Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'7-7-Internal Loop pdb1a51FA.n12-30
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
FLIPPED INTERNAL
Source: Resolution NOT APPLICABLE.
Position (4, 38), (12, 30)
Primary structure ('_': anchors) _GAGAGUA_-_GAUGGUA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		5: C2'-exo, 7: C2'-exo, 16: 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 2 3 ↑
3 2 16 →
4 3 4 ↑
5 4 5 ↑
6 5 6 ↑
7 6 7 ↑
8 7 11 →
9 8 9 ↑
10 10 11 ↑
11 11 12 ↑
12 12 13 ↑
13 13 14 ↑
14 14 15 ↑
15 15 16 ↑
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 17 Hoogsteen/Sugar trans
3 3 16 Watson-Crick/Hoogsteen trans
4 3 17 O2'/Bifurcated ?
5 4 15 Watson-Crick/Hoogsteen trans y
6 4 17 O2'/Hoogsteen ?
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