Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'4-5-Internal Loop pdb1vq810.n1545-1593
Source: [PDB-id:chain] 1vq8:0 (&rarr PDB)
Source: Information THE STRUCTURE OF CCDA-PHE-CAP-BIO AND THE ANTIBIOTIC SPARSOMYCIN BOUND TO THE LARGE RIBOSOMAL SUBUNIT OF HALOARCULA MARISMORTUI
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 2.20 ANGSTROMS.
Position (1549, 1589), (1554, 1583)
Primary structure ('_': anchors) _CAAC_-_CGAAC_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		2: C2'-endo, 10: C4'-exo, 12: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		2: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 3 4 ↑
2 3 10 →
3 4 5 ↑
4 5 6 ↑
5 7 8 ↑
6 8 9 ↑
7 10 11 ↑
8 11 13 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 13 Watson-Crick/Watson-Crick cis
2 2 3 Hoogsteen/O2' ?
3 2 9 Watson-Crick/O2' ?
4 2 11 Hoogsteen/Watson-Crick trans
5 3 9 Bifurcated/O2' ?
6 4 9 O2'/Bifurcated trans
7 6 7 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters