Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'7-7-Internal Loop pdb1a511A.n1-41
Source: [PDB-id:chain] 1a51:A (&rarr PDB)
Source: Information LOOP D/LOOP E ARM OF E. COLI 5S RRNA, NMR, 9 STRUCTURES
Source: Compound 5S RRNA LOOP D/LOOP E
Source: Resolution NOT APPLICABLE.
Position (4, 38), (12, 30)
Primary structure ('_': anchors) _GAUGGUA_-_GAGAGUA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		3: C2'-exo, 12: C2'-exo, 14: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		None
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 3 4 ↑
3 3 17 →
4 4 5 ↑
5 5 6 ↑
6 6 7 ↑
7 7 8 ↑
8 8 9 ↑
9 8 12 →
10 10 11 ↑
11 12 13 ↑
12 13 14 ↑
13 14 15 ↑
14 15 16 ↑
15 16 17 ↑
16 17 18 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 18 Watson-Crick/Watson-Crick cis
2 2 15 O2'/Hoogsteen ?
3 2 16 O2'/Bifurcated ?
4 2 17 Hoogsteen/Sugar trans
5 3 16 Watson-Crick/Hoogsteen trans
6 4 15 Watson-Crick/Hoogsteen trans y
7 5 14 Watson-Crick/Hoogsteen cis y
8 6 13 Bifurcated/Watson-Crick trans
9 7 12 Hoogsteen/Watson-Crick trans
10 8 11 O2'/Bifurcated trans
11 9 10 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters