Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'2-6-1-1-3-Multiloop pdb2vqe1A.m52-347
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 (54, 345), (57, 95), (102, 305), (307, 328), (330, 341)
Primary structure ('_': anchors) _AA_-_GGACGG_-_A_-_A_-_GCA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		3: C2'-endo, 8: C2'-endo, 14: C2'-endo, 22: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		7: syn, 8: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 2 23 →
2 4 6 →
3 5 6 ↑
4 9 10 ↑
5 10 11 ↑
6 11 12 ↑
7 12 14 →
8 13 14 ↑
9 15 17 →
10 15 20 ↓
11 17 18 ↑
12 19 20 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 23 Watson-Crick/Watson-Crick cis
2 3 6 O2'/Watson-Crick trans y
3 3 9 Watson-Crick/Hoogsteen trans y
4 3 10 Bifurcated/O2' ?
5 4 5 Watson-Crick/Watson-Crick cis
6 11 14 Watson-Crick/Watson-Crick cis
7 12 13 Watson-Crick/Watson-Crick cis
8 12 22 O2'/Sugar cis y
9 15 16 Watson-Crick/Watson-Crick cis
10 17 20 Watson-Crick/Watson-Crick cis
11 18 19 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters