Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'3-6-Internal Loop pdb2gya10.n61-92
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 (65, 88), (69, 81)
Primary structure ('_': anchors) _UAA_-_GUUUAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		4: C4'-exo, 10: 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 4 8 ↑
4 4 11 →
5 5 7 →
6 6 7 ↑
7 11 12 ↑
8 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 11 Hoogsteen/Sugar trans y
3 4 7 O2'/Watson-Crick ?
4 4 10 O2'/Bifurcated trans y
5 5 6 Watson-Crick/Watson-Crick cis
6 5 11 Watson-Crick/O2' ?
7 7 8 Hoogsteen/Sugar cis y
8 10 11 Hoogsteen/O2' ?
9 12 13 Bifurcated/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters