Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'9-4-Internal Loop pdb1vspFw.n1446-1602
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
FLIPPED INTERNAL
Source: Resolution 3.83 ANGSTROMS.
Position (1449, 1599), (1454, 1589)
Primary structure ('_': anchors) _CAAGAAAAG_-_GGAC_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		3: C2'-exo, 5: C2'-exo, 7: C2'-exo, 8: C3'-exo, 9: C3'-exo, 13: C3'-exo, 14: C2'-endo, 15: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		7: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 ↑
3 3 4 ↑
4 4 5 ↑
5 5 6 ↑
6 7 12 ↓
7 8 10 ↑
8 10 11 ↑
9 14 15 &larr
10 15 16 ↑
11 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 16 Hoogsteen/Bifurcated trans
3 3 15 O2'/Bifurcated trans
4 4 5 C/O2' ?
5 4 14 O2'/Bifurcated trans
6 5 13 Hoogsteen/Watson-Crick trans
7 5 14 O2'/Watson-Crick ?
8 7 10 Watson-Crick/Watson-Crick cis
9 8 9 Bifurcated/O2' ?
10 9 10 Hoogsteen/O2' ?
11 11 12 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters