Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'4-9-Internal Loop pdb2vhm1B.n1405-1561
Source: [PDB-id:chain] 2vhm:B (&rarr PDB)
Source: Information STRUCTURE OF PDF BINDING HELIX IN COMPLEX WITH THE RIBOSOME (PART 1 OF 4)
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 3.74 ANGSTROMS.
Position (1408, 1558), (1413, 1548)
Primary structure ('_': anchors) _GGAC_-_CAGGAAAAG_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		2: C2'-exo, 3: C2'-exo, 4: C1'-exo, 5: C2'-endo, 6: C2'-exo, 8: C3'-exo, 9: C3'-exo, 10: C3'-exo, 13: C4'-exo, 14: C2'-exo, 15: C2'-exo, 17: C4'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		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 8 10 ↑
6 12 13 ↑
7 13 14 ↑
8 14 15 ↑
9 15 16 ↑
10 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 Hoogsteen/Sugar trans
4 4 14 O2'/Bifurcated ?
5 6 7 Watson-Crick/Watson-Crick cis y
6 8 11 Watson-Crick/Watson-Crick cis
7 9 11 Bifurcated/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters