Thallium in PDB 4e8q: Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+
Protein crystallography data
The structure of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+, PDB code: 4e8q
was solved by
M.Marcia,
A.M.Pyle,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.51 /
2.84
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
89.459,
95.680,
225.144,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.8 /
25.2
|
Other elements in 4e8q:
The structure of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+ also contains other interesting chemical elements:
Thallium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
17;
Binding sites:
The binding sites of Thallium atom in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+
(pdb code 4e8q). This binding sites where shown within
5.0 Angstroms radius around Thallium atom.
In total 17 binding sites of Thallium where determined in the
Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+, PDB code: 4e8q:
Jump to Thallium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Thallium binding site 1 out
of 17 in 4e8q
Go back to
Thallium Binding Sites List in 4e8q
Thallium binding site 1 out
of 17 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+
Mono view
Stereo pair view
|
A full contact list of Thallium with other atoms in the Tl binding
site number 1 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Tl401
b:0.1
occ:0.41
|
O6
|
A:G15
|
3.4
|
86.3
|
1.0
|
O6
|
A:G14
|
3.9
|
93.2
|
1.0
|
N7
|
A:G15
|
4.0
|
81.8
|
1.0
|
C6
|
A:G15
|
4.3
|
86.3
|
1.0
|
N7
|
A:G14
|
4.4
|
69.3
|
1.0
|
O2'
|
A:A12
|
4.5
|
86.9
|
1.0
|
OP2
|
A:U13
|
4.5
|
0.2
|
1.0
|
C6
|
A:G14
|
4.5
|
76.4
|
1.0
|
C5
|
A:G15
|
4.5
|
84.5
|
1.0
|
C2'
|
A:A12
|
4.5
|
87.4
|
1.0
|
O4
|
A:U256
|
4.6
|
0.9
|
1.0
|
C5
|
A:G14
|
4.7
|
70.1
|
1.0
|
C3'
|
A:A12
|
4.9
|
92.0
|
1.0
|
|
Thallium binding site 2 out
of 17 in 4e8q
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Thallium Binding Sites List in 4e8q
Thallium binding site 2 out
of 17 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+
Mono view
Stereo pair view
|
A full contact list of Thallium with other atoms in the Tl binding
site number 2 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Tl402
b:0.8
occ:0.28
|
O
|
A:HOH512
|
2.2
|
67.8
|
1.0
|
O
|
A:HOH517
|
2.4
|
63.0
|
1.0
|
OP2
|
A:G269
|
2.5
|
73.8
|
1.0
|
N7
|
A:G270
|
3.4
|
79.5
|
1.0
|
N7
|
A:G269
|
3.5
|
79.9
|
1.0
|
OP2
|
A:A268
|
3.5
|
76.8
|
1.0
|
O5'
|
A:A268
|
3.6
|
75.3
|
1.0
|
O6
|
A:G270
|
3.6
|
81.0
|
1.0
|
P
|
A:G269
|
3.8
|
82.7
|
1.0
|
C8
|
A:G269
|
3.9
|
81.4
|
1.0
|
O5'
|
A:G269
|
4.0
|
81.6
|
1.0
|
C5
|
A:G270
|
4.2
|
78.3
|
1.0
|
C6
|
A:G270
|
4.2
|
79.8
|
1.0
|
P
|
A:A268
|
4.3
|
78.0
|
1.0
|
C3'
|
A:A268
|
4.4
|
83.8
|
1.0
|
C8
|
A:G270
|
4.5
|
83.0
|
1.0
|
N2
|
A:G284
|
4.6
|
67.3
|
1.0
|
O3'
|
A:A268
|
4.6
|
84.0
|
1.0
|
C5
|
A:G269
|
4.6
|
78.2
|
1.0
|
C5'
|
A:A268
|
4.6
|
84.0
|
1.0
|
O4
|
A:U271
|
4.9
|
79.7
|
1.0
|
OP2
|
A:G270
|
5.0
|
94.6
|
1.0
|
|
Thallium binding site 3 out
of 17 in 4e8q
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Thallium Binding Sites List in 4e8q
Thallium binding site 3 out
of 17 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+
Mono view
Stereo pair view
|
A full contact list of Thallium with other atoms in the Tl binding
site number 3 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Tl403
b:98.1
occ:0.29
|
O
|
A:HOH508
|
2.3
|
49.9
|
1.0
|
O
|
A:HOH523
|
2.7
|
63.5
|
1.0
|
O6
|
A:G266
|
2.8
|
67.1
|
1.0
|
N7
|
A:G267
|
3.0
|
67.1
|
1.0
|
C6
|
A:G266
|
3.4
|
67.2
|
1.0
|
N7
|
A:G266
|
3.6
|
74.2
|
1.0
|
C5
|
A:G266
|
3.7
|
68.4
|
1.0
|
O6
|
A:G267
|
3.8
|
65.0
|
1.0
|
C5
|
A:G267
|
3.9
|
71.2
|
1.0
|
C8
|
A:G267
|
4.0
|
71.0
|
1.0
|
C6
|
A:G267
|
4.2
|
69.8
|
1.0
|
N1
|
A:G266
|
4.4
|
65.6
|
1.0
|
C8
|
A:G266
|
4.7
|
76.4
|
1.0
|
C4
|
A:G266
|
4.9
|
70.2
|
1.0
|
|
Thallium binding site 4 out
of 17 in 4e8q
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Thallium Binding Sites List in 4e8q
Thallium binding site 4 out
of 17 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+
Mono view
Stereo pair view
|
A full contact list of Thallium with other atoms in the Tl binding
site number 4 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Tl404
b:98.0
occ:0.47
|
O
|
A:HOH518
|
2.0
|
49.0
|
1.0
|
O6
|
A:G320
|
3.0
|
95.4
|
1.0
|
N1
|
A:A297
|
3.1
|
97.8
|
1.0
|
N7
|
A:G320
|
3.1
|
93.0
|
1.0
|
O6
|
A:G321
|
3.4
|
0.9
|
1.0
|
C2
|
A:A297
|
3.6
|
0.3
|
1.0
|
C6
|
A:G320
|
3.6
|
92.3
|
1.0
|
C5
|
A:G320
|
3.7
|
90.4
|
1.0
|
OP2
|
A:G320
|
3.9
|
94.7
|
1.0
|
C6
|
A:A297
|
4.2
|
0.1
|
1.0
|
C6
|
A:G321
|
4.2
|
0.4
|
1.0
|
C8
|
A:G320
|
4.3
|
85.7
|
1.0
|
N6
|
A:A297
|
4.4
|
0.4
|
1.0
|
OP2
|
A:A319
|
4.5
|
94.1
|
1.0
|
N7
|
A:G321
|
4.6
|
0.8
|
1.0
|
O4
|
A:U298
|
4.7
|
93.1
|
1.0
|
C5
|
A:G321
|
4.7
|
98.7
|
1.0
|
N3
|
A:A297
|
4.9
|
0.7
|
1.0
|
O5'
|
A:A319
|
4.9
|
90.0
|
1.0
|
N1
|
A:G320
|
5.0
|
84.2
|
1.0
|
|
Thallium binding site 5 out
of 17 in 4e8q
Go back to
Thallium Binding Sites List in 4e8q
Thallium binding site 5 out
of 17 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+
Mono view
Stereo pair view
|
A full contact list of Thallium with other atoms in the Tl binding
site number 5 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Tl405
b:82.4
occ:0.24
|
N7
|
A:G170
|
2.5
|
59.7
|
1.0
|
O
|
A:HOH507
|
2.8
|
63.6
|
1.0
|
O
|
A:HOH536
|
2.9
|
69.3
|
1.0
|
O6
|
A:G170
|
2.9
|
54.8
|
1.0
|
C5
|
A:G170
|
3.3
|
56.7
|
1.0
|
C6
|
A:G170
|
3.4
|
54.8
|
1.0
|
C8
|
A:G170
|
3.7
|
60.9
|
1.0
|
N7
|
A:G169
|
3.8
|
56.3
|
1.0
|
O6
|
A:G169
|
4.0
|
56.5
|
1.0
|
C5
|
A:G169
|
4.2
|
53.5
|
1.0
|
N7
|
A:A171
|
4.2
|
61.7
|
1.0
|
N6
|
A:A171
|
4.2
|
63.0
|
1.0
|
C6
|
A:G169
|
4.3
|
53.9
|
1.0
|
C4
|
A:G170
|
4.6
|
55.6
|
1.0
|
C8
|
A:G169
|
4.6
|
56.9
|
1.0
|
N9
|
A:G170
|
4.7
|
58.5
|
1.0
|
N1
|
A:G170
|
4.8
|
53.7
|
1.0
|
C5
|
A:A171
|
4.9
|
57.1
|
1.0
|
C6
|
A:A171
|
5.0
|
57.8
|
1.0
|
|
Thallium binding site 6 out
of 17 in 4e8q
Go back to
Thallium Binding Sites List in 4e8q
Thallium binding site 6 out
of 17 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+
Mono view
Stereo pair view
|
A full contact list of Thallium with other atoms in the Tl binding
site number 6 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Tl406
b:90.0
occ:0.30
|
N3
|
A:C377
|
2.7
|
87.8
|
1.0
|
O2
|
A:C377
|
3.2
|
76.7
|
1.0
|
C2
|
A:C377
|
3.3
|
83.7
|
1.0
|
O
|
A:HOH524
|
3.3
|
59.4
|
1.0
|
O6
|
A:G382
|
3.4
|
0.7
|
1.0
|
N4
|
A:C381
|
3.7
|
91.8
|
1.0
|
C4
|
A:C377
|
3.7
|
89.2
|
1.0
|
N4
|
A:C377
|
3.9
|
93.6
|
1.0
|
N4
|
A:C361
|
4.1
|
92.3
|
1.0
|
N4
|
A:C360
|
4.3
|
0.6
|
1.0
|
C6
|
A:G382
|
4.5
|
0.9
|
1.0
|
N1
|
A:C377
|
4.6
|
84.5
|
1.0
|
O6
|
A:G383
|
4.6
|
0.2
|
1.0
|
MG
|
A:MG444
|
4.7
|
82.0
|
1.0
|
C4
|
A:C381
|
4.9
|
0.6
|
1.0
|
C5
|
A:C377
|
4.9
|
89.4
|
1.0
|
|
Thallium binding site 7 out
of 17 in 4e8q
Go back to
Thallium Binding Sites List in 4e8q
Thallium binding site 7 out
of 17 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+
Mono view
Stereo pair view
|
A full contact list of Thallium with other atoms in the Tl binding
site number 7 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Tl407
b:82.5
occ:0.30
|
O
|
A:HOH503
|
2.4
|
54.4
|
1.0
|
O4
|
A:U4
|
2.7
|
76.1
|
1.0
|
OP2
|
A:A376
|
3.1
|
69.8
|
1.0
|
O2'
|
A:U375
|
3.3
|
67.2
|
1.0
|
O3'
|
A:U375
|
3.3
|
76.3
|
1.0
|
O6
|
A:G107
|
3.4
|
67.1
|
1.0
|
C4
|
A:U4
|
3.7
|
71.1
|
1.0
|
P
|
A:A376
|
4.0
|
75.5
|
1.0
|
N3
|
A:U4
|
4.0
|
64.4
|
1.0
|
N7
|
A:A106
|
4.2
|
72.1
|
1.0
|
C3'
|
A:U375
|
4.3
|
72.1
|
1.0
|
C2'
|
A:U375
|
4.4
|
67.8
|
1.0
|
O6
|
A:G3
|
4.4
|
73.5
|
1.0
|
TL
|
A:TL415
|
4.4
|
0.8
|
0.2
|
C6
|
A:G107
|
4.5
|
69.8
|
1.0
|
C8
|
A:A106
|
4.5
|
74.8
|
1.0
|
N7
|
A:G107
|
4.7
|
78.6
|
1.0
|
C4'
|
A:U375
|
4.8
|
66.3
|
1.0
|
O2'
|
A:G1
|
4.8
|
0.8
|
1.0
|
N1
|
A:G5
|
4.8
|
66.7
|
1.0
|
OP1
|
A:A376
|
4.9
|
64.2
|
1.0
|
N7
|
A:G3
|
5.0
|
73.2
|
1.0
|
|
Thallium binding site 8 out
of 17 in 4e8q
Go back to
Thallium Binding Sites List in 4e8q
Thallium binding site 8 out
of 17 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+
Mono view
Stereo pair view
|
A full contact list of Thallium with other atoms in the Tl binding
site number 8 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Tl408
b:0.7
occ:0.40
|
O6
|
A:G275
|
3.2
|
90.2
|
1.0
|
N7
|
A:G275
|
3.2
|
83.0
|
1.0
|
C6
|
A:G275
|
3.8
|
82.1
|
1.0
|
C5
|
A:G275
|
3.8
|
81.2
|
1.0
|
C8
|
A:G275
|
4.3
|
82.5
|
1.0
|
OP2
|
A:A277
|
4.4
|
78.9
|
1.0
|
OP1
|
A:A277
|
4.6
|
84.1
|
1.0
|
O
|
A:HOH547
|
4.7
|
67.0
|
1.0
|
|
Thallium binding site 9 out
of 17 in 4e8q
Go back to
Thallium Binding Sites List in 4e8q
Thallium binding site 9 out
of 17 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+
Mono view
Stereo pair view
|
A full contact list of Thallium with other atoms in the Tl binding
site number 9 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Tl409
b:60.6
occ:0.21
|
O
|
A:HOH538
|
2.6
|
37.4
|
1.0
|
O6
|
A:G87
|
2.7
|
64.9
|
1.0
|
O4
|
A:U96
|
3.2
|
71.1
|
1.0
|
O6
|
A:G97
|
3.2
|
56.0
|
1.0
|
N6
|
A:A95
|
3.3
|
62.9
|
1.0
|
N4
|
A:C86
|
3.3
|
68.0
|
1.0
|
O4
|
A:U88
|
3.7
|
69.3
|
1.0
|
C6
|
A:G87
|
3.7
|
65.3
|
1.0
|
C4
|
A:U96
|
4.0
|
64.2
|
1.0
|
N3
|
A:U96
|
4.1
|
60.0
|
1.0
|
C6
|
A:G97
|
4.1
|
55.0
|
1.0
|
N7
|
A:G87
|
4.1
|
70.2
|
1.0
|
C4
|
A:C86
|
4.2
|
68.4
|
1.0
|
C5
|
A:G87
|
4.3
|
67.3
|
1.0
|
C6
|
A:A95
|
4.3
|
62.3
|
1.0
|
C4
|
A:U88
|
4.4
|
68.8
|
1.0
|
N1
|
A:G97
|
4.6
|
55.7
|
1.0
|
N1
|
A:A95
|
4.8
|
62.9
|
1.0
|
C5
|
A:C86
|
4.8
|
70.8
|
1.0
|
O
|
A:HOH537
|
4.8
|
62.3
|
1.0
|
N3
|
A:C86
|
4.9
|
67.2
|
1.0
|
N1
|
A:G87
|
4.9
|
63.6
|
1.0
|
N3
|
A:U88
|
5.0
|
67.8
|
1.0
|
|
Thallium binding site 10 out
of 17 in 4e8q
Go back to
Thallium Binding Sites List in 4e8q
Thallium binding site 10 out
of 17 in the Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+
Mono view
Stereo pair view
|
A full contact list of Thallium with other atoms in the Tl binding
site number 10 of Structure of Oceanobacillus Iheyensis Group II Intron in A Ligand-Free State in the Presence of Tl+ and MG2+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Tl410
b:83.9
occ:0.30
|
O2'
|
A:G32
|
2.9
|
83.4
|
1.0
|
O6
|
A:G34
|
3.0
|
68.3
|
1.0
|
N7
|
A:A33
|
3.2
|
73.5
|
1.0
|
C6
|
A:G34
|
3.9
|
68.0
|
1.0
|
C8
|
A:A33
|
4.1
|
72.8
|
1.0
|
N6
|
A:A33
|
4.2
|
79.2
|
1.0
|
O3'
|
A:G32
|
4.2
|
92.5
|
1.0
|
C5
|
A:A33
|
4.3
|
73.3
|
1.0
|
C2'
|
A:G32
|
4.3
|
82.1
|
1.0
|
N7
|
A:G34
|
4.5
|
69.5
|
1.0
|
C5
|
A:G34
|
4.5
|
69.0
|
1.0
|
C6
|
A:A33
|
4.7
|
75.9
|
1.0
|
C3'
|
A:G32
|
4.7
|
89.7
|
1.0
|
C4'
|
A:G32
|
4.7
|
89.4
|
1.0
|
N1
|
A:G34
|
4.9
|
68.7
|
1.0
|
|
Reference:
M.Marcia,
A.M.Pyle.
Visualizing Group II Intron Catalysis Through the Stages of Splicing. Cell(Cambridge,Mass.) V. 151 497 2012.
ISSN: ISSN 0092-8674
PubMed: 23101623
DOI: 10.1016/J.CELL.2012.09.033
Page generated: Fri Oct 11 09:54:38 2024
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