Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'3-7-Internal Loop pdb2vhm1B.n80-106
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 (81, 105), (85, 97)
Primary structure ('_': anchors) _UAA_-_GUUAUAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		1: C2'-exo, 3: C4'-exo, 4: C1'-exo, 5: C2'-exo, 7: C2'-exo, 9: C3'-exo, 11: C3'-exo, 12: C2'-exo, 13: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		8: syn, 10: syn, 11: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 4 12 →
3 5 7 →
4 6 7 ↑
5 7 8 &larr
6 9 10 →
7 12 13 ↑
8 13 14 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 14 Watson-Crick/Watson-Crick cis
2 3 4 C/O2' ?
3 3 10 O2'/Hoogsteen ?
4 3 12 Hoogsteen/Sugar trans y
5 4 7 O2'/Watson-Crick trans y
6 5 6 Watson-Crick/Watson-Crick cis
7 5 12 Sugar/Sugar trans
8 9 10 C/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters