#PDBTitleRNA source organismCompoundsMethodResolutionDate
12P7D|D (rep)A Minimal, 'Hinged' Hairpin Ribozyme Construct Solved with Mimics of the Product Strands at 2.25 Angstroms Resolution5' substrate strand, pentameric fragment, Ribozyme strand I, Ribozyme strand II, Ribozyme strand III, 3' substrate strand, octameric fragmentX-RAY DIFFRACTION2.252007-05-22
21X9C|DAn all-RNA Hairpin Ribozyme with mutation U39C5'-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'X-RAY DIFFRACTION2.192005-11-22
31X9K|DAn all-RNA Hairpin Ribozyme with mutation U39C5'-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'X-RAY DIFFRACTION3.172005-11-22
41ZFT|DThe crystal structure of an all-RNA minimal Hairpin Ribozyme with mutant G8I at the cleavage site5'-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'X-RAY DIFFRACTION2.332006-02-14
51ZFV|DThe structure of an all-RNA minimal Hairpin Ribozyme with Mutation G8A at the cleavage site5'-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'X-RAY DIFFRACTION2.42006-02-14
61ZFX|DThe Structure of a minimal all-RNA Hairpin Ribozyme with the mutant G8U at the cleavage site5'-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'X-RAY DIFFRACTION2.382006-02-14
72BCY|DCrystal Structure of a minimal, mutant all-RNA hairpin ribozyme (U39C, G8MTU)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'X-RAY DIFFRACTION2.72006-02-14
82BCZ|DCrystal Structure of a minimal, mutant all-RNA hairpin ribozyme (U39C, G8I, 2'deoxy A-1)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'X-RAY DIFFRACTION2.42006-02-14
92D2K|DCrystal Structure of a minimal, native (U39) all-RNA hairpin ribozyme5'-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'X-RAY DIFFRACTION2.652005-11-01
102FGP|DCrystal structure of a minimal, all RNA hairpin ribozyme with modifications (g8dap, u39c) at ph 8.65'-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'X-RAY DIFFRACTION2.42006-02-14
112NPY|DCrystal Structure of a junctioned hairpin ribozyme incorporating 9atom linker and 2'-deoxy 2'-amino U at A-15'-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'X-RAY DIFFRACTION2.652007-08-14
122NPZ|DCrystal structure of junctioned hairpin ribozyme incorporating synthetic propyl linker5'-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'X-RAY DIFFRACTION3.352007-08-14
132OUE|DCrystal structure of a junctionless all-RNA hairpin ribozyme at 2.05 angstroms resolutionSubstrate strand - Minimal Junctionless Hairpin Ribozyme, Loop A ribozyme strand, Loop B ribozyme strand, Loop B S-turn strandX-RAY DIFFRACTION2.052007-03-06
142P7E|DVanadate at the Active Site of a Small Ribozyme Suggests a Role for Water in Transition-State Stabilization5' substrate strand, pentameric fragment, Ribozyme strand I, Ribozyme strand II, Ribozyme strand III, 3' substrate strand, octameric fragmentX-RAY DIFFRACTION2.052007-05-22
152P7F|DThe Novel Use of a 2',5'-Phosphodiester Linkage as a Reaction Intermediate at the Active Site of a Small Ribozymesubstrate strand, Loop A ribozyme strand, Loop B ribozyme strand, Loop B S-turn strandX-RAY DIFFRACTION2.352007-05-22
163GS1|DAn all-RNA Hairpin Ribozyme with mutation A38N1dARNA (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')X-RAY DIFFRACTION2.852009-05-12
173GS5|CAn all-RNA hairpin ribozyme A38N1dA variant with a product mimic substrate strandRNA (25-MER), RNA (36-MER)X-RAY DIFFRACTION2.752009-04-21
183GS8|DAn all-RNA hairpin ribozyme A38N1dA38 variant with a transition-state mimic substrate strandRNA (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')X-RAY DIFFRACTION2.852009-04-21
194G6R|DMinimal Hairpin Ribozyme in the Transition State with G8I VariationLoop A Substrate strand, Loop A Ribozyme strand, Loop B Ribozyme Strand, Loop B S-turn strandX-RAY DIFFRACTION2.832012-08-15

Release history

Release0.830.840.850.860.870.880.890.900.910.920.930.940.950.960.970.980.990.1000.1010.1020.1030.1040.1050.1060.1070.1080.1090.1101.01.11.21.31.41.51.61.71.81.91.101.111.121.131.141.151.161.171.181.191.201.211.221.231.241.251.261.271.281.291.301.311.321.331.341.351.361.371.381.391.401.411.421.431.441.451.461.471.481.491.501.511.521.531.541.551.561.571.581.591.601.611.621.631.641.651.661.671.681.691.701.711.721.731.741.751.761.771.781.791.801.811.821.831.841.851.861.871.881.89
Date2012-08-182012-08-252012-09-012012-09-082012-09-152012-09-222012-09-292012-10-062012-10-132012-10-202012-10-272012-11-032012-11-102012-11-172012-11-242012-12-012012-12-082012-12-152012-12-222012-12-292013-01-052013-01-122013-01-192013-01-262013-02-022013-02-092013-02-162013-02-232013-03-022013-03-092013-03-162013-03-232013-03-302013-04-062013-04-132013-04-202013-04-272013-05-042013-05-112013-05-182013-05-252013-06-012013-06-082013-06-152013-06-222013-06-292013-07-062013-07-132013-07-202013-07-272013-08-032013-08-102013-08-172013-08-242013-08-312013-09-072013-09-142013-09-212013-09-282013-10-052013-10-122013-10-192013-10-262013-11-092013-11-162013-11-232013-11-302013-12-072013-12-142013-12-212013-12-282014-01-042014-01-112014-01-182014-01-252014-02-012014-02-082014-02-152014-02-222014-03-012014-03-082014-03-172014-03-222014-03-292014-04-052014-04-122014-04-192014-04-262014-05-032014-05-102014-05-172014-05-312014-06-072014-06-132014-06-202014-06-272014-07-042014-07-182014-07-252014-08-012014-08-082014-08-152014-08-222014-08-292014-09-052014-09-122014-09-192014-09-262014-10-032014-10-102014-10-172014-10-242014-10-312014-11-072014-11-142014-11-212014-11-282014-12-05

Parents

This classParent classesRelease idIntersectionAdded to this classOnly in parent

Children

This classDescendant 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
12NPZ|DCrystal structure of junctioned hairpin ribozyme incorporating synthetic propyl linkerX-RAY DIFFRACTION3.3519
23GS5|CAn all-RNA hairpin ribozyme A38N1dA variant with a product mimic substrate strandX-RAY DIFFRACTION2.7536
33GS1|DAn all-RNA Hairpin Ribozyme with mutation A38N1dAX-RAY DIFFRACTION2.8519
43GS8|DAn all-RNA hairpin ribozyme A38N1dA38 variant with a transition-state mimic substrate strandX-RAY DIFFRACTION2.8519
52NPY|DCrystal Structure of a junctioned hairpin ribozyme incorporating 9atom linker and 2'-deoxy 2'-amino U at A-1X-RAY DIFFRACTION2.6519
62P7F|DThe Novel Use of a 2',5'-Phosphodiester Linkage as a Reaction Intermediate at the Active Site of a Small RibozymeX-RAY DIFFRACTION2.3519
72P7D|DA Minimal, 'Hinged' Hairpin Ribozyme Construct Solved with Mimics of the Product Strands at 2.25 Angstroms ResolutionX-RAY DIFFRACTION2.2519
82P7E|DVanadate at the Active Site of a Small Ribozyme Suggests a Role for Water in Transition-State StabilizationX-RAY DIFFRACTION2.0519
91ZFT|DThe crystal structure of an all-RNA minimal Hairpin Ribozyme with mutant G8I at the cleavage siteX-RAY DIFFRACTION2.3319
102OUE|DCrystal structure of a junctionless all-RNA hairpin ribozyme at 2.05 angstroms resolutionX-RAY DIFFRACTION2.0519
111X9C|DAn all-RNA Hairpin Ribozyme with mutation U39CX-RAY DIFFRACTION2.1919
122D2K|DCrystal Structure of a minimal, native (U39) all-RNA hairpin ribozymeX-RAY DIFFRACTION2.6519
132FGP|DCrystal structure of a minimal, all RNA hairpin ribozyme with modifications (g8dap, u39c) at ph 8.6X-RAY DIFFRACTION2.419
144G6R|DMinimal Hairpin Ribozyme in the Transition State with G8I VariationX-RAY DIFFRACTION2.8319
151ZFX|DThe Structure of a minimal all-RNA Hairpin Ribozyme with the mutant G8U at the cleavage siteX-RAY DIFFRACTION2.3819
161ZFV|DThe structure of an all-RNA minimal Hairpin Ribozyme with Mutation G8A at the cleavage siteX-RAY DIFFRACTION2.419
172BCY|DCrystal Structure of a minimal, mutant all-RNA hairpin ribozyme (U39C, G8MTU)X-RAY DIFFRACTION2.719
182BCZ|DCrystal Structure of a minimal, mutant all-RNA hairpin ribozyme (U39C, G8I, 2'deoxy A-1)X-RAY DIFFRACTION2.419
191X9K|DAn all-RNA Hairpin Ribozyme with mutation U39CX-RAY DIFFRACTION3.1719