Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'3-9-Internal Loop pdb1vqn10.n1498-1633
Source: [PDB-id:chain] 1vqn:0 (&rarr PDB)
Source: Information THE STRUCTURE OF CC-HPMN AND CCA-PHE-CAP-BIO BOUND TO THE LARGE RIBOSOMAL SUBUNIT OF HALOARCULA MARISMORTUI
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 2.40 ANGSTROMS.
Position (1500, 1631), (1504, 1621)
Primary structure ('_': anchors) _GAC_-_CCAUGAAAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		3: C2'-endo, 4: C2'-endo, 7: C4'-exo, 8: C2'-endo, 9: C2'-endo, 10: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		4: syn, 11: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 &larr
3 5 11 ↓
4 7 10 ↑
5 12 13 ↑
6 13 14 ↑
7 14 15 ↑
8 15 16 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 16 Watson-Crick/Watson-Crick cis
2 2 15 Bifurcated/O2' trans
3 3 14 O2'/Bifurcated trans
4 4 13 O2'/Bifurcated trans y
5 5 6 Watson-Crick/Watson-Crick cis
6 7 11 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters