Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'6-4-Internal Loop pdb1q811B.n28-54
Source: [PDB-id:chain] 1q81:B (&rarr PDB)
Source: Information CRYSTAL STRUCTURE OF MINIHELIX WITH 3' PUROMYCIN BOUND TO A- SITE OF THE 50S RIBOSOMAL SUBUNIT.
Source: Compound 5S RIBOSOMAL RNA
Source: Resolution 2.95 ANGSTROMS.
Position (21, 59), (28, 54)
Primary structure ('_': anchors) _GUUGCC_-_UAAG_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		3: O4'-exo, 4: C3'-exo, 10: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		4: syn, 5: syn, 12: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 10 &larr
3 6 7 ↑
4 7 8 ↑
5 9 10 ↑
6 11 12 &larr
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 2 6 Watson-Crick/Sugar trans y
3 2 10 O2'/Hoogsteen ?
4 2 13 Watson-Crick/Watson-Crick cis y
5 7 10 Watson-Crick/Watson-Crick cis y
6 7 13 Watson-Crick/Bifurcated cis
7 8 9 Watson-Crick/Watson-Crick cis
8 8 12 Bifurcated/O2' ?
9 9 11 Hoogsteen/O2' cis y
10 13 14 Bifurcated/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters