Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-7-Internal Loop pdb2j281B.n1788-1797
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 (1782, 1805), (1788, 1797)
Primary structure ('_': anchors) _GCAAA_-_GACGUAU_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		2: C2'-endo, 3: C2'-endo, 4: C2'-endo, 10: C2'-endo, 13: C4'-exo, 14: C2'-endo, 15: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		2: 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 ?
4 2 14 O2'/Bifurcated ?
5 3 12 Watson-Crick/Watson-Crick trans
6 3 13 Watson-Crick/O2' ?
7 3 14 Hoogsteen/Hoogsteen trans y
8 5 9 Watson-Crick/O2' ?
9 5 10 Bifurcated/O2' trans
10 6 9 O2'/Bifurcated trans
11 7 8 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters