Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-5-Internal Loop pdb1vqmF0.n1884-1897
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
FLIPPED INTERNAL
Source: Resolution 2.30 ANGSTROMS.
Position (1878, 1903), (1884, 1897)
Primary structure ('_': anchors) _ACGAA_-_GAACA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		4: C4'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		4: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 ↑
3 3 12 →
4 4 5 &larr
5 4 13 ↑
6 5 6 ↑
7 6 7 ↑
8 8 9 ↑
9 9 10 ↑
10 10 11 ↑
11 11 12 ↑
12 13 14 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 14 Watson-Crick/Watson-Crick cis
2 2 13 Bifurcated/O2' trans
3 3 13 O2'/Watson-Crick ?
4 6 9 Watson-Crick/Watson-Crick cis y
5 7 8 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters