Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'3-5-Internal Loop pdb1vqm10.n1424-1459
Source: [PDB-id:chain] 1vqm:0 (&rarr PDB)
Source: Information THE STRUCTURE OF THE TRANSITION STATE ANALOGUE "DAN" BOUND TO THE LARGE RIBOSOMAL SUBUNIT OF HALOARCULA MARISMORTUI
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 2.30 ANGSTROMS.
Position (1425, 1458), (1429, 1452)
Primary structure ('_': anchors) _UAA_-_GAAAU_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		8: C2'-endo, 9: C2'-endo, 11: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		8: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 3 4 ↑
3 3 8 →
4 6 7 ↑
5 8 12 ↑
6 10 11 &larr
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 12 Watson-Crick/Watson-Crick cis
2 2 8 Hoogsteen/Watson-Crick trans
3 3 7 Watson-Crick/O2' ?
4 4 7 O2'/Bifurcated trans
5 5 6 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters