Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'3-7-Internal Loop pdb1qvf10.n925-1008
Source: [PDB-id:chain] 1qvf:0 (&rarr PDB)
Source: Information STRUCTURE OF A DEACYLATED TRNA MINIHELIX BOUND TO THE E SITE OF THE LARGE RIBOSOMAL SUBUNIT OF HALOARCULA MARISMORTUI
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 3.10 ANGSTROMS.
Position (930, 1003), (934, 995)
Primary structure ('_': anchors) _CGA_-_GUUUGAC_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		3: C2'-endo, 4: C1'-exo, 9: C2'-endo, 10: C1'-exo, 11: C1'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		10: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 ↑
3 4 12 →
4 5 7 →
5 6 7 ↑
6 7 8 ↑
7 12 13 ↑
8 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 11 O2'/Bifurcated ?
3 2 12 O2'/Bifurcated ?
4 2 13 Watson-Crick/Watson-Crick cis y
5 3 11 O2'/Bifurcated ?
6 3 12 O2'/Bifurcated trans y
7 4 7 O2'/Watson-Crick ?
8 4 11 Sugar/Hoogsteen trans
9 5 6 Watson-Crick/Watson-Crick cis y
10 5 12 Watson-Crick/O2' trans y
11 12 13 Bifurcated/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters