Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-4-Internal Loop pdb2gyaF0.n644-661
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 (639, 667), (644, 661)
Primary structure ('_': anchors) _GGAGG_-_UGAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		None
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		2: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 3 ↑
2 3 4 ↑
3 4 10 →
4 5 6 ↑
5 5 11 &larr
6 6 7 ↑
7 8 9 ↑
8 9 10 ↑
9 11 12 ↑
10 12 13 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 13 Watson-Crick/Watson-Crick cis
2 3 12 Watson-Crick/Watson-Crick cis y
3 4 11 Bifurcated/O2' ?
4 5 10 O2'/Bifurcated ?
5 6 9 O2'/Bifurcated trans
6 7 8 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters