Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'3-7-Internal Loop pdb1q811A.n2532-2685
Source: [PDB-id:chain] 1q81:A (&rarr PDB)
Source: Information CRYSTAL STRUCTURE OF MINIHELIX WITH 3' PUROMYCIN BOUND TO A- SITE OF THE 50S RIBOSOMAL SUBUNIT.
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 2.95 ANGSTROMS.
Position (2536, 2681), (2540, 2673)
Primary structure ('_': anchors) _UGA_-_GAAAAGA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		3: C2'-endo, 8: C2'-endo, 9: C2'-endo, 10: C2'-endo, 11: C2'-endo, 12: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		9: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 ↑
3 3 7 &larr
4 4 5 ↑
5 4 10 →
6 6 7 ↑
7 8 10 ↓
8 8 14 ↑
9 11 13 →
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 14 Watson-Crick/Watson-Crick cis
2 2 8 Hoogsteen/Watson-Crick trans
3 3 7 Bifurcated/O2' ?
4 3 8 O2'/Watson-Crick ?
5 3 10 Hoogsteen/Sugar trans
6 4 7 O2'/Bifurcated trans
7 5 6 Watson-Crick/Watson-Crick cis
8 8 14 Hoogsteen/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters