Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'6-7-18-7-31-4-4-6-4-Multiloop pdb2hgq1A.m1-2889
Source: [PDB-id:chain] 2hgq:A (&rarr PDB)
Source: Information CRYSTAL STRUCTURE OF THE 70S THERMUS THERMOPHILUS RIBOSOME WITH TRANSLOCATED AND ROTATED SHINE-DALGARNO DUPLEX. THIS ENTRY 2HGQ CONTAINS 50S RIBOSOMAL SUBUNIT. THE 30S RIBOSOMAL SUBUNIT CAN BE FOUND IN PDB ENTRY 2HGP.
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 5.50 ANGSTROMS.
Position (8, 2882), (15, 550), (558, 583), (602, 1285), (1293, 2011), (2043, 2615), (2620, 2779), (2784, 2792), (2799, 2877)
Primary structure ('_': anchors) _UGGUAA_-_ACAAGCA_-_GUGCCUAUUGAAGCAUGA_-_AUGAGUA_-_GAAAUUGAACUGGCCGUGAAGAUGCGGCCUA_-_CGCA_-_CACG_-_CGGUAA_-_GAGG_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		3: C4'-exo, 9: C4'-exo, 10: C2'-exo, 11: C4'-exo, 13: C4'-exo, 16: C4'-exo, 18: C2'-exo, 19: C2'-exo, 22: C4'-exo, 24: C4'-exo, 27: C2'-exo, 31: C4'-exo, 32: C4'-exo, 34: C2'-exo, 36: C4'-exo, 39: C4'-exo, 41: C2'-exo, 42: C4'-exo, 43: C4'-exo, 44: C2'-exo, 46: C2'-exo, 48: C4'-exo, 51: C4'-exo, 57: C2'-exo, 61: C4'-exo, 62: C4'-exo, 63: C4'-exo, 68: O4'-endo, 69: C2'-exo, 71: C4'-exo, 75: C4'-exo, 80: C2'-exo, 84: C2'-exo, 86: C2'-exo, 87: C4'-exo, 93: C4'-exo, 95: C4'-exo, 96: C2'-exo, 97: C2'-exo, 102: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		6: syn, 7: syn, 12: syn, 16: syn, 42: syn, 51: syn, 97: syn, 102: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 3 4 ↑
3 4 5 ↑
4 13 59 ↑
5 13 78 →
6 17 19 →
7 21 22 ↑
8 21 54 →
9 23 35 →
10 27 28 ↑
11 28 66 ↑
12 29 33 ↑
13 29 66 ↓
14 30 31 ↑
15 35 36 ↑
16 37 39 →
17 40 41 ↑
18 43 48 &larr
19 45 46 ↑
20 45 49 →
21 47 48 ↑
22 49 50 ↑
23 52 53 ↑
24 54 55 ↑
25 59 60 ↑
26 60 61 ↑
27 61 62 ↑
28 63 64 ↑
29 63 73 →
30 64 65 ↑
31 65 69 →
32 73 74 ↑
33 74 75 ↑
34 80 81 ↑
35 84 105 ↑
36 85 104 →
37 90 91 ↑
38 98 99 ↑
39 100 101 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 84 Hoogsteen/Watson-Crick trans y
2 1 105 Watson-Crick/Watson-Crick cis
3 7 10 Watson-Crick/Bifurcated cis y
4 7 80 O2'/Sugar ?
5 8 9 Watson-Crick/Watson-Crick cis
6 10 80 Sugar/Sugar trans y
7 11 12 Sugar/O2' ?
8 12 79 O2'/Watson-Crick ?
9 13 14 Hoogsteen/O2' ?
10 14 58 O2'/Bifurcated ?
11 15 16 O2'/Watson-Crick ?
12 15 19 Watson-Crick/O2' ?
13 16 57 Bifurcated/O2' ?
14 17 18 Watson-Crick/Watson-Crick cis
15 20 30 Sugar/Watson-Crick cis
16 21 36 Watson-Crick/Watson-Crick cis y
17 22 35 Watson-Crick/Watson-Crick cis
18 23 24 Watson-Crick/Watson-Crick cis y
19 23 34 Watson-Crick/Watson-Crick cis y
20 26 28 Hoogsteen/O2' ?
21 26 29 O2'/Watson-Crick ?
22 29 31 Hoogsteen/O2' ?
23 30 65 O2'/Bifurcated trans y
24 30 67 O2'/Bifurcated ?
25 31 67 O2'/Watson-Crick ?
26 37 38 Watson-Crick/Watson-Crick cis
27 41 42 Sugar/O2' ?
28 42 44 Bifurcated/C cis y
29 43 48 Bifurcated/O2' ?
30 44 48 Watson-Crick/O2' trans y
31 46 47 Watson-Crick/Watson-Crick cis y
32 50 51 Sugar/O2' ?
33 54 71 Watson-Crick/Watson-Crick cis y
34 56 70 Watson-Crick/Watson-Crick cis y
35 58 70 Watson-Crick/O2' ?
36 59 76 Watson-Crick/Watson-Crick cis
37 60 75 Watson-Crick/Watson-Crick cis
38 61 74 Watson-Crick/Watson-Crick cis
39 62 73 Watson-Crick/Watson-Crick cis
40 63 72 Watson-Crick/Watson-Crick cis
41 64 69 Hoogsteen/Watson-Crick trans
42 65 67 O2'/C ?
43 65 69 O2'/Bifurcated ?
44 71 72 Bifurcated/O2' ?
45 79 80 Watson-Crick/Watson-Crick cis
46 85 86 Watson-Crick/Watson-Crick cis
47 85 102 O2'/Sugar ?
48 86 102 Watson-Crick/O2' ?
49 87 103 Bifurcated/O2' ?
50 87 104 Hoogsteen/Watson-Crick cis y
51 88 103 O2'/Sugar ?
52 89 103 Hoogsteen/Hoogsteen trans y
53 91 92 Watson-Crick/Watson-Crick cis
54 95 102 Hoogsteen/Watson-Crick trans y
55 97 99 Hoogsteen/O2' ?
56 98 101 Sugar/Hoogsteen trans y
57 99 100 Watson-Crick/Watson-Crick cis
58 103 104 C/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters