Thallium in PDB 4en5: Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked
Protein crystallography data
The structure of Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked, PDB code: 4en5
was solved by
A.M.Ren,
K.R.Rajashankar,
D.J.Patel,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.36 /
2.96
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
58.205,
77.287,
42.597,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
22.9 /
27.1
|
Other elements in 4en5:
The structure of Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked also contains other interesting chemical elements:
Thallium Binding Sites:
The binding sites of Thallium atom in the Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked
(pdb code 4en5). This binding sites where shown within
5.0 Angstroms radius around Thallium atom.
In total 6 binding sites of Thallium where determined in the
Crystal Structure of Fluoride Riboswitch, Tl-Acetate Soaked, PDB code: 4en5:
Jump to Thallium binding site number:
1;
2;
3;
4;
5;
6;
Thallium binding site 1 out
of 6 in 4en5
Go back to
Thallium Binding Sites List in 4en5
Thallium binding site 1 out
of 6 in the Crystal Structure of Fluoride 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 Fluoride Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Tl111
b:0.8
occ:1.00
|
O
|
A:HOH220
|
2.5
|
81.8
|
1.0
|
O6
|
A:G39
|
2.5
|
66.1
|
1.0
|
O
|
A:HOH222
|
2.5
|
69.3
|
1.0
|
O
|
A:HOH219
|
2.5
|
75.2
|
1.0
|
O
|
A:HOH221
|
2.5
|
67.2
|
1.0
|
N7
|
A:G39
|
3.2
|
61.6
|
1.0
|
C6
|
A:G39
|
3.2
|
62.4
|
1.0
|
C5
|
A:G39
|
3.5
|
61.4
|
1.0
|
O4
|
A:U38
|
4.0
|
61.7
|
1.0
|
N3
|
A:U7
|
4.3
|
56.3
|
1.0
|
C4
|
A:U38
|
4.3
|
61.4
|
1.0
|
C8
|
A:G39
|
4.4
|
61.7
|
1.0
|
N1
|
A:G39
|
4.5
|
56.6
|
1.0
|
C5
|
A:U38
|
4.5
|
62.4
|
1.0
|
O4
|
A:U7
|
4.8
|
57.5
|
1.0
|
C4
|
A:G39
|
4.8
|
60.0
|
1.0
|
C2
|
A:U7
|
4.8
|
59.4
|
1.0
|
C4
|
A:U7
|
4.8
|
55.4
|
1.0
|
O2
|
A:U7
|
4.8
|
61.8
|
1.0
|
O
|
A:HOH213
|
4.9
|
56.1
|
1.0
|
|
Thallium binding site 2 out
of 6 in 4en5
Go back to
Thallium Binding Sites List in 4en5
Thallium binding site 2 out
of 6 in the Crystal Structure of Fluoride 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 Fluoride Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Tl112
b:0.6
occ:1.00
|
O
|
A:HOH232
|
2.5
|
97.7
|
1.0
|
O
|
A:HOH231
|
2.5
|
88.7
|
1.0
|
O
|
A:HOH233
|
2.5
|
98.5
|
1.0
|
O
|
A:HOH235
|
2.5
|
83.7
|
1.0
|
O
|
A:HOH234
|
2.5
|
79.0
|
1.0
|
O6
|
A:G3
|
3.2
|
80.0
|
1.0
|
N7
|
A:G3
|
3.2
|
72.9
|
1.0
|
N7
|
A:G2
|
3.7
|
78.0
|
1.0
|
O6
|
A:G2
|
3.8
|
82.3
|
1.0
|
C6
|
A:G3
|
3.8
|
76.3
|
1.0
|
C5
|
A:G2
|
3.9
|
78.4
|
1.0
|
C5
|
A:G3
|
3.9
|
73.5
|
1.0
|
C6
|
A:G2
|
3.9
|
79.6
|
1.0
|
C8
|
A:G3
|
4.3
|
72.8
|
1.0
|
C8
|
A:G2
|
4.4
|
79.2
|
1.0
|
O
|
A:HOH216
|
4.4
|
77.2
|
1.0
|
OP1
|
A:G2
|
4.6
|
86.3
|
1.0
|
C4
|
A:G2
|
4.7
|
76.8
|
1.0
|
N4
|
A:C4
|
4.8
|
77.2
|
1.0
|
N1
|
A:G2
|
4.8
|
74.2
|
1.0
|
N9
|
A:G2
|
5.0
|
76.5
|
1.0
|
|
Thallium binding site 3 out
of 6 in 4en5
Go back to
Thallium Binding Sites List in 4en5
Thallium binding site 3 out
of 6 in the Crystal Structure of Fluoride 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 Fluoride Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Tl113
b:0.6
occ:1.00
|
O
|
A:HOH228
|
2.5
|
71.4
|
1.0
|
O
|
A:HOH227
|
2.5
|
83.8
|
1.0
|
O6
|
A:G42
|
2.6
|
86.5
|
1.0
|
O
|
A:HOH226
|
2.7
|
81.5
|
1.0
|
N7
|
A:G42
|
3.0
|
78.7
|
1.0
|
C6
|
A:G42
|
3.4
|
84.6
|
1.0
|
C5
|
A:G42
|
3.6
|
80.3
|
1.0
|
O6
|
A:G5
|
3.7
|
78.3
|
1.0
|
C6
|
A:G5
|
3.9
|
79.8
|
1.0
|
N7
|
A:G5
|
3.9
|
75.1
|
1.0
|
C5
|
A:G5
|
3.9
|
77.3
|
1.0
|
C8
|
A:G42
|
4.1
|
78.6
|
1.0
|
O
|
A:HOH201
|
4.3
|
84.5
|
1.0
|
C8
|
A:G5
|
4.7
|
71.0
|
1.0
|
N1
|
A:G5
|
4.7
|
78.7
|
1.0
|
O6
|
A:G43
|
4.7
|
87.8
|
1.0
|
O2'
|
A:U41
|
4.8
|
73.7
|
1.0
|
N1
|
A:G42
|
4.8
|
82.8
|
1.0
|
C4
|
A:G5
|
4.8
|
76.8
|
1.0
|
MG
|
A:MG104
|
4.9
|
72.4
|
1.0
|
C4
|
A:G42
|
4.9
|
78.9
|
1.0
|
O3'
|
A:U41
|
5.0
|
66.3
|
1.0
|
OP1
|
A:G42
|
5.0
|
64.8
|
1.0
|
|
Thallium binding site 4 out
of 6 in 4en5
Go back to
Thallium Binding Sites List in 4en5
Thallium binding site 4 out
of 6 in the Crystal Structure of Fluoride 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 Fluoride Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Tl114
b:0.7
occ:1.00
|
O
|
A:HOH225
|
2.5
|
71.5
|
1.0
|
O
|
A:HOH223
|
2.5
|
76.5
|
1.0
|
O
|
A:HOH201
|
2.5
|
84.5
|
1.0
|
O6
|
A:G10
|
2.5
|
85.0
|
1.0
|
O
|
A:HOH224
|
2.5
|
82.1
|
1.0
|
O6
|
A:G11
|
2.5
|
89.1
|
1.0
|
C6
|
A:G10
|
3.1
|
81.5
|
1.0
|
N7
|
A:G10
|
3.3
|
78.7
|
1.0
|
C5
|
A:G10
|
3.4
|
79.1
|
1.0
|
C6
|
A:G11
|
3.6
|
87.4
|
1.0
|
N7
|
A:G11
|
3.9
|
84.0
|
1.0
|
C5
|
A:G11
|
4.1
|
85.7
|
1.0
|
N6
|
A:A9
|
4.3
|
73.5
|
1.0
|
N1
|
A:G10
|
4.3
|
82.8
|
1.0
|
C8
|
A:G10
|
4.4
|
79.1
|
1.0
|
O
|
A:HOH227
|
4.5
|
83.8
|
1.0
|
C6
|
A:A9
|
4.5
|
72.0
|
1.0
|
C4
|
A:G10
|
4.7
|
79.0
|
1.0
|
N4
|
A:C12
|
4.7
|
85.8
|
1.0
|
C5
|
A:A9
|
4.7
|
69.7
|
1.0
|
O6
|
A:G43
|
4.8
|
87.8
|
1.0
|
N1
|
A:G11
|
4.8
|
86.4
|
1.0
|
N7
|
A:A9
|
4.8
|
66.6
|
1.0
|
|
Thallium binding site 5 out
of 6 in 4en5
Go back to
Thallium Binding Sites List in 4en5
Thallium binding site 5 out
of 6 in the Crystal Structure of Fluoride 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 Fluoride Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Tl115
b:0.1
occ:1.00
|
O
|
A:HOH208
|
2.5
|
67.1
|
1.0
|
O
|
A:HOH230
|
2.5
|
61.7
|
1.0
|
O
|
A:HOH209
|
2.5
|
52.7
|
1.0
|
O
|
A:HOH229
|
2.5
|
64.7
|
1.0
|
O
|
A:HOH207
|
2.5
|
69.3
|
1.0
|
O6
|
A:G35
|
2.5
|
57.3
|
1.0
|
N7
|
A:G35
|
3.0
|
57.8
|
1.0
|
MG
|
A:MG106
|
3.1
|
53.5
|
1.0
|
MG
|
A:MG107
|
3.2
|
54.6
|
1.0
|
C6
|
A:G35
|
3.3
|
56.5
|
1.0
|
N7
|
A:G34
|
3.4
|
56.9
|
1.0
|
C5
|
A:G35
|
3.5
|
56.4
|
1.0
|
O6
|
A:G34
|
3.6
|
58.0
|
1.0
|
C5
|
A:G34
|
3.8
|
53.7
|
1.0
|
C6
|
A:G34
|
3.9
|
54.5
|
1.0
|
C8
|
A:G35
|
4.3
|
58.9
|
1.0
|
C8
|
A:G34
|
4.3
|
56.4
|
1.0
|
N1
|
A:G35
|
4.6
|
55.8
|
1.0
|
O6
|
A:G36
|
4.7
|
54.7
|
1.0
|
C4
|
A:G34
|
4.8
|
54.9
|
1.0
|
N4
|
A:C26
|
4.8
|
58.4
|
1.0
|
C4
|
A:G35
|
4.8
|
56.5
|
1.0
|
N7
|
A:G36
|
4.9
|
57.3
|
1.0
|
N1
|
A:G34
|
4.9
|
54.7
|
1.0
|
|
Thallium binding site 6 out
of 6 in 4en5
Go back to
Thallium Binding Sites List in 4en5
Thallium binding site 6 out
of 6 in the Crystal Structure of Fluoride 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 Fluoride Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Tl116
b:0.6
occ:1.00
|
OP1
|
A:U7
|
2.4
|
67.2
|
1.0
|
O
|
A:HOH218
|
2.5
|
66.5
|
1.0
|
O
|
A:HOH202
|
2.5
|
68.2
|
1.0
|
OP1
|
A:G5
|
2.5
|
71.6
|
1.0
|
O
|
A:HOH203
|
2.5
|
66.1
|
1.0
|
O3'
|
A:A6
|
2.6
|
63.1
|
1.0
|
OP1
|
A:A6
|
3.0
|
65.5
|
1.0
|
O5'
|
A:A6
|
3.0
|
60.9
|
1.0
|
P
|
A:U7
|
3.1
|
56.2
|
1.0
|
P
|
A:A6
|
3.5
|
58.3
|
1.0
|
P
|
A:G5
|
3.6
|
64.2
|
1.0
|
F
|
A:F110
|
3.7
|
67.4
|
1.0
|
C3'
|
A:A6
|
3.8
|
62.2
|
1.0
|
O5'
|
A:G5
|
4.0
|
63.3
|
1.0
|
MG
|
A:MG103
|
4.0
|
61.7
|
1.0
|
C4'
|
A:A6
|
4.0
|
63.0
|
1.0
|
OP2
|
A:U7
|
4.1
|
59.2
|
1.0
|
C5'
|
A:A6
|
4.1
|
65.7
|
1.0
|
OP2
|
A:G5
|
4.2
|
67.7
|
1.0
|
OP2
|
A:A6
|
4.2
|
66.5
|
1.0
|
O5'
|
A:U7
|
4.2
|
56.5
|
1.0
|
C5'
|
A:G5
|
4.3
|
65.2
|
1.0
|
MG
|
A:MG104
|
4.3
|
72.4
|
1.0
|
C5'
|
A:U7
|
4.3
|
61.2
|
1.0
|
OP1
|
A:G8
|
4.4
|
61.5
|
1.0
|
OP2
|
A:G8
|
4.8
|
60.2
|
1.0
|
MG
|
A:MG102
|
4.8
|
60.4
|
1.0
|
O3'
|
A:G5
|
4.9
|
67.1
|
1.0
|
O2'
|
A:A6
|
4.9
|
64.2
|
1.0
|
O3'
|
A:C4
|
4.9
|
69.3
|
1.0
|
C2'
|
A:A6
|
5.0
|
61.6
|
1.0
|
|
Reference:
A.Ren,
K.R.Rajashankar,
D.J.Patel.
Fluoride Ion Encapsulation By MG2+ Ions and Phosphates in A Fluoride Riboswitch. Nature V. 486 85 2012.
ISSN: ISSN 0028-0836
PubMed: 22678284
DOI: 10.1038/NATURE11152
Page generated: Fri Oct 11 09:57:57 2024
|