Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'4-8-Internal Loop pdb1y6910.n2400-2472
Source: [PDB-id:chain] 1y69:0 (&rarr PDB)
Source: Information RRF DOMAIN I IN COMPLEX WITH THE 50S RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 3.33 ANGSTROMS.
Position (2402, 2470), (2407, 2461)
Primary structure ('_': anchors) _UCGU_-_GCACGCGA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		2: C2'-exo, 8: C2'-exo, 9: C2'-exo, 10: C4'-exo, 11: C2'-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 4 5 ↑
4 4 12 →
5 5 6 ↑
6 8 9 ↑
7 12 13 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 16 Watson-Crick/Watson-Crick cis
2 2 13 Watson-Crick/Watson-Crick cis y
3 3 12 Watson-Crick/Watson-Crick cis
4 4 9 Watson-Crick/Watson-Crick cis
5 6 7 Watson-Crick/Watson-Crick cis
6 13 16 Hoogsteen/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters