Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-4-Internal Loop pdb2qa410.n198-225
Source: [PDB-id:chain] 2qa4:0 (&rarr PDB)
Source: Information A MORE COMPLETE STRUCTURE OF THE THE L7/L12 STALK OF THE HALOARCULA MARISMORTUI 50S LARGE RIBOSOMAL SUBUNIT
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 3.00 ANGSTROMS.
Position (202, 221), (208, 216)
Primary structure ('_': anchors) _UAGUA_-_GAAC_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		3: C2'-endo, 4: C2'-endo, 11: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		None
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 &larr
3 3 5 →
4 4 9 &larr
5 6 7 ↑
6 6 10 →
7 8 9 ↑
8 10 11 ↑
9 11 12 ↑
10 12 13 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 13 Watson-Crick/Watson-Crick cis
2 2 12 Hoogsteen/Watson-Crick trans y
3 3 11 O2'/Bifurcated trans
4 4 5 Hoogsteen/Sugar cis y
5 4 9 Watson-Crick/O2' ?
6 4 10 O2'/Bifurcated ?
7 5 9 Watson-Crick/O2' ?
8 5 10 Hoogsteen/Watson-Crick trans
9 6 9 O2'/Bifurcated 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