Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-5-Internal Loop pdb2b9nFA.n2388-2398
Source: [PDB-id:chain] 2b9n:A (&rarr PDB)
Source: Information 50S RIBOSOMAL SUBUNIT FROM A CRYSTAL STRUCTURE OF RELEASE FACTOR RF2, 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
FLIPPED INTERNAL
Source: Resolution 6.76 ANGSTROMS.
Position (2382, 2404), (2388, 2398)
Primary structure ('_': anchors) _GGCGG_-_CCCGA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		2: C4'-exo, 3: C2'-exo, 4: C2'-exo, 5: C2'-exo, 8: C4'-exo, 9: C1'-endo, 10: C2'-exo, 13: C4'-exo, 14: O4'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		None
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 1 13 →
3 2 12 →
4 3 4 ↑
5 5 9 →
6 6 10 &larr
7 8 9 ↑
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 10 O2'/Bifurcated ?
6 6 8 Sugar/Hoogsteen cis y
7 6 9 Sugar/Hoogsteen trans y
8 6 10 O2'/Bifurcated ?
9 7 8 Watson-Crick/Watson-Crick cis y
10 9 10 Hoogsteen/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters