Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-5-Internal Loop pdb2b661A.n2388-2398
Source: [PDB-id:chain] 2b66:A (&rarr PDB)
Source: Information 50S RIBOSOMAL SUBUNIT FROM A CRYSTAL STRUCTURE OF RELEASE FACTOR RF1, TRNAS AND MRNA BOUND TO THE RIBOSOME. THIS FILE CONTAINS THE 50S SUBUNIT FROM A CRYSTAL STRUCTURE OF RELEASE FACTOR RF1, TRNAS AND MRNA BOUND TO THE RIBOSOME AND IS DESCRIBED IN REMARK 400
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 5.90 ANGSTROMS.
Position (2382, 2404), (2388, 2398)
Primary structure ('_': anchors) _CCCGA_-_GGCGG_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		1: O4'-endo, 2: C4'-exo, 5: C2'-exo, 6: C1'-endo, 7: C4'-exo, 10: C2'-exo, 11: C2'-exo, 12: C2'-exo, 13: 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 14 →
3 3 4 ↑
4 3 13 →
5 5 9 &larr
6 6 7 ↑
7 6 10 →
8 11 12 ↑
9 13 14 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 14 Watson-Crick/Watson-Crick cis y
2 2 13 Watson-Crick/Bifurcated cis
3 3 12 Watson-Crick/Watson-Crick cis
4 4 11 Watson-Crick/Watson-Crick trans y
5 5 6 Hoogsteen/O2' ?
6 5 9 O2'/Bifurcated ?
7 5 10 O2'/Bifurcated ?
8 6 9 Sugar/Hoogsteen trans y
9 7 8 Watson-Crick/Watson-Crick cis y
10 7 9 Sugar/Hoogsteen cis y
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters