Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'7-7-Internal Loop pdb1vspFx.n79-98
Source: [PDB-id:chain] 1vsp:x (&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 5S LARGE SUBUNIT RIBOSOMAL RNA
FLIPPED INTERNAL
Source: Resolution 3.83 ANGSTROMS.
Position (71, 106), (79, 98)
Primary structure ('_': anchors) _GAGAGUA_-_GAUGGUA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		5: C2'-exo, 6: C2'-exo, 10: C2'-exo, 11: C2'-exo, 13: C4'-exo, 14: C2'-exo, 15: C2'-exo, 17: 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 4 5 ↑
4 5 6 ↑
5 6 7 ↑
6 7 11 →
7 8 9 ↑
8 12 13 ↑
9 14 15 ↑
10 15 16 ↑
11 17 18 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 18 Watson-Crick/Watson-Crick cis
2 2 17 Hoogsteen/Sugar trans y
3 3 16 Watson-Crick/Hoogsteen trans
4 4 15 Watson-Crick/Watson-Crick cis y
5 6 13 Watson-Crick/Hoogsteen trans y
6 7 12 Hoogsteen/Watson-Crick trans y
7 8 11 Sugar/Hoogsteen trans y
8 9 10 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters