Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'2-4-11-3-3-9-Multiloop pdb1qvg10.m25-440
Source: [PDB-id:chain] 1qvg:0 (&rarr PDB)
Source: Information STRUCTURE OF CCA OLIGONUCLEOTIDE BOUND TO THE TRNA BINDING SITES OF THE LARGE RIBOSOMAL SUBUNIT OF HALOARCULA MARISMORTUI
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 2.90 ANGSTROMS.
Position (30, 435), (33, 141), (146, 174), (186, 194), (198, 225), (229, 425)
Primary structure ('_': anchors) _CG_-_GAAC_-_AGGAACAGAAA_-_GAU_-_ACA_-_UAAACACAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		14: C2'-endo, 20: C2'-endo, 21: C2'-endo, 25: C2'-endo, 32: C2'-endo, 39: C2'-endo, 42: C2'-endo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		21: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 2 3 ↑
3 5 6 ↑
4 7 8 ↑
5 7 43 →
6 8 9 ↑
7 12 13 ↑
8 13 14 ↑
9 15 16 ↑
10 15 40 →
11 16 17 ↑
12 17 18 ↑
13 18 19 ↑
14 19 35 &larr
15 20 26 →
16 20 33 ↑
17 21 23 ↑
18 24 25 ↑
19 26 27 ↑
20 27 28 ↑
21 28 38 ↓
22 29 30 ↑
23 30 31 ↑
24 32 36 ↑
25 34 35 ↑
26 36 37 ↑
27 37 38 ↑
28 40 41 ↑
29 41 42 ↑
30 43 44 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 44 Watson-Crick/Watson-Crick cis
2 2 42 Watson-Crick/Watson-Crick cis
3 2 43 Watson-Crick/Watson-Crick cis y
4 3 7 Watson-Crick/Sugar trans y
5 3 41 Watson-Crick/Watson-Crick cis
6 4 5 Watson-Crick/Watson-Crick cis
7 4 13 O2'/Bifurcated ?
8 6 7 Hoogsteen/O2' ?
9 6 13 Hoogsteen/Watson-Crick trans y
10 6 14 Hoogsteen/Sugar trans y
11 8 14 Watson-Crick/Watson-Crick cis
12 8 41 O2'/Sugar cis y
13 9 13 Watson-Crick/Watson-Crick cis
14 9 40 Sugar/O2' ?
15 10 11 Watson-Crick/Watson-Crick cis
16 10 16 Sugar/O2' ?
17 13 15 O2'/Sugar cis y
18 14 40 Watson-Crick/Sugar trans y
19 18 27 O2'/Sugar ?
20 19 26 Sugar/O2' cis y
21 19 36 O2'/Bifurcated ?
22 20 32 O2'/Watson-Crick ?
23 20 33 Hoogsteen/O2' ?
24 20 35 Watson-Crick/Hoogsteen trans
25 21 25 Sugar/Hoogsteen trans
26 23 24 Watson-Crick/Watson-Crick cis
27 26 37 Watson-Crick/Watson-Crick trans
28 27 38 Watson-Crick/Watson-Crick trans
29 28 29 Watson-Crick/Watson-Crick cis
30 28 39 Watson-Crick/O2' ?
31 30 37 Sugar/O2' ?
32 31 36 Watson-Crick/O2' ?
33 32 35 O2'/Watson-Crick ?
34 32 36 Bifurcated/O2' ?
35 33 34 Watson-Crick/Watson-Crick cis
36 42 43 Hoogsteen/Sugar cis y
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters