Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-6-Internal Loop pdb2d3o10.n663-695
Source: [PDB-id:chain] 2d3o:0 (&rarr PDB)
Source: Information STRUCTURE OF RIBOSOME BINDING DOMAIN OF THE TRIGGER FACTOR ON THE 50S RIBOSOMAL SUBUNIT FROM D. RADIODURANS
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 3.35 ANGSTROMS.
Position (665, 693), (671, 686)
Primary structure ('_': anchors) _UGAAA_-_CGGAGG_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		7: C2'-exo, 10: C2'-exo, 13: C4'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		14: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 ↑
3 3 11 &larr
4 4 5 ↑
5 4 12 →
6 5 6 ↑
7 6 7 ↑
8 8 9 ↑
9 9 10 ↑
10 10 11 ↑
11 12 13 ↑
12 13 15 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 15 Watson-Crick/Watson-Crick cis
2 2 13 Watson-Crick/Watson-Crick cis
3 3 11 Bifurcated/O2' ?
4 4 10 Bifurcated/O2' ?
5 4 11 O2'/Bifurcated trans
6 5 10 O2'/Bifurcated trans y
7 6 9 Watson-Crick/Watson-Crick cis y
8 7 8 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters