Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'8-9-Internal Loop pdb2gya19.n27-45
Source: [PDB-id:chain] 2gya:9 (&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 5S RIBOSOMAL RNA
Source: Resolution 2.00 ANGSTROMS.
Position (18, 55), (27, 45)
Primary structure ('_': anchors) _GUCCCACC_-_GAAGUGAAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		13: C4'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		19: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 4 5 ↑
3 5 6 ↑
4 7 8 ↑
5 8 9 ↑
6 9 10 ↑
7 11 12 ↑
8 12 13 ↑
9 14 15 ↑
10 15 16 ↑
11 16 17 ↑
12 20 21 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 21 Watson-Crick/Watson-Crick cis y
2 6 17 Watson-Crick/Watson-Crick cis y
3 8 15 Watson-Crick/Watson-Crick cis
4 8 18 Watson-Crick/O2' ?
5 9 14 Watson-Crick/O2' cis y
6 10 11 Watson-Crick/Watson-Crick cis y
7 13 14 Hoogsteen/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters