Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-5-Internal Loop pdb2vqe1A.n1218-1273
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 (1224, 1267), (1230, 1261)
Primary structure ('_': anchors) _ACAAA_-_AAAAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		3: C2'-exo, 4: C4'-exo, 9: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		10: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 2 3 ↑
2 2 14 →
3 4 5 ↑
4 4 11 →
5 5 6 ↑
6 6 7 ↑
7 8 9 &larr
8 11 12 ↑
9 12 13 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 14 Watson-Crick/Watson-Crick cis
2 2 13 Hoogsteen/Watson-Crick trans y
3 3 12 Hoogsteen/Watson-Crick trans
4 7 8 Watson-Crick/Watson-Crick cis
5 9 10 Watson-Crick/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters