Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'4-5-Internal Loop pdb1vq410.n938-992
Source: [PDB-id:chain] 1vq4:0 (&rarr PDB)
Source: Information THE STRUCTURE OF THE TRANSITION STATE ANALOGUE "DAA" BOUND TO THE LARGE RIBOSOMAL SUBUNIT OF HALOARCULA MARISMORTUI
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 2.70 ANGSTROMS.
Position (946, 984), (951, 978)
Primary structure ('_': anchors) _GUAG_-_CCAAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		1: C2'-endo, 2: C2'-endo, 7: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		None
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 4 5 ↑
2 4 11 →
3 5 6 ↑
4 9 10 ↑
5 11 12 ↑
6 12 13 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 2 Hoogsteen/O2' ?
2 1 13 Watson-Crick/Watson-Crick cis
3 2 3 Hoogsteen/Sugar cis y
4 2 10 Bifurcated/O2' ?
5 2 11 O2'/Watson-Crick ?
6 3 11 Hoogsteen/Watson-Crick trans
7 4 10 O2'/Bifurcated trans y
8 5 9 Watson-Crick/Watson-Crick cis
9 6 7 Watson-Crick/Watson-Crick cis
10 7 8 Hoogsteen/Bifurcated cis
11 12 13 Bifurcated/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters