Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-4-Internal Loop pdb2otlF0.n1563-1573
Source: [PDB-id:chain] 2otl:0 (&rarr PDB)
Source: Information GIRODAZOLE BOUND TO THE LARGE SUBUNIT OF HALOARCULA MARISMORTUI
Source: Compound 23S RIBOSOMAL RNA
FLIPPED INTERNAL
Source: Resolution 2.70 ANGSTROMS.
Position (1558, 1579), (1563, 1573)
Primary structure ('_': anchors) _AGGAA_-_GGAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		4: C2'-endo, 5: C2'-endo, 6: C2'-endo, 8: C4'-exo, 9: C2'-endo, 11: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		6: syn, 9: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 ↑
3 3 10 →
4 6 9 →
5 6 10 &larr
6 11 12 ↑
7 12 13 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 13 Watson-Crick/Watson-Crick cis
2 2 12 Hoogsteen/Sugar trans
3 3 11 O2'/Bifurcated trans
4 3 12 O2'/Bifurcated ?
5 4 10 Sugar/Hoogsteen trans
6 4 11 O2'/Bifurcated ?
7 6 9 O2'/Bifurcated ?
8 7 8 Watson-Crick/Watson-Crick cis
9 7 10 O2'/Watson-Crick ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters