Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'2-3-Internal Loop pdb1ow9FA.n8-17
Source: [PDB-id:chain] 1ow9:A (&rarr PDB)
Source: Information NMR STRUCTURE OF THE ACTIVE CONFORMATION OF THE VS RIBOZYME CLEAVAGE SITE
Source: Compound A MIMIC OF THE VS RIBOZYME HAIRPIN SUBSTRATE
FLIPPED INTERNAL
Source: Resolution NOT APPLICABLE.
Position (4, 20), (8, 17)
Primary structure ('_': anchors) _GA_-_GAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		1: C2'-exo, 5: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		None
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 7 →
3 3 4 ↑
4 3 8 &larr
5 5 6 ↑
6 6 7 ↑
7 8 9 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 2 Hoogsteen/O2' ?
2 1 9 Watson-Crick/Watson-Crick cis
3 2 3 C/O2' ?
4 2 8 Bifurcated/O2' trans
5 3 7 O2'/Watson-Crick ?
6 4 5 Watson-Crick/Watson-Crick cis
7 7 8 Hoogsteen/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters