Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'8-5-Internal Loop pdb1rlgFD.n1-25
Source: [PDB-id:chain] 1rlg:D (&rarr PDB)
Source: Information MOLECULAR BASIS OF BOX C/D RNA-PROTEIN INTERACTION: CO- CRYSTAL STRUCTURE OF THE ARCHAEAL SRNP INTIATION COMPLEX
Source: Compound 25-MER
FLIPPED INTERNAL
Source: Resolution 2.70 ANGSTROMS.
Position (2, 24), (8, 15)
Primary structure ('_': anchors) _CGUGAUGA_-_UCUGA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		6: C2'-endo, 7: C3'-exo, 8: C2'-endo, 9: C4'-endo, 12: C3'-exo, 13: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		2: syn, 8: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 →
2 2 3 &larr
3 3 4 ↑
4 4 5 ↑
5 5 12 →
6 6 13 &larr
7 8 12 &larr
8 9 10 ↑
9 13 14 ↑
10 14 15 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 17 Watson-Crick/Watson-Crick cis
2 2 16 Watson-Crick/Watson-Crick cis y
3 3 15 Watson-Crick/Watson-Crick cis
4 4 14 Watson-Crick/Watson-Crick cis
5 5 11 Sugar/O2' ?
6 5 13 Hoogsteen/Sugar trans
7 6 12 Sugar/Hoogsteen trans
8 6 13 O2'/Bifurcated ?
9 9 12 O2'/Bifurcated ?
10 10 11 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters