Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'8-8-Internal Loop pdb2gya10.n233-307
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 (237, 303), (246, 294)
Primary structure ('_': anchors) _UGUGUGUU_-_AAUGCACA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		17: C2'-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 4 ↑
3 3 19 →
4 4 5 ↑
5 5 6 ↑
6 6 7 ↑
7 7 8 ↑
8 7 15 →
9 8 9 ↑
10 9 10 ↑
11 10 12 →
12 11 12 ↑
13 12 13 ↑
14 13 14 ↑
15 14 15 ↑
16 15 16 ↑
17 19 20 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 20 Watson-Crick/Watson-Crick cis y
2 2 19 Bifurcated/Sugar trans y
3 3 18 Hoogsteen/Hoogsteen trans y
4 4 17 Bifurcated/O2' ?
5 4 18 Watson-Crick/Hoogsteen trans y
6 6 15 Watson-Crick/Watson-Crick cis y
7 8 13 Watson-Crick/Watson-Crick cis y
8 10 11 Watson-Crick/Watson-Crick cis
9 16 17 Hoogsteen/Watson-Crick cis y
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters