Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'3-7-Internal Loop pdb2qexF0.n1107-1194
Source: [PDB-id:chain] 2qex:0 (&rarr PDB)
Source: Information NEGAMYCIN BINDS TO THE WALL OF THE NASCENT CHAIN EXIT TUNNEL OF THE 50S RIBOSOMAL SUBUNIT
Source: Compound 23S RIBOSOMAL RNA
FLIPPED INTERNAL
Source: Resolution 2.90 ANGSTROMS.
Position (1116, 1185), (1124, 1181)
Primary structure ('_': anchors) _CGA_-_CUAGACA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		2: C2'-endo, 3: C2'-endo, 10: C2'-endo, 11: C2'-endo, 12: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		None
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 2 9 →
2 3 4 ↑
3 3 10 &larr
4 4 5 ↑
5 6 7 ↑
6 7 8 ↑
7 8 9 ↑
8 13 14 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 9 O2'/Watson-Crick trans
2 1 14 Watson-Crick/Watson-Crick cis
3 2 10 Hoogsteen/Sugar trans
4 2 13 Watson-Crick/O2' ?
5 3 9 Sugar/Hoogsteen trans y
6 3 10 Watson-Crick/O2' ?
7 4 7 Watson-Crick/Watson-Crick trans y
8 5 6 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters