Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'6-5-Internal Loop pdb2vqe1A.n407-418
Source: [PDB-id:chain] 2vqe:A (&rarr PDB)
Source: Information MODIFIED URIDINES WITH C5-METHYLENE SUBSTITUENTS AT THE FIRST POSITION OF THE TRNA ANTICODON STABILIZE U-G WOBBLE PAIRING DURING DECODING
Source: Compound 16S RRNA
Source: Resolution 2.5 ANGSTROMS.
Position (400, 424), (407, 418)
Primary structure ('_': anchors) _GAAGAA_-_GUAAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		5: C2'-endo, 10: C2'-endo, 11: C2'-endo, 15: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		11: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 11 &larr
3 3 5 ↑
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'/Hoogsteen ?
3 2 13 O2'/Watson-Crick ?
4 2 14 Bifurcated/O2' trans
5 3 12 Hoogsteen/Watson-Crick trans
6 5 10 O2'/Bifurcated trans
7 5 11 O2'/Bifurcated ?
8 6 12 Watson-Crick/Hoogsteen trans
9 8 9 Watson-Crick/Watson-Crick cis
10 11 13 Hoogsteen/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters