Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'19-Segment pdb1vsp1w.i522-542
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 (522, 542)
Primary structure ('_': anchors) _AGUGAAAUAGAGCCUGAAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		2: C2'-exo, 3: C2'-exo, 7: C2'-exo, 8: C4'-exo, 9: C4'-exo, 11: C4'-exo, 12: C4'-exo, 14: C4'-exo, 16: C2'-exo, 18: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		None
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 ↑
3 3 4 ↑
4 4 5 ↑
5 6 7 ↑
6 7 10 ↑
7 8 10 ↓
8 8 11 ↑
9 15 16 ↑
10 16 17 ↑
11 18 19 ↑
12 19 20 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 3 11 Bifurcated/Watson-Crick trans
2 4 5 Hoogsteen/O2' ?
3 5 7 Hoogsteen/O2' ?
4 5 8 O2'/Bifurcated ?
5 5 10 Hoogsteen/Sugar trans y
6 20 21 Bifurcated/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters