Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'3-6-Internal Loop pdb1vqmF0.n1288-1307
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 (1281, 1311), (1288, 1307)
Primary structure ('_': anchors) _GGA_-_AUGGAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		2: C2'-endo, 3: C2'-endo, 9: C2'-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 2 8 →
2 3 4 ↑
3 3 9 &larr
4 4 5 ↑
5 6 7 ↑
6 7 8 ↑
7 12 13 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 8 O2'/Sugar ?
2 1 13 Watson-Crick/Watson-Crick cis
3 2 9 Hoogsteen/Sugar trans
4 2 12 Watson-Crick/O2' ?
5 3 8 Sugar/Hoogsteen trans y
6 3 9 O2'/Bifurcated ?
7 4 7 O2'/Bifurcated trans
8 4 8 Bifurcated/O2' ?
9 5 6 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters