Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-6-Internal Loop pdb2qnhFy.n407-418
Source: [PDB-id:chain] 2qnh:y (&rarr PDB)
Source: Information INTERACTIONS AND DYNAMICS OF THE SHINE-DALGARNO HELIX IN THE 70S RIBOSOME. THIS FILE, 2QNH, CONTAINS THE 30S RIBOSOME SUBUNIT, TWO TRNA, AND MRNA MOLECULES. 50S RIBOSOME SUBUNIT IS IN THE FILE 1VSP.
Source: Compound 16S RNA
FLIPPED INTERNAL
Source: Resolution 3.83 ANGSTROMS.
Position (400, 424), (407, 418)
Primary structure ('_': anchors) _GUAAA_-_GAAGAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		5: C3'-exo, 6: C4'-exo, 9: C2'-exo, 11: C3'-exo, 12: C4'-exo, 13: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		5: syn, 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 4 6 Hoogsteen/O2' ?
5 4 10 Watson-Crick/Hoogsteen trans y
6 5 14 O2'/C ?
7 6 11 O2'/Bifurcated trans y
8 6 13 O2'/Bifurcated ?
9 7 8 Watson-Crick/Watson-Crick cis
10 11 12 C/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters