Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'9-9-Internal Loop pdb1vqp10.n564-577
Source: [PDB-id:chain] 1vqp:0 (&rarr PDB)
Source: Information THE STRUCTURE OF THE TRANSITION STATE ANALOGUE "RAP" BOUND TO THE LARGE RIBOSOMAL SUBUNIT OF HALOARCULA MARISMORTUI
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 2.25 ANGSTROMS.
Position (554, 587), (564, 577)
Primary structure ('_': anchors) _CGAAUGACC_-_CAGUAAGAC_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		14: C2'-endo, 15: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		None
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 ↑
3 3 19 &larr
4 4 5 ↑
5 5 6 ↑
6 6 7 ↑
7 7 15 &larr
8 8 9 ↑
9 8 17 →
10 9 10 ↑
11 10 11 ↑
12 12 13 ↑
13 13 14 &larr
14 14 16 →
15 17 18 ↑
16 18 19 ↑
17 20 21 ↑
18 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 19 O2'/Bifurcated ?
3 4 19 O2'/Bifurcated ?
4 5 19 O2'/Bifurcated trans
5 6 18 Watson-Crick/Watson-Crick cis
6 7 16 O2'/Watson-Crick ?
7 7 17 Bifurcated/O2' trans
8 8 16 Watson-Crick/Hoogsteen trans
9 9 14 Bifurcated/O2' ?
10 10 13 Watson-Crick/Watson-Crick cis y
11 11 12 Watson-Crick/Watson-Crick cis
12 15 16 Hoogsteen/Sugar cis y
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters