Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'6-5-Internal Loop pdb2ognF0.n663-695
Source: [PDB-id:chain] 2ogn:0 (&rarr PDB)
Source: Information THE CRYSTAL STRUCTURE OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS COMPLEXED WITH THE PLEUROMUTILIN DERIVATIVE SB-280080
Source: Compound 23S RIBOSOMAL RNA
FLIPPED INTERNAL
Source: Resolution 3.56 ANGSTROMS.
Position (665, 693), (671, 686)
Primary structure ('_': anchors) _CGGAGG_-_UGAAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		2: C4'-exo, 3: O4'-endo, 13: C4'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		None
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 3 ↑
2 3 4 ↑
3 5 6 ↑
4 5 13 &larr
5 6 7 ↑
6 7 8 ↑
7 9 10 ↑
8 10 11 ↑
9 11 12 ↑
10 13 14 ↑
11 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 13 Watson-Crick/O2' ?
3 4 14 Bifurcated/Watson-Crick trans y
4 5 12 Bifurcated/O2' ?
5 5 13 Bifurcated/O2' ?
6 6 11 O2'/Bifurcated ?
7 6 12 Watson-Crick/O2' ?
8 7 10 Watson-Crick/Watson-Crick cis y
9 8 9 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters