Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'8-8-Internal Loop pdb2vhn1B.n1833-1877
Source: [PDB-id:chain] 2vhn:B (&rarr PDB)
Source: Information STRUCTURE OF PDF BINDING HELIX IN COMPLEX WITH THE RIBOSOME. (PART 2 OF 4)
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 3.74 ANGSTROMS.
Position (1835, 1875), (1844, 1866)
Primary structure ('_': anchors) _UAAUUGAU_-_UGAUCGAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		6: C4'-exo, 7: O4'-endo, 13: O4'-endo, 14: C2'-exo, 17: C4'-exo, 18: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		17: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 3 4 ↑
3 3 18 →
4 4 5 ↑
5 6 7 ↑
6 7 13 &larr
7 8 9 ↑
8 8 14 →
9 12 13 ↑
10 14 15 ↑
11 15 16 ↑
12 16 17 &larr
13 18 19 ↑
14 19 20 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 20 Watson-Crick/Watson-Crick cis
2 4 17 O2'/Bifurcated ?
3 7 8 Hoogsteen/O2' ?
4 7 13 O2'/Bifurcated ?
5 8 13 Sugar/Hoogsteen trans
6 10 11 Watson-Crick/Watson-Crick cis y
7 13 14 Hoogsteen/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters