Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'7-5-Internal Loop pdb2j28FB.n1776-1811
Source: [PDB-id:chain] 2j28:B (&rarr PDB)
Source: Information MODEL OF E. COLI SRP BOUND TO 70S RNCS
Source: Compound 23S RIBOSOMAL RNA
FLIPPED INTERNAL
Source: Resolution 8.00 ANGSTROMS.
Position (1782, 1805), (1788, 1797)
Primary structure ('_': anchors) _GACGUAU_-_GCAAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		2: C2'-endo, 3: C2'-endo, 4: C4'-exo, 7: C2'-endo, 13: C2'-endo, 14: C2'-endo, 15: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		15: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 3 →
2 3 15 ↓
3 3 16 ↑
4 4 5 ↑
5 5 7 →
6 7 8 &larr
7 8 9 ↑
8 10 11 ↑
9 11 12 ↑
10 12 14 →
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 16 Watson-Crick/Watson-Crick cis
2 3 14 Hoogsteen/Hoogsteen trans y
3 3 15 O2'/Bifurcated ?
4 4 14 Watson-Crick/O2' ?
5 4 15 O2'/Bifurcated ?
6 5 14 Watson-Crick/Watson-Crick trans
7 7 12 Bifurcated/O2' trans
8 8 11 O2'/Bifurcated trans
9 8 12 Watson-Crick/O2' ?
10 9 10 Watson-Crick/Watson-Crick cis
11 12 16 Sugar/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters