Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'12-Hairpin pdb2vqe1A.e311-324
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 (311, 324)
Primary structure ('_': anchors) _ACUGAGACACGG_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		8: C2'-endo, 9: C2'-endo, 10: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		8: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 ↑
3 2 14 →
4 3 4 ↑
5 4 5 ↑
6 6 7 ↑
7 8 10 ↑
8 10 13 ↑
9 13 14 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 14 Watson-Crick/Watson-Crick cis
2 2 10 O2'/Bifurcated ?
3 2 13 Watson-Crick/Watson-Crick cis
4 3 9 Bifurcated/O2' ?
5 3 10 Hoogsteen/Watson-Crick trans
6 4 8 Hoogsteen/Watson-Crick trans
7 5 7 Hoogsteen/O2' ?
8 5 8 O2'/Watson-Crick ?
9 10 13 Hoogsteen/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters