Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'4-9-Internal Loop pdb2j031A.n1371-1519
Source: [PDB-id:chain] 2j03:A (&rarr PDB)
Source: Information STRUCTURE OF THE THERMUS THERMOPHILUS 70S RIBOSOME COMPLEXED WITH MRNA, TRNA AND PAROMOMYCIN (PART 4 OF 4). THIS FILE CONTAINS THE 50S SUBUNIT FROM MOLECULE II.
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 2.80 ANGSTROMS.
Position (1374, 1516), (1379, 1506)
Primary structure ('_': anchors) _GGAC_-_CAAGAAAAG_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		4: C2'-endo, 5: C2'-endo, 8: C2'-endo, 9: C2'-endo, 10: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		5: syn, 11: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 ↑
3 3 4 &larr
4 6 11 ↓
5 7 8 ↑
6 8 10 ↑
7 12 13 ↑
8 13 14 ↑
9 14 15 ↑
10 15 16 ↑
11 16 17 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 17 Watson-Crick/Watson-Crick cis
2 2 16 Hoogsteen/Sugar trans y
3 3 15 Bifurcated/O2' trans
4 4 13 O2'/Sugar ?
5 4 14 Hoogsteen/Hoogsteen trans y
6 5 13 O2'/Bifurcated ?
7 6 7 Watson-Crick/Watson-Crick cis
8 8 11 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters