Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'2-7-Internal Loop pdb1vq5F0.n1483-1643
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 (1490, 1636), (1498, 1633)
Primary structure ('_': anchors) _GA_-_AGUGAAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		2: C2'-endo, 7: C2'-endo, 8: C2'-endo, 10: C3'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		7: syn, 9: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 12 →
2 2 3 &larr
3 2 8 →
4 3 4 ↑
5 5 6 ↑
6 6 7 ↑
7 8 9 ↓
8 10 11 ↑
9 11 12 ↑
10 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 7 Hoogsteen/Hoogsteen trans
3 3 6 Sugar/Hoogsteen trans
4 4 5 Watson-Crick/Watson-Crick cis
5 8 9 O2'/Bifurcated ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters