Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'9-9-Internal Loop pdb1yl31A.n1858-1893
Source: [PDB-id:chain] 1yl3:A (&rarr PDB)
Source: Information CRYSTAL STRUCTURE OF 70S RIBOSOME WITH THRS OPERATOR AND TRNAS. LARGE SUBUNIT. THE COORDINATES FOR THE SMALL SUBUNIT ARE IN THE PDB ENTRY 1YL4.
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 5.50 ANGSTROMS.
Position (1860, 1891), (1870, 1881)
Primary structure ('_': anchors) _CAAGGGGAG_-_CGAACCGAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		2: C4'-exo, 5: C2'-exo, 12: C2'-exo, 14: C4'-exo, 15: C2'-exo, 21: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		19: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 3 4 ↑
3 4 5 ↑
4 5 6 ↑
5 6 18 →
6 8 16 →
7 10 11 ↑
8 16 17 ↑
9 18 19 &larr
10 20 21 ↑
11 21 22 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 22 Watson-Crick/Watson-Crick cis
2 2 20 Hoogsteen/Watson-Crick trans y
3 6 7 Sugar/Hoogsteen trans y
4 6 17 Watson-Crick/Watson-Crick cis
5 7 15 Watson-Crick/Watson-Crick cis y
6 7 16 Bifurcated/O2' ?
7 8 15 O2'/Bifurcated ?
8 9 14 O2'/Bifurcated trans
9 9 15 O2'/Watson-Crick ?
10 11 12 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters