Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'4-9-Internal Loop pdb2aar10.n1370-1526
Source: [PDB-id:chain] 2aar:0 (&rarr PDB)
Source: Information STRUCTURE OF TRIGGER FACTOR BINDING DOMAIN IN BIOLOGICALLY HOMOLOGOUS COMPLEX WITH EUBACTERIAL RIBOSOME.
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 3.50 ANGSTROMS.
Position (1372, 1524), (1377, 1514)
Primary structure ('_': anchors) _GGAC_-_CAAGAAAAG_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		8: C4'-exo, 9: C4'-exo, 10: C4'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		4: syn, 9: syn, 11: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 ↑
3 6 11 ↓
4 8 10 ↑
5 12 13 ↑
6 13 14 ↑
7 14 15 ↑
8 15 16 ↑
9 16 17 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 17 Watson-Crick/Watson-Crick cis
2 3 4 Hoogsteen/Hoogsteen cis y
3 3 15 Bifurcated/O2' ?
4 4 5 Hoogsteen/O2' ?
5 5 12 Hoogsteen/Watson-Crick cis y
6 6 7 Watson-Crick/Watson-Crick cis
7 8 11 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters