Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'29-Segment pdb3dll1X.i2120-2150
Source: [PDB-id:chain] 3dll:X (&rarr PDB)
Source: Information THE OXAZOLIDINONE ANTIBIOTICS PERTURB THE RIBOSOMAL PEPTIDYL-TRANSFERASE CENTER AND EFFECT TRNA POSITIONING
Source: Compound RRNA-23S RIBOSOMAL RNA
Source: Resolution 3.50 ANGSTROMS.
Position (2120, 2150)
Primary structure ('_': anchors) _GUAGAGCGCAAAGGUAGAAGGUGGCUUGA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		4: C4'-exo, 8: C4'-exo, 12: C4'-exo, 18: O4'-endo, 19: C4'-exo, 20: C4'-exo, 23: C2'-exo, 27: C2'-exo, 29: C2'-exo, 30: C4'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		5: syn, 16: syn, 20: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 4 17 ↓
3 6 7 ↑
4 7 8 ↑
5 11 12 ↑
6 12 13 ↑
7 13 14 ↑
8 14 15 ↑
9 15 16 &larr
10 17 19 →
11 19 21 ↑
12 21 22 ↑
13 22 23 ↑
14 24 25 ↑
15 25 26 ↑
16 26 27 ↑
17 29 31 →
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 3 4 C/O2' ?
2 4 6 C/O2' ?
3 4 17 Bifurcated/O2' ?
4 8 15 Watson-Crick/Watson-Crick cis
5 15 20 Bifurcated/O2' ?
6 16 20 Hoogsteen/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters