Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-6-Internal Loop pdb2ogoF0.n221-229
Source: [PDB-id:chain] 2ogo:0 (&rarr PDB)
Source: Information THE CRYSTAL STRUCTURE OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS COMPLEXED WITH THE PLEUROMUTILIN DERIVATIVE RETAPAMULIN (SB-275833)
Source: Compound 23S RIBOSOMAL RNA
FLIPPED INTERNAL
Source: Resolution 3.66 ANGSTROMS.
Position (214, 235), (221, 229)
Primary structure ('_': anchors) _GAACC_-_UUAGUA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		11: C2'-exo, 13: C4'-exo
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 4 5 ↑
4 5 9 →
5 6 7 ↑
6 6 11 &larr
7 10 12 →
8 12 13 &larr
9 13 14 ↑
10 14 15 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 15 Watson-Crick/Watson-Crick cis
2 4 12 Hoogsteen/Hoogsteen trans
3 5 11 O2'/Bifurcated ?
4 6 10 Watson-Crick/O2' ?
5 6 11 Bifurcated/O2' ?
6 7 8 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters