Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'3-6-Internal Loop pdb1vsp1w.n84-96
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 (80, 103), (84, 96)
Primary structure ('_': anchors) _GGA_-_GUGGAU_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		2: C2'-exo, 3: C2'-exo, 6: C2'-exo, 7: C2'-exo, 9: C2'-exo, 10: C4'-exo, 11: 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 5 7 →
3 11 12 ↑
4 12 13 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 2 Hoogsteen/O2' ?
2 1 13 Watson-Crick/Watson-Crick cis
3 2 11 O2'/Bifurcated ?
4 3 10 O2'/Bifurcated ?
5 3 11 Hoogsteen/Sugar trans y
6 4 11 Bifurcated/O2' ?
7 5 6 Watson-Crick/Watson-Crick cis
8 5 11 Watson-Crick/O2' ?
9 12 13 Bifurcated/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters