Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-7-Internal Loop pdb1vsp1w.n1801-1836
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 (1807, 1830), (1813, 1822)
Primary structure ('_': anchors) _GCGAA_-_GAGGUAU_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		2: C3'-exo, 5: C2'-exo, 10: C3'-exo, 11: C2'-exo, 13: C3'-exo, 14: C3'-exo, 15: C3'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		2: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 3 5 →
2 5 6 ↑
3 8 9 ↑
4 9 10 &larr
5 10 12 →
6 12 13 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 5 Sugar/O2' cis y
2 1 16 Watson-Crick/Watson-Crick cis y
3 3 12 Watson-Crick/Watson-Crick trans
4 5 9 Bifurcated/O2' ?
5 5 10 Bifurcated/O2' trans
6 6 9 O2'/Bifurcated trans
7 7 8 Watson-Crick/Watson-Crick cis
8 9 10 O2'/Hoogsteen ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters