Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'4-5-Internal Loop pdb2gyaF0.n199-207
Source: [PDB-id:chain] 2gya:0 (&rarr PDB)
Source: Information STRUCTURE OF THE 50S SUBUNIT OF A PRE-TRANSLOCATIONAL E. COLI RIBOSOME OBTAINED BY FITTING ATOMIC MODELS FOR RNA AND PROTEIN COMPONENTS INTO CRYO-EM MAP EMD-1056
Source: Compound 23S RIBOSOMAL RNA
FLIPPED INTERNAL
Source: Resolution 2.00 ANGSTROMS.
Position (193, 212), (199, 207)
Primary structure ('_': anchors) _GAAC_-_CAGUA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		10: C4'-exo, 11: 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 2 3 ↑
3 3 4 ↑
4 4 8 →
5 5 6 ↑
6 5 10 &larr
7 7 8 ↑
8 8 9 ↑
9 9 11 →
10 12 13 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 13 Watson-Crick/Watson-Crick cis y
2 2 12 Hoogsteen/Watson-Crick trans y
3 3 11 O2'/Bifurcated ?
4 4 9 Hoogsteen/Watson-Crick trans
5 4 10 O2'/Bifurcated ?
6 5 8 O2'/Bifurcated trans
7 6 7 Watson-Crick/Watson-Crick cis
8 11 12 Hoogsteen/Watson-Crick cis y
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters