Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-6-Internal Loop pdb2vqfFA.n397-427
Source: [PDB-id:chain] 2vqf: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
FLIPPED INTERNAL
Source: Resolution 2.9 ANGSTROMS.
Position (400, 424), (407, 418)
Primary structure ('_': anchors) _GUAAA_-_GAAGAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		1: C2'-exo, 5: C2'-endo, 6: C2'-endo, 10: C2'-exo, 11: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		5: syn, 12: 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 14 &larr
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 Hoogsteen/Sugar trans
3 3 5 Hoogsteen/Watson-Crick cis
4 3 14 O2'/Watson-Crick ?
5 4 10 Watson-Crick/Hoogsteen trans y
6 4 13 Hoogsteen/Watson-Crick trans
7 5 11 O2'/Bifurcated ?
8 5 14 O2'/Hoogsteen ?
9 6 11 Bifurcated/O2' trans
10 7 8 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters