BGSU RNA Site //

Equivalence class NR_2.5_98705.4 Current

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodÅDate
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

Release history

Release3.523.533.543.553.563.573.583.593.603.613.623.633.643.653.663.673.683.693.703.713.723.733.743.753.763.773.783.793.803.813.823.833.843.853.863.873.883.893.903.913.923.933.943.953.963.973.983.993.1003.1013.1023.1033.1043.1053.1063.1073.1083.1093.1103.1113.1123.1133.1143.1153.1163.1173.1183.1193.1203.1213.1223.1233.1243.1253.1263.1273.1283.1293.1303.1313.1323.1333.1343.1353.1363.1373.1383.1393.1403.1413.1423.1433.1443.1453.1463.1473.1483.1493.1503.1513.1523.1533.1543.1553.1563.1573.1583.1593.1603.1613.1623.1633.1643.1653.1663.1673.1683.1693.1703.1713.1723.1733.1743.1753.1763.1773.1783.1793.1803.1813.1823.1833.1843.1853.1863.1873.1883.1893.1903.1913.1923.1933.1943.1953.1963.1973.1983.1993.2003.2013.2023.2033.2043.2053.2063.2073.2083.2093.2103.2113.2123.2133.2143.2153.2163.2173.2183.2193.2203.2213.2223.2233.2243.2253.2263.2273.2283.2293.2303.2313.2323.2333.2343.2353.2363.2373.2383.2393.2403.2413.2423.2433.2443.2453.2463.2473.2483.2493.2503.2513.2523.2533.2543.2553.2563.2573.2583.2593.2603.2613.2623.2633.2643.2653.2663.2673.2683.2693.2703.2713.2723.2733.2743.2753.2763.2773.2783.2793.2803.281
Date2018-12-142018-12-212018-12-282019-01-042019-01-112019-01-182019-01-252019-02-012019-02-082019-02-152019-02-222019-03-012019-03-082019-03-152019-03-222019-03-292019-04-052019-04-122019-04-192019-04-262019-05-032019-05-102019-05-172019-05-242019-05-312019-06-072019-06-142019-06-212019-06-282019-07-052019-07-122019-07-192019-07-262019-08-022019-08-092019-08-162019-08-232019-08-282019-09-042019-09-112019-09-192019-09-252019-10-032019-10-092019-10-162019-10-232019-10-302019-11-062019-11-132019-11-202019-11-272019-12-042019-12-112019-12-182019-12-252020-01-012020-01-082020-01-152020-01-222020-01-292020-02-052020-02-122020-02-192020-02-262020-03-042020-03-112020-03-182020-03-252020-04-012020-04-082020-04-152020-04-222020-04-292020-05-062020-05-132020-05-202020-05-272020-06-032020-06-102020-06-172020-06-242020-07-012020-07-082020-07-152020-07-222020-07-292020-08-052020-08-122020-08-192020-08-262020-09-022020-09-092020-09-162020-09-232020-09-302020-10-072020-10-142020-10-212020-10-282020-11-042020-11-112020-11-182020-11-252020-12-022020-12-092020-12-162020-12-232020-12-302021-01-062021-01-132021-01-202021-01-272021-02-032021-02-102021-02-172021-02-242021-03-032021-03-102021-03-172021-03-242021-03-312021-04-072021-04-142021-04-212021-04-282021-05-052021-05-122021-05-192021-05-262021-06-022021-06-092021-06-162021-06-232021-06-302021-07-072021-07-142021-07-212021-07-282021-08-042021-08-112021-08-182021-08-252021-09-012021-09-082021-09-152021-09-222021-09-292021-10-062021-10-132021-10-202021-10-272021-11-032021-11-102021-11-172021-11-242021-12-012021-12-082021-12-152021-12-222021-12-292022-01-052022-01-122022-01-192022-01-262022-02-022022-02-092022-02-162022-02-232022-03-022022-03-092022-03-162022-03-232022-03-302022-04-062022-04-132022-04-202022-04-272022-05-042022-05-112022-05-182022-05-252022-06-012022-06-082022-06-152022-06-222022-06-292022-07-062022-07-132022-07-202022-07-272022-08-032022-08-102022-08-172022-08-242022-08-312022-09-072022-09-142022-09-212022-09-282022-10-052022-10-122022-10-192022-10-262022-11-022022-11-092022-11-162022-11-232022-11-302022-12-072022-12-142022-12-212022-12-282023-01-042023-01-112023-01-182023-01-252023-02-012023-02-082023-02-152023-02-222023-03-012023-03-082023-03-152023-03-222023-03-292023-04-052023-04-122023-04-192023-04-262023-05-03

Parents

This classParent classesRelease idIntersectionAdded to this classOnly in parent
NR_2.5_98705.4NR_2.5_98705.33.52(11) 2P7E|1|D+2P7E|1|C+2P7E|1|P, 2BCZ|1|D+2BCZ|1|C+2BCZ|1|A+2BCZ|1|B, 2FGP|1|D+2FGP|1|C+2FGP|1|A+2FGP|1|B, 1ZFT|1|D+1ZFT|1|C+1ZFT|1|A+1ZFT|1|B, 2P7D|1|D+2P7D|1|C+2P7D|1|P, 1ZFX|1|D+1ZFX|1|C+1ZFX|1|A+1ZFX|1|B, 2P7F|1|D+2P7F|1|C+2P7F|1|A+2P7F|1|B, 2D2L|1|D+2D2L|1|C+2D2L|1|A+2D2L|1|B, 1X9C|1|D+1X9C|1|C+1X9C|1|A+1X9C|1|B, 2OUE|1|D+2OUE|1|C+2OUE|1|A+2OUE|1|B, 1ZFV|1|D+1ZFV|1|C+1ZFV|1|A+1ZFV|1|B(0) (1) 3CR1|1|C

Children

This class Descendant classesRelease idIntersectionOnly in this classAdded to child

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
11ZFV|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
22FGP|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
31ZFX|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
42BCZ|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
51ZFT|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
62P7D|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
72P7F|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
82P7E|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
92OUE|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
101X9C|1|D+1X9C|1|C+1X9C|1|A+1X9C|1|BAn all-RNA Hairpin Ribozyme with mutation U39CX-RAY DIFFRACTION2.1919
112D2L|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
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