Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'6-4-Internal Loop pdb2qnhFy.n231-277
Source: [PDB-id:chain] 2qnh:y (&rarr PDB)
Source: Information INTERACTIONS AND DYNAMICS OF THE SHINE-DALGARNO HELIX IN THE 70S RIBOSOME. THIS FILE, 2QNH, CONTAINS THE 30S RIBOSOME SUBUNIT, TWO TRNA, AND MRNA MOLECULES. 50S RIBOSOME SUBUNIT IS IN THE FILE 1VSP.
Source: Compound 16S RNA
FLIPPED INTERNAL
Source: Resolution 3.83 ANGSTROMS.
Position (233, 275), (238, 268)
Primary structure ('_': anchors) _GACGAC_-_AUCA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		2: C2'-exo, 3: C2'-exo, 4: C3'-exo, 5: C3'-exo, 6: C3'-exo, 10: C2'-endo, 12: O4'-endo, 13: C4'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		None
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 1 11 →
3 2 3 ↑
4 7 8 ↑
5 7 9 →
6 11 13 ↓
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 14 Watson-Crick/Watson-Crick cis
2 2 3 Bifurcated/O2' ?
3 3 4 Hoogsteen/O2' ?
4 3 7 C/O2' ?
5 3 9 Watson-Crick/O2' ?
6 3 13 O2'/Bifurcated ?
7 4 5 Hoogsteen/O2' ?
8 4 10 Sugar/Hoogsteen trans
9 4 13 O2'/Bifurcated ?
10 8 9 Watson-Crick/Watson-Crick cis
11 9 10 O2'/Sugar ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters