Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'7-9-Internal Loop pdb1m5p1E.n27-54
Source: [PDB-id:chain] 1m5p:E (&rarr PDB)
Source: Information TRANSITION STATE STABILIZATION BY A CATALYTIC RNA
Source: Compound RNA HAIRPIN RIBOZYME
Source: Resolution 2.60 ANGSTROMS.
Position (19, 64), (27, 54)
Primary structure ('_': anchors) _AGAAACA_-_GUAUAUUAC_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		8: C2'-exo, 11: C3'-exo, 12: C3'-exo, 13: C3'-exo, 14: C2'-endo, 16: C2'-endo, 17: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		13: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 ↑
3 3 16 &larr
4 4 5 ↑
5 4 18 →
6 5 6 ↑
7 6 7 ↑
8 8 9 ↑
9 10 11 ↑
10 13 15 ↑
11 15 16 ↑
12 18 19 ↑
13 19 20 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 20 Watson-Crick/Watson-Crick cis
2 2 19 Watson-Crick/Watson-Crick cis y
3 3 18 Bifurcated/O2' trans
4 4 16 Watson-Crick/Hoogsteen trans
5 5 15 Watson-Crick/Hoogsteen trans
6 5 17 Watson-Crick/Watson-Crick cis
7 8 11 Watson-Crick/Watson-Crick cis
8 9 10 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters