Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-3-Internal Loop pdb3cmaF0.n241-252
Source: [PDB-id:chain] 3cma:0 (&rarr PDB)
Source: Information THE STRUCTURE OF CCA AND CCA-PHE-CAP-BIO BOUND TO THE LARGE RIBOSOMAL SUBUNIT OF HALOARCULA MARISMORTUI
Source: Compound 23S RIBOSOMAL RNA
FLIPPED INTERNAL
Source: Resolution 2.80 ANGSTROMS.
Position (237, 258), (241, 252)
Primary structure ('_': anchors) _AAUGU_-_GAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		3: C3'-exo, 4: C2'-endo, 5: C2'-endo, 10: C2'-endo, 11: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		5: syn, 9: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 10 →
3 3 11 &larr
4 5 10 &larr
5 6 7 ↑
6 11 12 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 12 Watson-Crick/Watson-Crick cis
2 2 8 O2'/Sugar ?
3 2 9 Watson-Crick/Watson-Crick cis
4 2 11 Hoogsteen/Sugar trans y
5 3 10 Sugar/Hoogsteen trans
6 5 10 Bifurcated/O2' ?
7 6 10 O2'/Watson-Crick ?
8 7 8 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters