Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'3-6-Internal Loop pdb1vspFw.n2127-2161
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 (2129, 2159), (2136, 2155)
Primary structure ('_': anchors) _GGA_-_UGUGAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		3: C4'-exo, 4: C2'-exo, 8: C2'-exo, 9: C4'-exo, 10: C2'-exo, 11: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		None
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 3 4 ↑
2 4 5 ↑
3 6 7 ↑
4 7 8 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 13 Watson-Crick/Watson-Crick cis
2 2 3 C/O2' ?
3 2 9 Bifurcated/O2' trans y
4 3 8 O2'/Bifurcated trans
5 4 7 O2'/Bifurcated trans
6 4 8 Bifurcated/O2' ?
7 5 6 Watson-Crick/Watson-Crick cis
8 8 9 Hoogsteen/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters