Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'6-4-Internal Loop pdb2vqeFA.n238-268
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
FLIPPED INTERNAL
Source: Resolution 2.5 ANGSTROMS.
Position (233, 275), (238, 268)
Primary structure ('_': anchors) _GACGAC_-_AUCA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		3: C2'-exo, 4: C2'-endo, 5: C2'-endo, 6: C2'-endo, 10: C1'-exo, 12: C2'-endo, 13: C1'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		6: syn, 13: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 1 11 →
3 2 3 ↑
4 3 10 →
5 6 10 &larr
6 7 8 ↑
7 7 9 →
8 10 13 ↑
9 11 13 ↓
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 14 Watson-Crick/Watson-Crick cis
2 2 11 Watson-Crick/Watson-Crick cis y
3 3 9 Watson-Crick/O2' trans y
4 3 13 O2'/Bifurcated trans
5 4 10 Sugar/Hoogsteen trans
6 4 13 O2'/Bifurcated ?
7 6 7 Watson-Crick/Sugar cis y
8 6 10 Bifurcated/O2' ?
9 7 10 O2'/Watson-Crick ?
10 8 9 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters