Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'6-5-Internal Loop pdb1n331A.n397-427
Source: [PDB-id:chain] 1n33:A (&rarr PDB)
Source: Information STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT BOUND TO CODON AND NEAR-COGNATE TRANSFER RNA ANTICODON STEM-LOOP MISMATCHED AT THE SECOND CODON POSITION AT THE A SITE WITH PAROMOMYCIN
Source: Compound 16S RIBOSOMAL RNA
Source: Resolution 3.35 ANGSTROMS.
Position (400, 424), (407, 418)
Primary structure ('_': anchors) _GAAGAA_-_GUAAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		4: C4'-exo, 11: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		3: syn, 11: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 11 &larr
3 6 7 ↑
4 7 8 ↑
5 9 10 &larr
6 10 12 →
7 12 13 ↑
8 13 14 ↑
9 14 15 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 15 Watson-Crick/Watson-Crick cis
2 2 13 O2'/Watson-Crick ?
3 3 5 O2'/Sugar ?
4 5 10 Bifurcated/O2' ?
5 6 10 Bifurcated/O2' ?
6 6 12 Watson-Crick/Hoogsteen trans y
7 8 9 Watson-Crick/Watson-Crick cis
8 11 13 Hoogsteen/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters