Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'6-4-Internal Loop pdb2e5l1A.n860-885
Source: [PDB-id:chain] 2e5l:A (&rarr PDB)
Source: Information A SNAPSHOT OF THE 30S RIBOSOMAL SUBUNIT CAPTURING MRNA VIA THE SHINE- DALGARNO INTERACTION
Source: Compound 16S RIBOSOMAL RNA
Source: Resolution 3.30 ANGSTROMS.
Position (861, 884), (868, 879)
Primary structure ('_': anchors) _GAGUAC_-_GAAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		3: C4'-exo, 4: C4'-exo, 11: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		None
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 3 5 →
3 6 7 ↑
4 6 11 →
5 7 8 ↑
6 9 10 ↑
7 11 12 ↑
8 12 13 ↑
9 13 14 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 14 Watson-Crick/Watson-Crick cis
2 2 13 Bifurcated/O2' trans
3 4 10 Watson-Crick/O2' ?
4 4 11 O2'/Bifurcated ?
5 5 10 Watson-Crick/O2' ?
6 5 11 Hoogsteen/Watson-Crick trans
7 6 10 O2'/Bifurcated trans
8 8 9 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters