Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'15-Segment pdb1vsp1w.i472-488
Source: [PDB-id:chain] 1vsp:w (&rarr PDB)
Source: Information INTERACTIONS AND DYNAMICS OF THE SHINE-DALGARNO HELIX IN THE 70S RIBOSOME. THIS FILE, 1VSP, CONTAINS THE 50S RIBOSOME SUBUNIT. 30S RIBOSOME SUBUNIT IS IN THE FILE 2QNH
Source: Compound 23S LARGE SUBUNIT RIBOSOMAL RNA
Source: Resolution 3.83 ANGSTROMS.
Position (472, 488)
Primary structure ('_': anchors) _GAUAGCGCACCAGUA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		2: C4'-exo, 3: C4'-exo, 4: O4'-endo, 5: C2'-exo, 6: C4'-exo, 8: C4'-exo, 10: C2'-exo, 12: C3'-exo, 13: C4'-exo, 14: C4'-exo, 16: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		None
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 3 10 ↓
2 5 6 ↑
3 8 9 ↑
4 8 14 →
5 16 17 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 5 Sugar/O2' ?
2 2 5 Watson-Crick/O2' ?
3 2 10 Watson-Crick/Bifurcated trans y
4 3 10 O2'/Sugar ?
5 5 6 Hoogsteen/O2' ?
6 6 9 O2'/Hoogsteen ?
7 6 10 O2'/Bifurcated ?
8 7 10 O2'/Bifurcated ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters