Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'4-9-Internal Loop pdb2d3o10.n1370-1526
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 (1372, 1524), (1377, 1514)
Primary structure ('_': anchors) _GGAC_-_CAAGAAAAG_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		4: C2'-exo, 8: C4'-exo, 10: C2'-exo, 17: C4'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		9: syn, 11: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 ↑
3 6 11 ↓
4 12 13 ↑
5 13 14 ↑
6 14 15 ↑
7 16 17 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 2 Hoogsteen/O2' ?
2 1 17 Watson-Crick/Watson-Crick cis
3 3 15 Bifurcated/O2' ?
4 4 13 O2'/C ?
5 5 12 Hoogsteen/Bifurcated cis y
6 6 7 Watson-Crick/Watson-Crick cis
7 8 11 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters