Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-7-Internal Loop pdb1n341A.n231-277
Source: [PDB-id:chain] 1n34:A (&rarr PDB)
Source: Information STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT IN THE PRESENCE OF CODON AND CRYSTALLOGRAPHICALLY DISORDERED NEAR-COGNATE TRANSFER RNA ANTICODON STEM-LOOP MISMATCHED AT THE FIRST CODON POSITION
Source: Compound 16S RIBOSOMAL RNA
Source: Resolution 3.80 ANGSTROMS.
Position (233, 275), (239, 267)
Primary structure ('_': anchors) _AUCAG_-_CGACGAC_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		2: C4'-exo, 3: C2'-endo, 5: C2'-endo, 12: C2'-endo, 13: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		None
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 2 4 ↓
2 2 5 ↑
3 4 16 →
4 5 11 ↑
5 5 14 →
6 6 7 ↑
7 6 10 →
8 8 9 ↑
9 9 10 ↑
10 14 15 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 16 Watson-Crick/Watson-Crick cis
2 2 13 O2'/Bifurcated ?
3 2 14 Hoogsteen/Watson-Crick trans
4 4 15 Watson-Crick/Watson-Crick cis y
5 5 10 O2'/Watson-Crick ?
6 5 13 Sugar/Hoogsteen trans
7 6 14 Watson-Crick/O2' ?
8 7 8 Watson-Crick/Watson-Crick cis
9 14 15 Bifurcated/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters