Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'5-8-Internal Loop pdb1rlg1D.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
Source: Resolution 2.70 ANGSTROMS.
Position (2, 24), (8, 15)
Primary structure ('_': anchors) _UCUGA_-_CGUGAUGA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		5: C2'-endo, 6: C3'-exo, 9: C4'-endo, 10: C2'-endo, 11: C3'-exo, 12: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		10: syn, 16: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 3 4 ↑
2 4 5 ↑
3 5 12 &larr
4 6 10 &larr
5 6 13 →
6 8 9 ↑
7 13 14 ↑
8 14 15 ↑
9 15 16 &larr
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 Watson-Crick/Watson-Crick cis y
3 3 15 Watson-Crick/Watson-Crick cis
4 4 14 Watson-Crick/Watson-Crick cis
5 5 12 O2'/Bifurcated ?
6 5 13 Hoogsteen/Sugar trans
7 6 9 O2'/Bifurcated ?
8 6 12 Sugar/Hoogsteen trans
9 7 8 Watson-Crick/Watson-Crick cis
10 7 13 Sugar/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters