Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-9-Internal Loop pdb2hgjFA.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
FLIPPED INTERNAL
Source: Resolution 5.00 ANGSTROMS.
Position (1065, 1138), (1075, 1132)
Primary structure ('_': anchors) _CGAGU_-_GCGAAGACA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		2: C2'-exo, 5: C4'-exo, 6: C4'-exo, 7: C4'-exo, 8: C2'-exo, 10: C2'-exo, 13: C4'-exo, 18: C4'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		13: syn, 14: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 5 6 ↑
2 5 12 &larr
3 6 7 ↑
4 11 15 →
5 16 17 ↑
6 17 18 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 18 Watson-Crick/Watson-Crick cis
2 3 15 O2'/Watson-Crick trans y
3 4 15 O2'/Sugar ?
4 5 11 Bifurcated/O2' ?
5 6 11 Bifurcated/O2' ?
6 7 8 Watson-Crick/Watson-Crick cis
7 9 10 Hoogsteen/Watson-Crick cis y
8 12 15 Sugar/O2' ?
9 15 16 Hoogsteen/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters