Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-4-Internal Loop pdb2gya10.n190-215
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
Source: Resolution 2.00 ANGSTROMS.
Position (193, 212), (199, 207)
Primary structure ('_': anchors) _CAGUA_-_GAAC_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		3: C4'-exo, 4: 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 3 5 →
3 4 9 &larr
4 5 6 ↑
5 6 7 ↑
6 6 10 →
7 8 9 ↑
8 10 11 ↑
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 y
2 2 3 Hoogsteen/Watson-Crick cis y
3 2 12 Hoogsteen/Watson-Crick trans y
4 3 11 O2'/Bifurcated ?
5 4 10 O2'/Bifurcated ?
6 5 10 Hoogsteen/Watson-Crick trans
7 6 9 O2'/Bifurcated trans
8 7 8 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters