Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'4-5-Internal Loop pdb1vqoF9.n71-110
Source: [PDB-id:chain] 1vqo:9 (&rarr PDB)
Source: Information THE STRUCTURE OF CCPMN BOUND TO THE LARGE RIBOSOMAL SUBUNIT HALOARCULA MARISMORTUI
Source: Compound 5S RIBOSOMAL RNA
FLIPPED INTERNAL
Source: Resolution 2.20 ANGSTROMS.
Position (75, 106), (81, 101)
Primary structure ('_': anchors) _GAAA_-_GAGUA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		10: C2'-endo, 11: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		None
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 ↑
3 3 4 ↑
4 4 8 →
5 5 6 ↑
6 5 10 &larr
7 7 8 ↑
8 8 9 ↑
9 9 11 →
10 11 12 &larr
11 12 13 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 13 Watson-Crick/Watson-Crick cis
2 2 12 Bifurcated/O2' trans
3 3 11 Hoogsteen/Hoogsteen trans
4 4 9 Hoogsteen/Watson-Crick trans
5 4 10 O2'/Watson-Crick ?
6 5 8 O2'/Bifurcated trans
7 5 9 Watson-Crick/O2' ?
8 5 10 Watson-Crick/O2' ?
9 6 7 Watson-Crick/Watson-Crick cis
10 9 10 Hoogsteen/Sugar cis y
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters