Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'9-9-Internal Loop pdb1qvg10.n553-588
Source: [PDB-id:chain] 1qvg:0 (&rarr PDB)
Source: Information STRUCTURE OF CCA OLIGONUCLEOTIDE BOUND TO THE TRNA BINDING SITES OF THE LARGE RIBOSOMAL SUBUNIT OF HALOARCULA MARISMORTUI
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 2.90 ANGSTROMS.
Position (554, 587), (564, 577)
Primary structure ('_': anchors) _CGAAUGACC_-_CAGUAAGAC_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		8: C2'-exo, 12: C4'-exo, 14: C2'-endo, 15: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		15: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 ↑
3 4 5 ↑
4 5 6 ↑
5 6 7 ↑
6 8 9 ↑
7 8 17 →
8 9 10 ↑
9 10 11 ↑
10 12 13 ↑
11 13 14 &larr
12 14 16 →
13 17 18 ↑
14 18 19 ↑
15 20 21 ↑
16 21 22 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 22 Watson-Crick/Watson-Crick cis
2 2 21 Watson-Crick/Watson-Crick cis y
3 3 20 O2'/Bifurcated ?
4 4 19 O2'/Bifurcated ?
5 5 19 O2'/Bifurcated trans
6 6 18 Watson-Crick/Watson-Crick cis
7 7 16 O2'/Watson-Crick ?
8 7 17 Bifurcated/O2' trans
9 8 15 Bifurcated/O2' ?
10 8 16 Watson-Crick/Hoogsteen trans
11 9 14 Bifurcated/O2' ?
12 10 13 Watson-Crick/Watson-Crick cis y
13 11 12 Watson-Crick/Watson-Crick cis
14 15 16 Hoogsteen/Sugar cis y
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters