Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'7-9-Internal Loop pdb1n331A.n1239-1250
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 (1231, 1260), (1239, 1250)
Primary structure ('_': anchors) _GAUGCCA_-_GAGCUAAUC_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		15: C4'-endo, 17: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		3: syn, 4: syn, 15: syn, 16: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 2 16 ↑
2 2 20 →
3 5 6 ↑
4 8 9 ↑
5 8 12 →
6 10 11 ↑
7 12 13 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 20 Watson-Crick/Watson-Crick cis
2 2 5 Sugar/O2' ?
3 3 4 Hoogsteen/O2' ?
4 3 16 Bifurcated/O2' ?
5 6 20 Sugar/O2' ?
6 8 11 Sugar/Hoogsteen trans
7 9 10 Watson-Crick/Watson-Crick cis y
8 16 19 Bifurcated/O2' ?
9 18 19 Bifurcated/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters