Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'4-5-Internal Loop pdb1vql10.n1554-1583
Source: [PDB-id:chain] 1vql:0 (&rarr PDB)
Source: Information THE STRUCTURE OF THE TRANSITION STATE ANALOGUE "DCSN" BOUND TO THE LARGE RIBOSOMAL SUBUNIT OF HALOARCULA MARISMORTUI
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 2.30 ANGSTROMS.
Position (1558, 1579), (1563, 1573)
Primary structure ('_': anchors) _GGAA_-_AGGAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		3: C2'-endo, 5: C2'-endo, 8: C2'-endo, 9: C2'-endo, 10: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		5: syn, 8: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 ↑
3 4 8 &larr
4 4 11 →
5 5 8 →
6 11 12 ↑
7 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 11 O2'/Bifurcated ?
3 2 12 Bifurcated/O2' trans
4 3 10 O2'/Bifurcated ?
5 3 11 Hoogsteen/Sugar trans y
6 4 7 O2'/Watson-Crick ?
7 4 10 Sugar/Hoogsteen trans
8 5 8 O2'/Bifurcated ?
9 6 7 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters