Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'7-10-20-7-31-4-4-6-4-Multiloop pdb2hgj1A.m1-2889
Source: [PDB-id:chain] 2hgj:A (&rarr PDB)
Source: Information CRYSTAL STRUCTURE OF THE 70S THERMUS THERMOPHILUS RIBOSOME SHOWING HOW THE 16S 3'-END MIMICKS MRNA E AND P CODONS. THIS ENTRY 2HGJ CONTAINS 50S RIBOSOMAL SUBUNIT. THE 30S RIBOSOMAL SUBUNIT CAN BE FOUND IN PDB ENTRY 2HGI.
Source: Compound 23S RIBOSOMAL RNA
Source: Resolution 5.00 ANGSTROMS.
Position (8, 2882), (16, 549), (560, 581), (602, 1285), (1293, 2011), (2043, 2615), (2620, 2779), (2784, 2792), (2799, 2877)
Primary structure ('_': anchors) _UGGUAAG_-_UACAAGCAGU_-_GCGUGCCUAUUGAAGCAUGA_-_AUGAGUA_-_GAAAUUGAACUGGCCGUGAAGAUGCGGCCUA_-_CGCA_-_CACG_-_CGGUAA_-_GAGG_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		3: C4'-exo, 6: C2'-exo, 11: C4'-exo, 13: C4'-exo, 14: C2'-exo, 15: C4'-exo, 16: C2'-exo, 18: C4'-exo, 20: C4'-exo, 23: C2'-exo, 25: C2'-exo, 30: C2'-exo, 35: C4'-exo, 36: C2'-exo, 37: C4'-exo, 38: C4'-exo, 40: C2'-exo, 42: C4'-exo, 47: C2'-exo, 48: C4'-exo, 49: C4'-exo, 50: C2'-exo, 51: C2'-exo, 54: C4'-exo, 57: C4'-exo, 58: C2'-exo, 59: C4'-exo, 63: C2'-exo, 64: C4'-exo, 68: C4'-exo, 69: C4'-exo, 73: C2'-exo, 74: C1'-exo, 75: C2'-exo, 76: C2'-exo, 77: C4'-exo, 81: C4'-exo, 83: C4'-exo, 84: C4'-exo, 86: C2'-exo, 87: C2'-exo, 93: C4'-exo, 101: C4'-exo, 103: C4'-exo, 106: C4'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		6: syn, 7: syn, 14: syn, 18: syn, 57: syn, 72: syn, 94: syn, 103: syn, 108: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 2 ↑
2 3 4 ↑
3 4 5 ↑
4 8 9 ↑
5 15 65 ↑
6 15 84 →
7 19 20 ↑
8 19 25 →
9 22 23 ↑
10 23 24 ↑
11 24 25 ↑
12 27 28 ↑
13 27 60 →
14 29 41 →
15 33 34 ↑
16 35 39 ↑
17 35 72 ↓
18 36 37 ↑
19 41 42 ↑
20 45 46 ↑
21 46 47 ↑
22 49 54 &larr
23 51 52 ↑
24 51 55 →
25 53 54 ↑
26 55 56 ↑
27 60 61 ↑
28 61 62 ↑
29 65 66 ↑
30 65 83 →
31 66 67 ↑
32 67 68 ↑
33 69 70 ↑
34 69 79 →
35 71 75 →
36 75 78 ↑
37 79 80 ↑
38 80 81 ↑
39 83 84 ↑
40 86 87 ↑
41 90 111 ↑
42 91 110 →
43 92 93 ↑
44 104 105 ↑
45 106 107 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 111 Watson-Crick/Watson-Crick cis
2 5 88 O2'/Watson-Crick ?
3 7 8 Hoogsteen/O2' ?
4 7 12 Watson-Crick/Watson-Crick cis y
5 7 86 O2'/Sugar ?
6 9 10 Watson-Crick/Watson-Crick cis
7 11 12 Hoogsteen/O2' ?
8 12 86 Sugar/Sugar trans
9 13 14 Sugar/O2' ?
10 14 85 O2'/Watson-Crick ?
11 15 16 Watson-Crick/O2' ?
12 15 65 O2'/Watson-Crick ?
13 16 64 O2'/Watson-Crick ?
14 17 18 O2'/Bifurcated ?
15 17 25 Watson-Crick/O2' ?
16 18 63 Bifurcated/O2' ?
17 19 24 Watson-Crick/Watson-Crick cis
18 21 22 Watson-Crick/Watson-Crick cis
19 27 42 Watson-Crick/Watson-Crick cis y
20 28 41 Watson-Crick/Watson-Crick cis
21 29 30 Watson-Crick/Watson-Crick cis y
22 29 40 Watson-Crick/Watson-Crick trans y
23 32 34 Hoogsteen/O2' ?
24 32 35 O2'/Watson-Crick ?
25 35 37 C/O2' ?
26 36 71 O2'/Bifurcated ?
27 40 41 Hoogsteen/Watson-Crick cis y
28 43 44 Watson-Crick/Watson-Crick cis
29 47 48 Hoogsteen/Hoogsteen cis y
30 47 56 O2'/Watson-Crick ?
31 48 50 Watson-Crick/C cis y
32 49 54 Watson-Crick/O2' ?
33 50 54 Bifurcated/Hoogsteen trans y
34 52 53 Watson-Crick/Watson-Crick cis
35 56 57 Sugar/O2' ?
36 60 77 Watson-Crick/Watson-Crick cis y
37 62 64 Watson-Crick/Hoogsteen trans
38 62 76 Watson-Crick/Watson-Crick cis y
39 64 76 Watson-Crick/O2' ?
40 65 82 Watson-Crick/Watson-Crick cis
41 66 81 Watson-Crick/Watson-Crick cis
42 67 80 Watson-Crick/Watson-Crick cis
43 68 79 Watson-Crick/Watson-Crick cis
44 69 78 Watson-Crick/Watson-Crick cis
45 70 71 C/O2' ?
46 70 75 Hoogsteen/Watson-Crick trans
47 71 73 O2'/C ?
48 71 75 O2'/Watson-Crick ?
49 77 78 Bifurcated/O2' ?
50 85 86 Watson-Crick/Watson-Crick cis
51 91 92 Watson-Crick/Watson-Crick cis
52 92 108 Watson-Crick/O2' ?
53 93 109 Bifurcated/O2' trans y
54 93 110 Bifurcated/Watson-Crick cis y
55 95 109 Hoogsteen/Hoogsteen trans y
56 97 98 Watson-Crick/Watson-Crick cis
57 101 108 Hoogsteen/Watson-Crick trans y
58 103 105 Hoogsteen/O2' ?
59 104 107 Sugar/Hoogsteen trans y
60 105 106 Watson-Crick/Watson-Crick cis
61 109 110 C/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters