Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-8-Internal Loop pdb1vsp1w.n704-825
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 (698, 834), (704, 825)
Primary structure ('_': anchors) _CGAAA_-_AGAUAGCU_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		8: C2'-exo, 10: C4'-exo, 11: C2'-exo, 14: C4'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		5: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 2 3 ↑
2 3 13 &larr
3 6 7 ↑
4 11 12 ↑
5 12 13 ↑
6 16 17 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 17 Watson-Crick/Watson-Crick cis
2 2 10 Sugar/O2' ?
3 2 16 Watson-Crick/Watson-Crick cis y
4 3 15 Watson-Crick/Watson-Crick cis
5 4 12 Watson-Crick/Hoogsteen trans
6 5 11 Watson-Crick/Watson-Crick trans y
7 6 9 Watson-Crick/Watson-Crick trans
8 7 8 Watson-Crick/Watson-Crick cis
9 9 10 O2'/Sugar ?
10 9 11 O2'/Sugar ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters