Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'6-3-Internal Loop pdb1pnu10.n2078-2095
Source: [PDB-id:chain] 1pnu:0 (&rarr PDB)
Source: Information CRYSTAL STRUCTURE OF A STREPTOMYCIN DEPENDENT RIBOSOME FROM ESCHERICHIA COLI, 50S SUBUNIT OF 70S RIBOSOME. THIS FILE, 1PNU, CONTAINS ONLY MOLECULES OF THE 50S RIBOSOMAL SUBUNIT. THE 30S SUBUNIT, MRNA, P-SITE TRNA, AND A-SITE TRNA ARE IN THE PDB FILE 1PNS.
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 8.70 ANGSTROMS.
Position (2071, 2099), (2078, 2095)
Primary structure ('_': anchors) _GAAGAA_-_GGA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		3: C2'-endo, 4: C2'-endo, 5: C2'-endo, 12: C2'-endo, 13: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		3: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 13 →
3 3 5 ↑
4 3 12 &larr
5 6 7 ↑
6 6 12 →
7 7 8 ↑
8 9 10 ↑
9 10 11 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 13 Watson-Crick/Watson-Crick cis
2 2 12 Watson-Crick/O2' ?
3 3 12 O2'/Bifurcated ?
4 5 11 Watson-Crick/O2' ?
5 5 12 Hoogsteen/Sugar trans
6 6 10 Bifurcated/O2' ?
7 6 11 Sugar/Hoogsteen trans
8 6 13 O2'/Watson-Crick trans y
9 7 10 Sugar/Hoogsteen trans
10 8 9 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters