Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-4-Internal Loop pdb2jl81A.n227-235
Source: [PDB-id:chain] 2jl8:A (&rarr PDB)
Source: Information INSIGHTS INTO TRANSLATIONAL TERMINATION FROM THE STRUCTURE OF RF2 BOUND TO THE RIBOSOME (PART 4 OF 4). THIS FILE CONTAINS THE 50S SUBUNIT.
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 3.45 ANGSTROMS.
Position (221, 240), (227, 235)
Primary structure ('_': anchors) _GAGUA_-_GAAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		3: C2'-endo, 4: C2'-endo
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 &larr
3 3 5 →
4 4 9 &larr
5 5 6 ↑
6 6 7 ↑
7 6 10 →
8 8 9 ↑
9 10 11 ↑
10 11 12 ↑
11 12 13 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 13 Watson-Crick/Watson-Crick cis
2 2 12 Bifurcated/O2' trans
3 3 11 Hoogsteen/Hoogsteen trans
4 4 5 Hoogsteen/Sugar cis y
5 4 10 O2'/Bifurcated ?
6 5 9 Bifurcated/O2' ?
7 5 10 Hoogsteen/Watson-Crick trans
8 6 9 O2'/Bifurcated trans
9 7 8 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters