Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'27-Segment pdb2v471A.i460-488
Source: [PDB-id:chain] 2v47:A (&rarr PDB)
Source: Information STRUCTURE OF THE RIBOSOME RECYCLING FACTOR BOUND TO THE THERMUS THERMOPHILUS 70S RIBOSOME WITH MRNA, ASL-PHE AND TRNA-FMET (PART 2 OF 4). THIS FILE CONTAINS THE 50S SUBUNIT FOR MOLECULE 1.
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 3.8 ANGSTROMS.
Position (460, 488)
Primary structure ('_': anchors) _GAUAGCGCACCAGUACCGUGAGGGAAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		2: C2'-endo, 3: C2'-endo, 4: C2'-endo, 10: C2'-endo, 11: C2'-endo, 12: C2'-endo, 13: C2'-endo, 14: C2'-endo, 16: C4'-exo, 26: 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 10 ↓
3 3 29 ↑
4 5 6 ↑
5 7 9 &larr
6 8 9 ↑
7 8 14 →
8 11 28 &larr
9 13 15 →
10 14 25 &larr
11 16 17 ↑
12 16 26 →
13 17 18 ↑
14 18 19 ↑
15 19 23 →
16 20 21 ↑
17 21 22 ↑
18 23 24 ↑
19 24 25 ↑
20 26 27 ↑
21 27 28 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 5 Sugar/O2' ?
2 2 10 Watson-Crick/Sugar trans y
3 3 10 O2'/Watson-Crick ?
4 3 29 Hoogsteen/O2' ?
5 5 10 Hoogsteen/Watson-Crick trans
6 6 10 O2'/Bifurcated ?
7 7 10 O2'/Bifurcated ?
8 8 13 Watson-Crick/O2' trans
9 9 28 Bifurcated/O2' ?
10 13 27 Hoogsteen/Hoogsteen trans
11 14 25 Watson-Crick/O2' ?
12 14 26 O2'/Bifurcated ?
13 15 25 Watson-Crick/O2' ?
14 15 26 Hoogsteen/Watson-Crick trans
15 16 25 O2'/Bifurcated trans
16 17 24 Watson-Crick/Watson-Crick cis
17 19 21 Hoogsteen/O2' ?
18 19 22 O2'/Bifurcated trans y
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters