Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-4-Internal Loop pdb1vq5F0.n938-992
Source: [PDB-id:chain] 1vq5:0 (&rarr PDB)
Source: Information THE STRUCTURE OF THE TRANSITION STATE ANALOGUE "RAA" BOUND TO THE LARGE RIBOSOMAL SUBUNIT OF HALOARCULA MARISMORTUI
Source: Compound 23S RIBOSOMAL RNA
FLIPPED INTERNAL
Source: Resolution 2.60 ANGSTROMS.
Position (946, 984), (951, 978)
Primary structure ('_': anchors) _CCAAA_-_GUAG_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		7: C2'-endo, 12: C2'-endo, 13: C1'-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 3 10 →
4 4 5 ↑
5 4 12 &larr
6 8 9 ↑
7 9 10 ↑
8 10 11 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 13 Watson-Crick/Watson-Crick cis
2 3 11 Hoogsteen/Watson-Crick trans
3 4 10 O2'/Bifurcated trans y
4 4 12 Bifurcated/O2' ?
5 5 9 Watson-Crick/Watson-Crick cis
6 6 7 Hoogsteen/Bifurcated cis
7 7 8 Watson-Crick/Watson-Crick cis
8 11 12 Hoogsteen/Sugar cis y
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters