Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'8-8-Internal Loop pdb1y6910.n1775-1810
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 (1777, 1808), (1786, 1799)
Primary structure ('_': anchors) _CAAGUGGA_-_GAAAUGAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		1: C2'-exo, 7: C2'-exo, 12: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		17: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 3 4 ↑
2 3 18 →
3 4 5 ↑
4 5 6 ↑
5 6 7 ↑
6 8 9 ↑
7 8 14 →
8 9 10 ↑
9 11 12 ↑
10 12 13 ↑
11 14 15 ↑
12 15 16 ↑
13 16 17 &larr
14 18 19 ↑
15 19 20 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 20 Watson-Crick/Watson-Crick cis y
2 3 17 O2'/Bifurcated ?
3 4 17 O2'/Bifurcated ?
4 6 15 Watson-Crick/Watson-Crick cis
5 7 13 Watson-Crick/Watson-Crick cis y
6 7 14 Hoogsteen/Sugar trans y
7 8 13 O2'/Bifurcated ?
8 9 13 O2'/Bifurcated trans y
9 10 11 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters