Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-6-Internal Loop pdb2e5lFA.n408-419
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
FLIPPED INTERNAL
Source: Resolution 3.30 ANGSTROMS.
Position (401, 425), (408, 419)
Primary structure ('_': anchors) _GUAAA_-_GAAGAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		4: C2'-exo, 5: O4'-endo, 6: C4'-exo, 12: O4'-endo, 13: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		13: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 ↑
3 3 4 ↑
4 4 6 →
5 5 13 →
6 6 7 &larr
7 8 9 ↑
8 9 10 ↑
9 11 13 ↑
10 14 15 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 15 Watson-Crick/Watson-Crick cis
2 2 14 Bifurcated/O2' trans y
3 3 5 Hoogsteen/Watson-Crick cis
4 3 14 O2'/Watson-Crick ?
5 4 13 Hoogsteen/Watson-Crick trans
6 6 9 Hoogsteen/Hoogsteen trans y
7 6 10 Bifurcated/O2' ?
8 6 11 O2'/Bifurcated trans
9 7 8 Watson-Crick/Watson-Crick cis y
10 11 13 O2'/Sugar ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters