Thallium in PDB 3oxm: Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked
Protein crystallography data
The structure of Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked, PDB code: 3oxm
was solved by
L.Huang,
A.Serganov,
D.J.Patel,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.95
|
Space group
|
P 32 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
83.783,
83.783,
200.066,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
20 /
22.5
|
Other elements in 3oxm:
The structure of Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked also contains other interesting chemical elements:
Thallium Binding Sites:
The binding sites of Thallium atom in the Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked
(pdb code 3oxm). This binding sites where shown within
5.0 Angstroms radius around Thallium atom.
In total 10 binding sites of Thallium where determined in the
Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked, PDB code: 3oxm:
Jump to Thallium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Thallium binding site 1 out
of 10 in 3oxm
Go back to
Thallium Binding Sites List in 3oxm
Thallium binding site 1 out
of 10 in the Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked
Mono view
Stereo pair view
|
A full contact list of Thallium with other atoms in the Tl binding
site number 1 of Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Tl201
b:0.3
occ:0.50
|
O2'
|
B:U20
|
3.1
|
80.1
|
1.0
|
O4
|
B:U18
|
3.1
|
51.8
|
1.0
|
O2
|
B:U20
|
3.3
|
77.4
|
1.0
|
O4
|
B:U23
|
3.5
|
78.8
|
1.0
|
OP2
|
B:A22
|
3.6
|
92.4
|
1.0
|
O6
|
B:G17
|
3.7
|
47.5
|
1.0
|
C2
|
B:U20
|
3.9
|
77.8
|
1.0
|
N4
|
B:C24
|
4.1
|
46.6
|
1.0
|
C4
|
B:U18
|
4.1
|
52.4
|
1.0
|
C1'
|
B:U20
|
4.1
|
79.3
|
1.0
|
C2'
|
B:U20
|
4.1
|
80.3
|
1.0
|
C5
|
B:U23
|
4.2
|
77.3
|
1.0
|
C4
|
B:U23
|
4.2
|
77.8
|
1.0
|
N1
|
B:U20
|
4.3
|
78.5
|
1.0
|
C6
|
B:G17
|
4.4
|
47.9
|
1.0
|
O3'
|
B:U20
|
4.5
|
84.1
|
1.0
|
C5
|
B:U18
|
4.6
|
52.4
|
1.0
|
C4
|
B:C24
|
4.7
|
47.4
|
1.0
|
N1
|
B:G17
|
4.8
|
47.8
|
1.0
|
N3
|
B:U20
|
4.8
|
77.8
|
1.0
|
N3
|
B:C24
|
4.8
|
48.1
|
1.0
|
C3'
|
B:U20
|
5.0
|
81.0
|
1.0
|
P
|
B:A22
|
5.0
|
92.0
|
1.0
|
|
Thallium binding site 2 out
of 10 in 3oxm
Go back to
Thallium Binding Sites List in 3oxm
Thallium binding site 2 out
of 10 in the Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked
Mono view
Stereo pair view
|
A full contact list of Thallium with other atoms in the Tl binding
site number 2 of Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Tl202
b:0.0
occ:1.00
|
N7
|
B:G25
|
3.1
|
44.0
|
1.0
|
O6
|
B:G25
|
3.2
|
44.0
|
1.0
|
C5
|
B:G25
|
3.7
|
44.1
|
1.0
|
N7
|
B:G26
|
3.7
|
42.3
|
1.0
|
C6
|
B:G25
|
3.8
|
44.0
|
1.0
|
N4
|
B:C24
|
4.0
|
46.6
|
1.0
|
O6
|
B:G26
|
4.1
|
41.3
|
1.0
|
C4
|
B:C24
|
4.1
|
47.4
|
1.0
|
C8
|
B:G25
|
4.2
|
44.3
|
1.0
|
C5
|
B:C24
|
4.2
|
47.7
|
1.0
|
OP2
|
B:U23
|
4.2
|
82.0
|
1.0
|
OP1
|
B:U23
|
4.4
|
81.5
|
1.0
|
C5
|
B:G26
|
4.5
|
42.2
|
1.0
|
C6
|
B:G26
|
4.6
|
41.7
|
1.0
|
C8
|
B:G26
|
4.7
|
43.0
|
1.0
|
P
|
B:U23
|
4.7
|
82.1
|
1.0
|
N3
|
B:C24
|
4.8
|
48.1
|
1.0
|
C6
|
B:C24
|
4.9
|
48.8
|
1.0
|
C4
|
B:G25
|
5.0
|
44.6
|
1.0
|
|
Thallium binding site 3 out
of 10 in 3oxm
Go back to
Thallium Binding Sites List in 3oxm
Thallium binding site 3 out
of 10 in the Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked
Mono view
Stereo pair view
|
A full contact list of Thallium with other atoms in the Tl binding
site number 3 of Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Tl203
b:0.4
occ:0.80
|
O6
|
B:G80
|
2.8
|
52.5
|
1.0
|
O6
|
B:G8
|
3.1
|
50.2
|
1.0
|
N7
|
B:G8
|
3.2
|
48.1
|
1.0
|
C6
|
B:G8
|
3.7
|
48.8
|
1.0
|
C5
|
B:G8
|
3.8
|
48.0
|
1.0
|
C6
|
B:G80
|
3.8
|
51.2
|
1.0
|
TL
|
B:TL208
|
4.2
|
0.9
|
0.2
|
C8
|
B:G8
|
4.3
|
47.2
|
1.0
|
C5
|
B:G80
|
4.7
|
51.0
|
1.0
|
OP2
|
B:G7
|
4.7
|
51.1
|
1.0
|
N1
|
B:G80
|
4.7
|
50.3
|
1.0
|
N7
|
B:G80
|
4.8
|
51.6
|
1.0
|
N7
|
B:G7
|
4.9
|
50.2
|
1.0
|
|
Thallium binding site 4 out
of 10 in 3oxm
Go back to
Thallium Binding Sites List in 3oxm
Thallium binding site 4 out
of 10 in the Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked
Mono view
Stereo pair view
|
A full contact list of Thallium with other atoms in the Tl binding
site number 4 of Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Tl204
b:0.0
occ:1.00
|
O6
|
A:G80
|
2.8
|
62.3
|
1.0
|
N7
|
A:G8
|
3.0
|
57.1
|
1.0
|
O6
|
A:G8
|
3.0
|
59.7
|
1.0
|
C5
|
A:G8
|
3.6
|
57.3
|
1.0
|
C6
|
A:G8
|
3.6
|
58.2
|
1.0
|
C6
|
A:G80
|
3.9
|
61.5
|
1.0
|
C8
|
A:G8
|
4.1
|
56.4
|
1.0
|
OP2
|
A:G7
|
4.6
|
60.9
|
1.0
|
N1
|
A:G80
|
4.6
|
60.8
|
1.0
|
N7
|
A:G7
|
4.7
|
59.5
|
1.0
|
C5
|
A:G80
|
4.9
|
61.5
|
1.0
|
C4
|
A:G8
|
4.9
|
56.6
|
1.0
|
N1
|
A:G8
|
4.9
|
57.9
|
1.0
|
|
Thallium binding site 5 out
of 10 in 3oxm
Go back to
Thallium Binding Sites List in 3oxm
Thallium binding site 5 out
of 10 in the Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked
Mono view
Stereo pair view
|
A full contact list of Thallium with other atoms in the Tl binding
site number 5 of Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Tl205
b:0.2
occ:1.00
|
OP2
|
A:A71
|
2.5
|
72.1
|
1.0
|
OP2
|
A:C70
|
2.6
|
71.7
|
1.0
|
O3'
|
A:U69
|
3.5
|
69.7
|
1.0
|
P
|
A:C70
|
3.5
|
71.9
|
1.0
|
O6
|
A:G72
|
3.6
|
57.7
|
1.0
|
N7
|
A:G72
|
3.8
|
59.3
|
1.0
|
O2'
|
A:U69
|
3.8
|
66.5
|
1.0
|
O5'
|
A:C70
|
3.9
|
72.6
|
1.0
|
P
|
A:A71
|
3.9
|
72.5
|
1.0
|
N7
|
A:A71
|
4.0
|
66.2
|
1.0
|
TL
|
A:TL207
|
4.3
|
43.0
|
0.1
|
C6
|
A:G72
|
4.4
|
57.2
|
1.0
|
C8
|
A:A71
|
4.4
|
67.3
|
1.0
|
O5'
|
A:A71
|
4.4
|
71.3
|
1.0
|
C5
|
A:G72
|
4.5
|
58.1
|
1.0
|
C3'
|
A:U69
|
4.6
|
68.2
|
1.0
|
OP1
|
A:A71
|
4.8
|
73.9
|
1.0
|
C2'
|
A:U69
|
4.8
|
66.8
|
1.0
|
C3'
|
A:C70
|
4.9
|
73.4
|
1.0
|
O3'
|
A:C70
|
4.9
|
73.7
|
1.0
|
C8
|
A:G72
|
4.9
|
59.6
|
1.0
|
OP1
|
A:C70
|
4.9
|
72.3
|
1.0
|
|
Thallium binding site 6 out
of 10 in 3oxm
Go back to
Thallium Binding Sites List in 3oxm
Thallium binding site 6 out
of 10 in the Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked
Mono view
Stereo pair view
|
A full contact list of Thallium with other atoms in the Tl binding
site number 6 of Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Tl206
b:0.0
occ:0.80
|
O6
|
A:G42
|
2.5
|
58.1
|
1.0
|
N7
|
A:G42
|
3.3
|
57.7
|
1.0
|
N4
|
A:C43
|
3.3
|
66.9
|
1.0
|
O6
|
A:G60
|
3.4
|
82.6
|
1.0
|
N2
|
A:G62
|
3.4
|
61.0
|
1.0
|
C6
|
A:G42
|
3.4
|
58.8
|
1.0
|
OP2
|
A:A41
|
3.7
|
59.5
|
1.0
|
C5
|
A:G42
|
3.7
|
58.3
|
1.0
|
O4
|
A:U61
|
3.7
|
74.0
|
1.0
|
C2
|
A:G62
|
3.8
|
62.0
|
1.0
|
N7
|
A:A41
|
3.8
|
55.7
|
1.0
|
MG
|
A:MG128
|
4.1
|
70.6
|
1.0
|
C4
|
A:C43
|
4.1
|
67.5
|
1.0
|
N3
|
A:U61
|
4.2
|
75.0
|
1.0
|
C8
|
A:A41
|
4.2
|
54.8
|
1.0
|
N1
|
A:G62
|
4.3
|
62.8
|
1.0
|
N3
|
A:G62
|
4.3
|
62.8
|
1.0
|
C6
|
A:G60
|
4.4
|
83.8
|
1.0
|
C4
|
A:U61
|
4.4
|
75.4
|
1.0
|
C8
|
A:G42
|
4.5
|
57.5
|
1.0
|
N3
|
A:C43
|
4.5
|
68.8
|
1.0
|
N1
|
A:G42
|
4.7
|
59.9
|
1.0
|
O5'
|
A:A41
|
4.8
|
57.8
|
1.0
|
P
|
A:A41
|
4.9
|
58.7
|
1.0
|
C5
|
A:A41
|
4.9
|
55.6
|
1.0
|
C5
|
A:C43
|
5.0
|
67.2
|
1.0
|
N1
|
A:G60
|
5.0
|
84.0
|
1.0
|
|
Thallium binding site 7 out
of 10 in 3oxm
Go back to
Thallium Binding Sites List in 3oxm
Thallium binding site 7 out
of 10 in the Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked
Mono view
Stereo pair view
|
A full contact list of Thallium with other atoms in the Tl binding
site number 7 of Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Tl207
b:43.0
occ:0.05
|
O6
|
A:G73
|
2.8
|
59.3
|
1.0
|
N7
|
A:G73
|
3.2
|
58.4
|
1.0
|
C6
|
A:G73
|
3.6
|
58.1
|
1.0
|
C5
|
A:G73
|
3.7
|
57.8
|
1.0
|
N7
|
A:G72
|
3.9
|
59.3
|
1.0
|
O6
|
A:G72
|
4.1
|
57.7
|
1.0
|
TL
|
A:TL205
|
4.3
|
0.2
|
1.0
|
C5
|
A:G72
|
4.3
|
58.1
|
1.0
|
C6
|
A:G72
|
4.4
|
57.2
|
1.0
|
C8
|
A:G73
|
4.4
|
57.7
|
1.0
|
C8
|
A:G72
|
4.7
|
59.6
|
1.0
|
N1
|
A:G73
|
4.9
|
57.2
|
1.0
|
|
Thallium binding site 8 out
of 10 in 3oxm
Go back to
Thallium Binding Sites List in 3oxm
Thallium binding site 8 out
of 10 in the Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked
Mono view
Stereo pair view
|
A full contact list of Thallium with other atoms in the Tl binding
site number 8 of Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Tl208
b:0.9
occ:0.20
|
O6
|
B:G8
|
2.7
|
50.2
|
1.0
|
O4
|
B:U6
|
3.2
|
54.3
|
1.0
|
C6
|
B:G8
|
3.7
|
48.8
|
1.0
|
C4
|
B:U6
|
3.7
|
53.8
|
1.0
|
C5
|
B:U6
|
4.0
|
53.9
|
1.0
|
O6
|
B:G7
|
4.0
|
50.0
|
1.0
|
TL
|
B:TL203
|
4.2
|
0.4
|
0.8
|
N1
|
B:G8
|
4.3
|
48.6
|
1.0
|
N7
|
B:G7
|
4.5
|
50.2
|
1.0
|
C5
|
B:G8
|
4.6
|
48.0
|
1.0
|
N3
|
B:U6
|
4.7
|
53.5
|
1.0
|
C6
|
B:G7
|
4.9
|
49.5
|
1.0
|
N7
|
B:G8
|
5.0
|
48.1
|
1.0
|
C6
|
B:U6
|
5.0
|
53.9
|
1.0
|
|
Thallium binding site 9 out
of 10 in 3oxm
Go back to
Thallium Binding Sites List in 3oxm
Thallium binding site 9 out
of 10 in the Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked
Mono view
Stereo pair view
|
A full contact list of Thallium with other atoms in the Tl binding
site number 9 of Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Tl209
b:0.5
occ:0.50
|
O6
|
B:G1
|
3.2
|
88.5
|
1.0
|
O6
|
B:G2
|
3.4
|
83.4
|
1.0
|
N7
|
B:G2
|
3.6
|
82.4
|
1.0
|
C6
|
B:G1
|
3.8
|
88.4
|
1.0
|
C6
|
B:G2
|
4.1
|
83.3
|
1.0
|
O4
|
B:U87
|
4.1
|
79.6
|
1.0
|
C5
|
B:G2
|
4.2
|
83.0
|
1.0
|
N4
|
B:CCC88
|
4.3
|
85.5
|
1.0
|
C5
|
B:G1
|
4.3
|
88.1
|
1.0
|
N7
|
B:G1
|
4.3
|
87.7
|
1.0
|
N4
|
B:C3
|
4.5
|
72.1
|
1.0
|
O6
|
B:G86
|
4.7
|
69.4
|
1.0
|
N1
|
B:G1
|
4.7
|
88.6
|
1.0
|
C8
|
B:G2
|
4.8
|
82.5
|
1.0
|
|
Thallium binding site 10 out
of 10 in 3oxm
Go back to
Thallium Binding Sites List in 3oxm
Thallium binding site 10 out
of 10 in the Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked
Mono view
Stereo pair view
|
A full contact list of Thallium with other atoms in the Tl binding
site number 10 of Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Tl210
b:0.5
occ:0.30
|
OP2
|
A:A78
|
2.4
|
62.5
|
1.0
|
P
|
A:A78
|
3.8
|
62.5
|
1.0
|
N7
|
A:G79
|
3.9
|
58.5
|
1.0
|
O6
|
A:G79
|
4.0
|
57.0
|
1.0
|
O6
|
A:G80
|
4.0
|
62.3
|
1.0
|
N7
|
A:A78
|
4.0
|
60.1
|
1.0
|
O5'
|
A:A78
|
4.1
|
62.1
|
1.0
|
C8
|
A:A78
|
4.3
|
60.6
|
1.0
|
OP2
|
A:A77
|
4.5
|
62.1
|
1.0
|
OP1
|
A:A77
|
4.5
|
63.5
|
1.0
|
O5'
|
A:A77
|
4.6
|
62.6
|
1.0
|
OP1
|
A:A78
|
4.7
|
63.4
|
1.0
|
C5
|
A:G79
|
4.7
|
57.9
|
1.0
|
C6
|
A:G79
|
4.7
|
57.5
|
1.0
|
C6
|
A:G80
|
4.7
|
61.5
|
1.0
|
P
|
A:A77
|
4.7
|
62.9
|
1.0
|
O3'
|
A:A77
|
4.8
|
62.3
|
1.0
|
C8
|
A:G79
|
4.9
|
58.9
|
1.0
|
C3'
|
A:A77
|
4.9
|
62.1
|
1.0
|
|
Reference:
L.Huang,
A.Serganov,
D.J.Patel.
Structural Insights Into Ligand Recognition By A Sensing Domain of the Cooperative Glycine Riboswitch. Mol.Cell V. 40 774 2010.
ISSN: ISSN 1097-2765
PubMed: 21145485
DOI: 10.1016/J.MOLCEL.2010.11.026
Page generated: Fri Oct 11 09:51:12 2024
|