Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-7-Internal Loop pdb1yij10.n1819-1854
Source: [PDB-id:chain] 1yij:0 (&rarr PDB)
Source: Information CRYSTAL STRUCTURE OF TELITHROMYCIN BOUND TO THE G2099A MUTANT 50S RIBOSOMAL SUBUNIT OF HALOARCULA MARISMORTUI
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 2.60 ANGSTROMS.
Position (1825, 1848), (1831, 1840)
Primary structure ('_': anchors) _GCAAA_-_CUCGUAC_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		2: C2'-endo, 3: C1'-exo, 4: C2'-endo, 10: C2'-endo, 11: C2'-endo, 13: C2'-endo, 14: C2'-endo, 15: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		2: syn, 4: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 14 ↑
2 2 14 ↓
3 3 5 →
4 5 6 ↑
5 6 7 ↑
6 8 9 ↑
7 9 10 &larr
8 10 12 →
9 12 13 ↑
10 14 16 →
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 5 Sugar/O2' ?
2 1 16 Watson-Crick/Watson-Crick cis
3 2 13 O2'/Bifurcated trans y
4 2 14 O2'/Bifurcated ?
5 3 12 Watson-Crick/Watson-Crick trans
6 3 13 Watson-Crick/O2' ?
7 5 10 Hoogsteen/Hoogsteen trans y
8 6 9 Watson-Crick/Watson-Crick cis y
9 7 8 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters