Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'9-5-Internal Loop pdb2hgj1A.n1058-1145
Source: [PDB-id:chain] 2hgj:A (&rarr PDB)
Source: Information CRYSTAL STRUCTURE OF THE 70S THERMUS THERMOPHILUS RIBOSOME SHOWING HOW THE 16S 3'-END MIMICKS MRNA E AND P CODONS. THIS ENTRY 2HGJ CONTAINS 50S RIBOSOMAL SUBUNIT. THE 30S RIBOSOMAL SUBUNIT CAN BE FOUND IN PDB ENTRY 2HGI.
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 5.00 ANGSTROMS.
Position (1065, 1138), (1075, 1132)
Primary structure ('_': anchors) _GCGAAGACA_-_CGAGU_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		1: C4'-exo, 6: C4'-exo, 9: C2'-exo, 11: C2'-exo, 12: C4'-exo, 13: C4'-exo, 14: C4'-exo, 17: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		5: syn, 6: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 ↑
3 4 8 →
4 7 14 &larr
5 12 13 ↑
6 13 14 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 18 Watson-Crick/Watson-Crick cis
2 3 4 Hoogsteen/O2' ?
3 4 7 Sugar/O2' ?
4 4 15 O2'/Sugar ?
5 4 16 O2'/Watson-Crick trans y
6 8 13 Bifurcated/O2' ?
7 8 14 Bifurcated/O2' ?
8 9 10 Hoogsteen/Watson-Crick cis y
9 11 12 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters