Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'29-Segment pdb1y6910.i2209-2239
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 (2209, 2239)
Primary structure ('_': anchors) _GUAGAGCGCAAAGGUAGAAGGUGGCUUGA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		8: C4'-exo, 9: C2'-exo, 12: C2'-exo, 16: C4'-exo, 18: C4'-exo, 19: C4'-exo, 23: C2'-exo, 29: C4'-exo, 30: C4'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		5: syn, 20: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 6 7 ↑
3 7 8 ↑
4 11 12 ↑
5 12 13 ↑
6 13 14 ↑
7 14 15 ↑
8 17 19 →
9 19 21 ↑
10 21 22 ↑
11 22 23 ↑
12 24 25 ↑
13 25 26 ↑
14 26 27 ↑
15 29 31 →
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 4 5 Hoogsteen/O2' ?
2 4 6 Hoogsteen/O2' ?
3 4 17 Bifurcated/O2' ?
4 5 6 Hoogsteen/O2' ?
5 8 15 Watson-Crick/Watson-Crick cis
6 16 17 Hoogsteen/O2' ?
7 19 20 C/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters