Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-6-Internal Loop pdb1n33FA.n407-418
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
FLIPPED INTERNAL
Source: Resolution 3.35 ANGSTROMS.
Position (400, 424), (407, 418)
Primary structure ('_': anchors) _GUAAA_-_GAAGAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		5: C2'-endo, 12: C4'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		5: syn, 13: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 ↑
3 3 4 ↑
4 4 6 →
5 5 14 &larr
6 6 7 &larr
7 8 9 ↑
8 9 10 ↑
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 3 5 Hoogsteen/Watson-Crick cis
3 3 14 O2'/Watson-Crick ?
4 4 10 Watson-Crick/Hoogsteen trans y
5 6 10 Bifurcated/O2' ?
6 6 11 Bifurcated/O2' ?
7 7 8 Watson-Crick/Watson-Crick cis
8 11 13 O2'/Sugar ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters