Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'8-8-Internal Loop pdb2j281B.n1833-1877
Source: [PDB-id:chain] 2j28:B (&rarr PDB)
Source: Information MODEL OF E. COLI SRP BOUND TO 70S RNCS
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 8.00 ANGSTROMS.
Position (1835, 1875), (1844, 1866)
Primary structure ('_': anchors) _UAAUUGAU_-_UGAUCGAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		6: C4'-exo, 7: C4'-exo, 17: C4'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		17: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 3 4 ↑
3 3 18 →
4 4 5 ↑
5 7 13 &larr
6 8 9 ↑
7 8 14 →
8 11 12 ↑
9 12 13 ↑
10 14 15 ↑
11 16 17 &larr
12 18 19 ↑
13 19 20 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 20 Watson-Crick/Watson-Crick cis
2 2 19 Hoogsteen/Watson-Crick trans y
3 3 17 O2'/Bifurcated ?
4 4 17 O2'/Bifurcated ?
5 5 16 Watson-Crick/Watson-Crick cis
6 6 15 Watson-Crick/Watson-Crick cis
7 7 13 Bifurcated/O2' ?
8 7 14 O2'/Bifurcated trans
9 8 13 O2'/Bifurcated trans
10 9 12 Watson-Crick/Watson-Crick cis
11 10 11 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters