Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'8-4-0-1-7-11-3-2-5-Multiloop pdb2hgj1A.m43-461
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 (44, 460), (53, 114), (119, 128), (129, 148), (150, 165), (173, 201), (213, 220), (224, 251), (254, 454)
Primary structure ('_': anchors) _CCGAUGAA_-_GAAU_-__-_A_-_GGGGAAC_-_AGGAGAGGAAA_-_GAC_-_CC_-_AAGUA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		9: C2'-exo, 14: C2'-exo, 15: C2'-exo, 16: C2'-exo, 17: C2'-exo, 20: C2'-exo, 21: C4'-exo, 26: C2'-exo, 27: C2'-exo, 34: C4'-exo, 36: C2'-exo, 39: C4'-exo, 40: C2'-exo, 41: C4'-exo, 45: C2'-exo, 46: C2'-exo, 51: C4'-exo, 57: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		20: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 3 4 ↑
2 4 24 →
3 5 23 →
4 8 13 →
5 9 10 ↑
6 11 12 ↑
7 13 14 →
8 16 18 →
9 16 19 ↓
10 20 21 &larr
11 24 25 ↑
12 25 26 ↑
13 27 28 ↑
14 28 29 ↑
15 33 34 ↑
16 35 58 →
17 36 37 ↑
18 37 38 ↑
19 38 39 ↑
20 40 46 →
21 41 43 ↑
22 46 47 ↑
23 47 48 ↑
24 58 59 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 59 Watson-Crick/Watson-Crick cis
2 3 24 Watson-Crick/Watson-Crick cis
3 4 13 Watson-Crick/O2' ?
4 4 23 O2'/Bifurcated ?
5 5 7 C/O2' ?
6 5 15 Watson-Crick/Bifurcated cis y
7 7 13 Bifurcated/O2' trans
8 7 14 Watson-Crick/O2' ?
9 7 15 Watson-Crick/Watson-Crick trans y
10 8 12 Watson-Crick/O2' ?
11 8 14 Watson-Crick/Hoogsteen trans y
12 8 24 O2'/Watson-Crick ?
13 10 11 Watson-Crick/Watson-Crick cis
14 13 14 Hoogsteen/O2' ?
15 15 23 Sugar/Hoogsteen trans y
16 16 17 Watson-Crick/Watson-Crick cis
17 18 19 Watson-Crick/Watson-Crick cis
18 21 22 Watson-Crick/Watson-Crick cis y
19 26 27 Hoogsteen/O2' ?
20 28 59 O2'/Sugar ?
21 29 34 Watson-Crick/Watson-Crick cis
22 29 58 Sugar/O2' ?
23 30 31 Watson-Crick/Watson-Crick cis
24 30 36 Sugar/O2' ?
25 32 36 O2'/Sugar ?
26 38 47 O2'/Sugar cis y
27 39 46 Sugar/O2' ?
28 39 54 O2'/Watson-Crick ?
29 41 45 Sugar/Hoogsteen trans y
30 43 44 Watson-Crick/Watson-Crick cis
31 46 55 Watson-Crick/Watson-Crick trans y
32 47 56 Watson-Crick/Watson-Crick trans y
33 48 49 Watson-Crick/Watson-Crick cis
34 49 56 O2'/Sugar ?
35 52 53 Watson-Crick/Watson-Crick cis
36 53 54 C/Watson-Crick cis y
37 55 56 C/O2' ?
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters