Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'6-5-Internal Loop pdb2qnh1y.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
Source: Resolution 3.83 ANGSTROMS.
Position (400, 424), (407, 418)
Primary structure ('_': anchors) _GAAGAA_-_GUAAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		3: C2'-exo, 4: C4'-exo, 5: C3'-exo, 7: C2'-exo, 10: C4'-exo, 11: C3'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		3: syn, 11: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 3 5 ↑
3 3 11 →
4 6 7 ↑
5 7 8 ↑
6 9 10 &larr
7 10 12 →
8 12 13 ↑
9 13 14 ↑
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 11 O2'/C ?
3 2 14 Bifurcated/O2' trans y
4 3 10 O2'/Bifurcated ?
5 4 5 C/O2' ?
6 5 10 O2'/Bifurcated trans y
7 6 12 Watson-Crick/Hoogsteen trans y
8 8 9 Watson-Crick/Watson-Crick cis
9 10 12 Hoogsteen/O2' ?
10 11 13 Hoogsteen/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters