Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-4-Internal Loop pdb2r8s1R.n26-94
Source: [PDB-id:chain] 2r8s:R (&rarr PDB)
Source: Information HIGH RESOLUTION STRUCTURE OF A SPECIFIC SYNTHETIC FAB BOUND TO P4-P6 RNA RIBOZYME DOMAIN
Source: Compound P4-P6 RNA RIBOZYME DOMAIN
Source: Resolution 1.95 ANGSTROMS.
Position (20, 99), (26, 94)
Primary structure ('_': anchors) _AACAG_-_ACAU_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		2: C4'-exo, 3: C2'-endo, 5: C1'-exo, 11: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		12: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 2 11 ↓
2 3 10 &larr
3 4 6 ↑
4 6 7 ↑
5 8 9 ↑
6 9 10 ↑
7 11 13 →
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 3 Sugar/O2' ?
2 1 13 Watson-Crick/Watson-Crick cis
3 2 11 O2'/Bifurcated ?
4 3 10 Bifurcated/O2' ?
5 3 11 Hoogsteen/Watson-Crick trans
6 4 10 Watson-Crick/Hoogsteen trans y
7 6 9 Watson-Crick/Watson-Crick cis
8 7 8 Watson-Crick/Watson-Crick cis
9 10 13 Sugar/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters