Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'9-9-Internal Loop pdb1qvfF0.n553-588
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
FLIPPED INTERNAL
Source: Resolution 3.10 ANGSTROMS.
Position (554, 587), (564, 577)
Primary structure ('_': anchors) _CAGUAAGAC_-_CGAAUGACC_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		8: C3'-exo, 9: C1'-exo, 11: C4'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		8: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 ↑
3 4 5 ↑
4 4 20 &larr
5 5 6 ↑
6 6 15 →
7 7 9 →
8 9 10 &larr
9 10 11 ↑
10 12 13 ↑
11 13 14 ↑
12 14 15 ↑
13 16 17 ↑
14 17 18 ↑
15 18 19 ↑
16 20 21 ↑
17 21 22 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 22 Watson-Crick/Watson-Crick cis
2 3 20 O2'/Bifurcated ?
3 4 18 O2'/Bifurcated trans
4 4 19 O2'/Bifurcated ?
5 5 17 Watson-Crick/Watson-Crick cis
6 6 16 Bifurcated/O2' trans
7 7 8 Hoogsteen/Sugar cis y
8 7 15 Watson-Crick/Hoogsteen trans
9 7 16 O2'/Watson-Crick ?
10 8 15 Bifurcated/O2' ?
11 9 14 Bifurcated/O2' ?
12 10 13 Watson-Crick/Watson-Crick cis y
13 11 12 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters