Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-7-Internal Loop pdb2zjp1X.n1707-1717
Source: [PDB-id:chain] 2zjp:X (&rarr PDB)
Source: Information THIOPEPTIDE ANTIBIOTIC NOSIHEPTIDE BOUND TO THE LARGE RIBOSOMAL SUBUNIT OF DEINOCOCCUS RADIODURANS
Source: Compound RIBOSOMAL 23S RNA
Source: Resolution 3.70 ANGSTROMS.
Position (1701, 1725), (1707, 1717)
Primary structure ('_': anchors) _GCCAA_-_GACGUAU_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		10: C4'-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 14 ↑
2 2 14 ↓
3 5 6 ↑
4 8 9 ↑
5 9 10 &larr
6 10 12 →
7 12 13 ↑
8 14 16 →
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 5 Sugar/O2' ?
2 1 16 Watson-Crick/Watson-Crick cis
3 2 3 Hoogsteen/Sugar cis y
4 2 13 O2'/Bifurcated ?
5 2 14 O2'/Bifurcated ?
6 3 12 Watson-Crick/Watson-Crick trans
7 3 13 O2'/Bifurcated ?
8 5 9 Bifurcated/O2' ?
9 5 10 Bifurcated/O2' ?
10 6 7 Bifurcated/O2' ?
11 6 9 O2'/Bifurcated trans
12 7 8 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters