'-Phosphodiester Linkage as a Reaction Intermediate at the Active Site of a Small Ribozyme | X-ray diffraction | 2.35 | 2007-05-22 | ||||
| 5 | 3CR1|1|C | RNA (5'-R(*UP*CP*GP*UP*GP*GP*UP*CP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3') | crystal structure of a minimal, mutant, all-RNA hairpin ribozyme (A38C, A-1OMA) grown from MgCl2 | X-ray diffraction | 2.25 | 2008-08-26 | ||||
| 6 | 1ZFV|1|D+ 1ZFV|1|C+ 1ZFV|1|A+ 1ZFV|1|B | 5'-R(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*G)-3', 5'-R(*CP*GP*GP*UP*GP*AP*AP*AP*AP*GP*GP*G)-3', 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3', 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3' | The structure of an all-RNA minimal Hairpin Ribozyme with Mutation G8A at the cleavage site | X-ray diffraction | 2.4 | 2006-02-14 | ||||
| 7 | 2OUE|1|D+ 2OUE|1|C+ 2OUE|1|A+ 2OUE|1|B | Substrate strand - Minimal Junctionless Hairpin Ribozyme, Loop A ribozyme strand, Loop B ribozyme strand, Loop B S-turn strand | Crystal structure of a junctionless all-RNA hairpin ribozyme at 2.05 angstroms resolution | X-ray diffraction | 2.05 | 2007-03-06 | ||||
| 8 | 2P7D|1|D+ 2P7D|1|C+ 2P7D|1|P | Ribozyme strand II, Ribozyme strand III, 3' substrate strand, octameric fragment | A Minimal, 'Hinged' Hairpin Ribozyme Construct Solved with Mimics of the Product Strands at 2.25 Angstroms Resolution | X-ray diffraction | 2.25 | 2007-05-22 | ||||
| 9 | 2D2L|1|D+ 2D2L|1|C+ 2D2L|1|A+ 2D2L|1|B | 5'-R(*UP*CP*CP*CP*(A2M)P*GP*UP*CP*CP*AP*CP*CP*G)-3', 5'-R(*CP*GP*GP*UP*GP*AP*GP*AP*AP*GP*GP*G)-3', 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3', 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*(P1P)P*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3' | Crystal Structure of a minimal, all-RNA hairpin ribozyme with a propyl linker (C3) at position U39 | X-ray diffraction | 2.5 | 2005-11-01 | ||||
| 10 | 2FGP|1|D+ 2FGP|1|C+ 2FGP|1|A+ 2FGP|1|B | 5'-R(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*G)-3', 5'-R(*CP*GP*GP*UP*GP*AP*(N6G)P*AP*AP*GP*GP*G)-3', 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3', 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C) -3' | Crystal structure of a minimal, all RNA hairpin ribozyme with modifications (g8dap, u39c) at ph 8.6 | X-ray diffraction | 2.4 | 2006-02-14 | ||||
| 11 | 1X9C|1|D+ 1X9C|1|C+ 1X9C|1|A+ 1X9C|1|B | 5'-R(*UP*CP*CP*CP*(A2M)P*GP*UP*CP*CP*AP*CP*CP*G)-3', 5'-R(*CP*GP*GP*UP*GP*AP*GP*AP*AP*GP*GP*G)-3', 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3', 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3' | An all-RNA Hairpin Ribozyme with mutation U39C | X-ray diffraction | 2.19 | 2005-11-22 | ||||
| 12 | 3CQS|1|C | 19-mer ribozyme strand | A 3'-OH, 2',5'-phosphodiester substitution in the hairpin ribozyme active site reveals similarities with protein ribonucleases | X-ray diffraction | 2.8 | 2008-05-20 | ||||
| 13 | 1ZFX|1|D+ 1ZFX|1|C+ 1ZFX|1|A+ 1ZFX|1|B | 5'-R(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*G)-3', 5'-R(*CP*GP*GP*UP*GP*AP*UP*AP*AP*GP*GP*G)-3', 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3', 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3' | The Structure of a minimal all-RNA Hairpin Ribozyme with the mutant G8U at the cleavage site | X-ray diffraction | 2.38 | 2006-02-14 | ||||
| 14 | 2BCZ|1|D+ 2BCZ|1|C+ 2BCZ|1|A+ 2BCZ|1|B | 5'-R(*UP*CP*CP*CP*(DA)P*GP*UP*CP*CP*AP*CP*CP*G)-3'), 5'-R(*CP*GP*GP*UP*GP*AP*IP*AP*AP*GP*GP*G)-3', 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3', 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3' | Crystal Structure of a minimal, mutant all-RNA hairpin ribozyme (U39C, G8I, 2'deoxy A-1) | X-ray diffraction | 2.4 | 2006-02-14 | ||||
| 15 | 2D2K|1|D+ 2D2K|1|C+ 2D2K|1|A+ 2D2K|1|B | 5'-R(*UP*CP*CP*CP*(A2M)P*GP*UP*CP*CP*AP*CP*CP*G)-3', 5'-R(*CP*GP*GP*UP*GP*AP*GP*AP*AP*GP*GP*G)-3', 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3', 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*UP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3' | Crystal Structure of a minimal, native (U39) all-RNA hairpin ribozyme | X-ray diffraction | 2.65 | 2005-11-01 | ||||
| 16 | 2BCY|1|D+ 2BCY|1|C+ 2BCY|1|A+ 2BCY|1|B | 5'-R(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*G)-3', 5'-R(*CP*GP*GP*UP*GP*AP*(MTU)P*AP*AP*GP*GP*G)-3', 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3', 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3' | Crystal Structure of a minimal, mutant all-RNA hairpin ribozyme (U39C, G8MTU) | X-ray diffraction | 2.7 | 2006-02-14 | ||||
| 17 | 2NPZ|1|D+ 2NPZ|1|C+ 2NPZ|1|A+ 2NPZ|1|B | 5'-R(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*G)-3', 5'-R(*CP*GP*GP*UP*GP*AP*GP*AP*AP*GP*GP*G)-3', 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3', 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3' | Crystal structure of junctioned hairpin ribozyme incorporating synthetic propyl linker | X-ray diffraction | 3.35 | 2007-08-14 | ||||
| 18 | 1X9K|1|D+ 1X9K|1|C+ 1X9K|1|A+ 1X9K|1|B | 5'-R(*UP*CP*GP*CP*AP*GP*UP*CP*CP*UP*AP*UP*U)-3', 5'-R(*AP*AP*UP*AP*GP*AP*GP*AP*AP*GP*CP*GP*A)-3', 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3', 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3' | An all-RNA Hairpin Ribozyme with mutation U39C | X-ray diffraction | 3.17 | 2005-11-22 | ||||
| 19 | 4G6R|1|D+ 4G6R|1|C+ 4G6R|1|A+ 4G6R|1|B | Loop A Substrate strand, Loop A Ribozyme strand, Loop B Ribozyme Strand, Loop B S-turn strand | Minimal Hairpin Ribozyme in the Transition State with G8I Variation | X-ray diffraction | 2.83 | 2012-08-15 | ||||
| 20 | 3I2Q|1|C | 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3' | Crystal structure of the hairpin ribozyme with 2'OMe substrate strand and N1-deazaadenosine at position A9 | X-ray diffraction | 2.9 | 2009-11-03 | ||||
| 21 | 3I2S|1|C | 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3' | Crystal structure of the hairpin ribozyme with a 2'OMe substrate and N1-deazaadenosine at position A10 | X-ray diffraction | 2.75 | 2009-11-03 | ||||
| 22 | 3GS8|1|D+ 3GS8|1|C+ 3GS8|1|A+ 3GS8|1|B | RNA (5'-R(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*GP*U)-3'), RNA (5'-R(*CP*GP*GP*UP*GP*AP*GP*AP*AP*GP*GP*G)-3'), RNA (5'-R(P*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3'), RNA (5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3') | An all-RNA hairpin ribozyme A38N1dA38 variant with a transition-state mimic substrate strand | X-ray diffraction | 2.85 | 2009-04-21 | ||||
| 23 | 3GS1|1|D+ 3GS1|1|C+ 3GS1|1|A+ 3GS1|1|B | RNA (5'-R(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*GP*U)-3'), RNA (5'-R(*CP*GP*GP*UP*GP*AP*GP*AP*AP*GP*GP*G)-3'), RNA (5'-R(P*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3'), RNA (5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3') | An all-RNA Hairpin Ribozyme with mutation A38N1dA | X-ray diffraction | 2.85 | 2009-05-12 | ||||
| 24 | 3I2R|1|C | 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3' | Crystal structure of the hairpin ribozyme with a 2',5'-linked substrate with N1-deazaadenosine at position A9 | X-ray diffraction | 2.8 | 2009-11-03 | ||||
| 25 | 3I2U|1|C | 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3' | Crystal structure of the haiprin ribozyme with a 2',5'-linked substrate and N1-deazaadenosine at position A10 | X-ray diffraction | 2.8 | 2009-11-03 |
Release history
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Heat map of mutual geometric discrepancy, in Angstroms per nucleotide. Instances are ordered to put similar structures near each other. The colorbar ranges from 0 to the maximum observed discrepancy, up to 0.5
#S - ordering by similarity (same as in the heat map).| #S | PDB | Title | Method | Resolution | Length | NAKB_NA_annotation | NAKB_protein_annotation |
|---|---|---|---|---|---|---|---|
| 1 | 2NPZ|1|D+2NPZ|1|C+2NPZ|1|A+2NPZ|1|B | Title: Crystal structure of junctioned hairpin ribozyme incorporating synthetic propyl linker | X-RAY DIFFRACTION | 3.35 | 19 | ||
| 2 | 1X9K|1|D+1X9K|1|C+1X9K|1|A+1X9K|1|B | Title: An all-RNA Hairpin Ribozyme with mutation U39C | X-RAY DIFFRACTION | 3.17 | 19 | ||
| 3 | 1ZFV|1|D+1ZFV|1|C+1ZFV|1|A+1ZFV|1|B | Title: The structure of an all-RNA minimal Hairpin Ribozyme with Mutation G8A at the cleavage site | X-RAY DIFFRACTION | 2.4 | 19 | ||
| 4 | 1ZFX|1|D+1ZFX|1|C+1ZFX|1|A+1ZFX|1|B | Title: The Structure of a minimal all-RNA Hairpin Ribozyme with the mutant G8U at the cleavage site | X-RAY DIFFRACTION | 2.38 | 19 | ||
| 5 | 3GS8|1|D+3GS8|1|C+3GS8|1|A+3GS8|1|B | Title: An all-RNA hairpin ribozyme A38N1dA38 variant with a transition-state mimic substrate strand | X-RAY DIFFRACTION | 2.85 | 19 | ||
| 6 | 3I2U|1|C | Title: Crystal structure of the haiprin ribozyme with a 2',5'-linked substrate and N1-deazaadenosine at position A10 | X-RAY DIFFRACTION | 2.8 | 19 | ||
| 7 | 3I2R|1|C | Title: Crystal structure of the hairpin ribozyme with a 2',5'-linked substrate with N1-deazaadenosine at position A9 | X-RAY DIFFRACTION | 2.8 | 19 | ||
| 8 | 3CQS|1|C | Title: A 3'-OH, 2',5'-phosphodiester substitution in the hairpin ribozyme active site reveals similarities with protein ribonucleases | X-RAY DIFFRACTION | 2.8 | 19 | ||
| 9 | 4G6R|1|D+4G6R|1|C+4G6R|1|A+4G6R|1|B | Title: Minimal Hairpin Ribozyme in the Transition State with G8I Variation | X-RAY DIFFRACTION | 2.83 | 19 | ||
| 10 | 2OUE|1|D+2OUE|1|C+2OUE|1|A+2OUE|1|B | Title: Crystal structure of a junctionless all-RNA hairpin ribozyme at 2.05 angstroms resolution | X-RAY DIFFRACTION | 2.05 | 19 | ||
| 11 | 3I2Q|1|C | Title: Crystal structure of the hairpin ribozyme with 2'OMe substrate strand and N1-deazaadenosine at position A9 | X-RAY DIFFRACTION | 2.9 | 19 | ||
| 12 | 3I2S|1|C | Title: Crystal structure of the hairpin ribozyme with a 2'OMe substrate and N1-deazaadenosine at position A10 | X-RAY DIFFRACTION | 2.75 | 19 | ||
| 13 | 1ZFT|1|D+1ZFT|1|C+1ZFT|1|A+1ZFT|1|B | Title: The crystal structure of an all-RNA minimal Hairpin Ribozyme with mutant G8I at the cleavage site | X-RAY DIFFRACTION | 2.33 | 19 | ||
| 14 | 2P7E|1|D+2P7E|1|C+2P7E|1|P | Title: Vanadate at the Active Site of a Small Ribozyme Suggests a Role for Water in Transition-State Stabilization | X-RAY DIFFRACTION | 2.05 | 19 | ||
| 15 | 2P7D|1|D+2P7D|1|C+2P7D|1|P | Title: A Minimal, 'Hinged' Hairpin Ribozyme Construct Solved with Mimics of the Product Strands at 2.25 Angstroms Resolution | X-RAY DIFFRACTION | 2.25 | 19 | ||
| 16 | 2NPY|1|D+2NPY|1|C+2NPY|1|A+2NPY|1|B | Title: Crystal Structure of a junctioned hairpin ribozyme incorporating 9atom linker and 2'-deoxy 2'-amino U at A-1 | X-RAY DIFFRACTION | 2.65 | 19 | ||
| 17 | 3CR1|1|C | Title: crystal structure of a minimal, mutant, all-RNA hairpin ribozyme (A38C, A-1OMA) grown from MgCl2 | X-RAY DIFFRACTION | 2.25 | 19 | ||
| 18 | 2D2K|1|D+2D2K|1|C+2D2K|1|A+2D2K|1|B | Title: Crystal Structure of a minimal, native (U39) all-RNA hairpin ribozyme | X-RAY DIFFRACTION | 2.65 | 22 | ||
| 19 | 2D2L|1|D+2D2L|1|C+2D2L|1|A+2D2L|1|B | Title: Crystal Structure of a minimal, all-RNA hairpin ribozyme with a propyl linker (C3) at position U39 | X-RAY DIFFRACTION | 2.5 | 18 | ||
| 20 | 1X9C|1|D+1X9C|1|C+1X9C|1|A+1X9C|1|B | Title: An all-RNA Hairpin Ribozyme with mutation U39C | X-RAY DIFFRACTION | 2.19 | 19 | ||
| 21 | 2BCY|1|D+2BCY|1|C+2BCY|1|A+2BCY|1|B | Title: Crystal Structure of a minimal, mutant all-RNA hairpin ribozyme (U39C, G8MTU) | X-RAY DIFFRACTION | 2.7 | 19 | ||
| 22 | 2BCZ|1|D+2BCZ|1|C+2BCZ|1|A+2BCZ|1|B | Title: Crystal Structure of a minimal, mutant all-RNA hairpin ribozyme (U39C, G8I, 2'deoxy A-1) | X-RAY DIFFRACTION | 2.4 | 19 | ||
| 23 | 3GS1|1|D+3GS1|1|C+3GS1|1|A+3GS1|1|B | Title: An all-RNA Hairpin Ribozyme with mutation A38N1dA | X-RAY DIFFRACTION | 2.85 | 19 | ||
| 24 | 2FGP|1|D+2FGP|1|C+2FGP|1|A+2FGP|1|B | Title: Crystal structure of a minimal, all RNA hairpin ribozyme with modifications (g8dap, u39c) at ph 8.6 | X-RAY DIFFRACTION | 2.4 | 19 | ||
| 25 | 2P7F|1|D+2P7F|1|C+2P7F|1|A+2P7F|1|B | Title: The Novel Use of a 2',5'-Phosphodiester Linkage as a Reaction Intermediate at the Active Site of a Small Ribozyme | X-RAY DIFFRACTION | 2.35 | 19 |
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