Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'4-7-10-19-0-4-Multiloop pdb2vhn1B.m812-1179
Source: [PDB-id:chain] 2vhn:B (&rarr PDB)
Source: Information STRUCTURE OF PDF BINDING HELIX IN COMPLEX WITH THE RIBOSOME. (PART 2 OF 4)
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 3.74 ANGSTROMS.
Position (817, 1174), (822, 835), (843, 919), (930, 955), (975, 1147), (1148, 1169)
Primary structure ('_': anchors) _GAAA_-_GCCUCGU_-_ACGGGAGACA_-_AAGAGGGAAACAACCCAGA_-__-_GGUA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		2: C2'-exo, 3: C2'-exo, 4: C2'-exo, 6: C4'-exo, 9: C2'-exo, 13: C2'-exo, 15: C2'-exo, 22: C4'-exo, 25: C2'-exo, 26: O4'-endo, 29: C4'-exo, 30: C2'-endo, 31: C1'-exo, 32: C2'-exo, 33: C2'-exo, 34: C2'-exo, 35: C4'-exo, 36: C4'-exo, 39: O4'-endo, 40: C4'-exo, 41: C3'-exo, 42: C2'-exo, 43: C2'-exo, 45: C2'-exo, 46: C4'-exo, 47: C1'-endo, 48: C2'-exo, 53: C2'-exo, 55: C2'-exo, 56: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		31: syn, 39: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 3 4 ↑
3 3 55 →
4 4 5 ↑
5 5 27 ↑
6 6 8 →
7 7 8 ↑
8 8 9 ↑
9 10 11 ↑
10 12 13 ↑
11 12 20 →
12 13 14 ↑
13 15 17 →
14 16 17 ↑
15 17 18 ↑
16 19 20 ↑
17 20 21 ↑
18 21 22 ↑
19 22 23 ↑
20 23 24 ↑
21 24 25 ↑
22 28 29 ↑
23 29 30 &larr
24 30 54 →
25 31 46 ↓
26 31 52 ↑
27 32 33 ↑
28 32 47 →
29 33 34 ↑
30 34 35 ↑
31 35 43 →
32 37 38 ↑
33 40 41 ↑
34 43 44 ↑
35 44 45 ↑
36 48 51 ↓
37 49 50 ↑
38 52 53 ↑
39 55 56 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 56 Watson-Crick/Watson-Crick cis y
2 2 54 O2'/Bifurcated ?
3 3 53 Bifurcated/O2' ?
4 3 54 Watson-Crick/Hoogsteen trans y
5 4 8 Bifurcated/O2' ?
6 4 24 O2'/Sugar ?
7 4 30 Bifurcated/O2' trans
8 5 29 Sugar/Hoogsteen trans y
9 6 7 Watson-Crick/Watson-Crick cis
10 8 9 Hoogsteen/Hoogsteen cis y
11 9 23 Watson-Crick/Watson-Crick cis
12 10 21 Watson-Crick/Watson-Crick cis
13 12 19 Watson-Crick/Watson-Crick cis
14 13 18 Watson-Crick/Bifurcated cis
15 15 16 Watson-Crick/Watson-Crick cis
16 22 56 O2'/Sugar ?
17 23 55 Sugar/O2' ?
18 27 28 Watson-Crick/Watson-Crick cis
19 28 31 Bifurcated/O2' ?
20 28 40 Sugar/O2' ?
21 31 52 Bifurcated/O2' ?
22 33 44 Watson-Crick/Watson-Crick cis y
23 37 39 Bifurcated/O2' ?
24 41 42 Bifurcated/O2' ?
25 47 52 O2'/Bifurcated ?
26 48 49 Watson-Crick/Watson-Crick cis
27 50 51 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters