Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'3-6-Internal Loop pdb1vspFw.n1230-1265
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 (1232, 1263), (1239, 1259)
Primary structure ('_': anchors) _GGA_-_GAUGAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		2: C2'-endo, 3: C3'-exo, 5: C2'-exo, 9: C3'-exo, 10: C3'-exo, 11: C3'-exo, 12: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		None
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 2 8 →
2 3 4 ↑
3 3 9 &larr
4 4 5 ↑
5 6 7 ↑
6 7 8 ↑
7 12 13 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 13 Watson-Crick/Watson-Crick cis
2 2 9 Hoogsteen/Sugar trans
3 3 8 Sugar/Hoogsteen trans
4 3 9 Bifurcated/O2' ?
5 4 7 Sugar/Hoogsteen trans
6 5 6 Watson-Crick/Watson-Crick cis
7 8 9 Hoogsteen/O2' ?
8 11 12 Hoogsteen/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters