Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-6-Internal Loop pdb1yi210.n288-347
Source: [PDB-id:chain] 1yi2:0 (&rarr PDB)
Source: Information CRYSTAL STRUCTURE OF ERYTHROMYCIN BOUND TO THE G2099A MUTANT 50S RIBOSOMAL SUBUNIT OF HALOARCULA MARISMORTUI
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 2.65 ANGSTROMS.
Position (282, 354), (288, 347)
Primary structure ('_': anchors) _CGACC_-_CAGUAC_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		10: C2'-endo, 11: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		11: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 ↑
3 3 11 &larr
4 4 5 ↑
5 4 13 →
6 5 6 ↑
7 6 7 ↑
8 8 9 ↑
9 9 10 &larr
10 10 12 →
11 12 13 ↑
12 13 14 ↑
13 14 15 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 15 Watson-Crick/Watson-Crick cis
2 3 12 O2'/Watson-Crick ?
3 3 13 Bifurcated/O2' trans
4 4 11 Bifurcated/O2' ?
5 4 12 Watson-Crick/Hoogsteen trans
6 6 9 Watson-Crick/Watson-Crick cis y
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