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Equivalence class NR_2.5_98705.3 Obsolete

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. ÅDate
12P7E|1|D+ 2P7E|1|C+ 2P7E|1|P (rep)Ribozyme strand III, Ribozyme strand II, 3' substrate strand, octameric fragmentVanadate at the Active Site of a Small Ribozyme Suggests a Role for Water in Transition-State StabilizationX-ray diffraction2.052007-05-22
21ZFT|1|D+ 1ZFT|1|C+ 1ZFT|1|A+ 1ZFT|1|B5'-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 siteX-ray diffraction2.332006-02-14
32P7F|1|D+ 2P7F|1|C+ 2P7F|1|A+ 2P7F|1|Bsubstrate strand, Loop A ribozyme strand, Loop B ribozyme strand, Loop B S-turn strandThe Novel Use of a 2',5'-Phosphodiester Linkage as a Reaction Intermediate at the Active Site of a Small RibozymeX-ray diffraction2.352007-05-22
41ZFV|1|D+ 1ZFV|1|C+ 1ZFV|1|A+ 1ZFV|1|B5'-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 siteX-ray diffraction2.42006-02-14
52OUE|1|D+ 2OUE|1|C+ 2OUE|1|A+ 2OUE|1|BSubstrate strand - Minimal Junctionless Hairpin Ribozyme, Loop A ribozyme strand, Loop B ribozyme strand, Loop B S-turn strandCrystal structure of a junctionless all-RNA hairpin ribozyme at 2.05 angstroms resolutionX-ray diffraction2.052007-03-06
62P7D|1|D+ 2P7D|1|C+ 2P7D|1|PRibozyme strand III, Ribozyme strand II, 3' substrate strand, octameric fragmentA Minimal, 'Hinged' Hairpin Ribozyme Construct Solved with Mimics of the Product Strands at 2.25 Angstroms ResolutionX-ray diffraction2.252007-05-22
72D2L|1|D+ 2D2L|1|C+ 2D2L|1|A+ 2D2L|1|B5'-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 U39X-ray diffraction2.52005-11-01
82FGP|1|D+ 2FGP|1|C+ 2FGP|1|A+ 2FGP|1|B5'-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 8.6X-ray diffraction2.42006-02-14
91X9C|1|D+ 1X9C|1|C+ 1X9C|1|A+ 1X9C|1|B5'-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 U39CX-ray diffraction2.192005-11-22
101ZFX|1|D+ 1ZFX|1|C+ 1ZFX|1|A+ 1ZFX|1|B5'-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 siteX-ray diffraction2.382006-02-14
112BCZ|1|D+ 2BCZ|1|C+ 2BCZ|1|A+ 2BCZ|1|B5'-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 diffraction2.42006-02-14
123CR1|1|CRNA (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 MgCl2X-ray diffraction2.252008-08-26

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).
#SPDBTitleMethodResolutionLength
12D2L|1|D+2D2L|1|C+2D2L|1|A+2D2L|1|BCrystal Structure of a minimal, all-RNA hairpin ribozyme with a propyl linker (C3) at position U39X-RAY DIFFRACTION2.518
22BCZ|1|D+2BCZ|1|C+2BCZ|1|A+2BCZ|1|BCrystal Structure of a minimal, mutant all-RNA hairpin ribozyme (U39C, G8I, 2'deoxy A-1)X-RAY DIFFRACTION2.419
32P7D|1|D+2P7D|1|C+2P7D|1|PA Minimal, 'Hinged' Hairpin Ribozyme Construct Solved with Mimics of the Product Strands at 2.25 Angstroms ResolutionX-RAY DIFFRACTION2.2519
42P7F|1|D+2P7F|1|C+2P7F|1|A+2P7F|1|BThe Novel Use of a 2',5'-Phosphodiester Linkage as a Reaction Intermediate at the Active Site of a Small RibozymeX-RAY DIFFRACTION2.3519
52P7E|1|D+2P7E|1|C+2P7E|1|PVanadate at the Active Site of a Small Ribozyme Suggests a Role for Water in Transition-State StabilizationX-RAY DIFFRACTION2.0519
61X9C|1|D+1X9C|1|C+1X9C|1|A+1X9C|1|BAn all-RNA Hairpin Ribozyme with mutation U39CX-RAY DIFFRACTION2.1919
71ZFT|1|D+1ZFT|1|C+1ZFT|1|A+1ZFT|1|BThe crystal structure of an all-RNA minimal Hairpin Ribozyme with mutant G8I at the cleavage siteX-RAY DIFFRACTION2.3319
82OUE|1|D+2OUE|1|C+2OUE|1|A+2OUE|1|BCrystal structure of a junctionless all-RNA hairpin ribozyme at 2.05 angstroms resolutionX-RAY DIFFRACTION2.0519
92FGP|1|D+2FGP|1|C+2FGP|1|A+2FGP|1|BCrystal structure of a minimal, all RNA hairpin ribozyme with modifications (g8dap, u39c) at ph 8.6X-RAY DIFFRACTION2.419
101ZFV|1|D+1ZFV|1|C+1ZFV|1|A+1ZFV|1|BThe structure of an all-RNA minimal Hairpin Ribozyme with Mutation G8A at the cleavage siteX-RAY DIFFRACTION2.419
111ZFX|1|D+1ZFX|1|C+1ZFX|1|A+1ZFX|1|BThe Structure of a minimal all-RNA Hairpin Ribozyme with the mutant G8U at the cleavage siteX-RAY DIFFRACTION2.3819
123CR1|1|Ccrystal structure of a minimal, mutant, all-RNA hairpin ribozyme (A38C, A-1OMA) grown from MgCl2X-RAY DIFFRACTION2.2519
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