Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'4-5-Internal Loop pdb2j011A.n859-929
Source: [PDB-id:chain] 2j01:A (&rarr PDB)
Source: Information STRUCTURE OF THE THERMUS THERMOPHILUS 70S RIBOSOME COMPLEXED WITH MRNA, TRNA AND PAROMOMYCIN (PART 2 OF 4). THIS FILE CONTAINS THE 50S SUBUNIT FROM MOLECULE I.
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 2.80 ANGSTROMS.
Position (867, 921), (872, 915)
Primary structure ('_': anchors) _GUAG_-_CCGAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		1: C2'-endo, 2: C2'-endo, 5: C2'-exo, 7: C2'-endo, 9: C4'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		3: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 4 5 ↑
2 4 11 →
3 5 6 ↑
4 9 10 ↑
5 11 12 ↑
6 12 13 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 2 C/O2' ?
2 1 13 Watson-Crick/Watson-Crick cis
3 2 3 Watson-Crick/Sugar cis
4 2 11 O2'/Bifurcated ?
5 3 10 Watson-Crick/O2' ?
6 3 11 Hoogsteen/Hoogsteen trans
7 4 10 O2'/Bifurcated trans
8 5 9 Watson-Crick/Watson-Crick cis
9 6 7 Watson-Crick/Watson-Crick cis
10 7 8 Hoogsteen/Bifurcated cis y
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters