Magnesium in PDB 6j7t: Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant D82A From Mycobacterium Tuberculosis
Protein crystallography data
The structure of Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant D82A From Mycobacterium Tuberculosis, PDB code: 6j7t
was solved by
X.Yu,
X.Gao,
K.Zhu,
J.A.Wojdyla,
M.Wang,
S.Cui,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.37 /
1.90
|
Space group
|
P 32 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
94.692,
94.692,
61.836,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
18.8 /
20.6
|
Magnesium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
15;
Binding sites:
The binding sites of Magnesium atom in the Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant D82A From Mycobacterium Tuberculosis
(pdb code 6j7t). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 15 binding sites of Magnesium where determined in the
Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant D82A From Mycobacterium Tuberculosis, PDB code: 6j7t:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 15 in 6j7t
Go back to
Magnesium Binding Sites List in 6j7t
Magnesium binding site 1 out
of 15 in the Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant D82A From Mycobacterium Tuberculosis
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant D82A From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg301
b:40.5
occ:1.00
|
H
|
A:MSE225
|
2.1
|
33.2
|
1.0
|
HB2
|
A:MSE225
|
2.6
|
41.0
|
1.0
|
H
|
A:LEU224
|
2.8
|
34.3
|
1.0
|
N
|
A:MSE225
|
2.9
|
27.7
|
1.0
|
HB3
|
A:LEU224
|
3.0
|
38.1
|
1.0
|
O
|
A:ALA222
|
3.1
|
34.9
|
1.0
|
HA
|
A:ALA222
|
3.2
|
46.8
|
1.0
|
O
|
A:ASP221
|
3.2
|
33.9
|
1.0
|
N
|
A:LEU224
|
3.3
|
28.5
|
1.0
|
CB
|
A:MSE225
|
3.4
|
34.2
|
1.0
|
C
|
A:ALA222
|
3.4
|
38.1
|
1.0
|
HE2
|
A:MSE225
|
3.5
|
43.5
|
1.0
|
HD3
|
A:PRO226
|
3.6
|
39.8
|
1.0
|
HB3
|
A:MSE225
|
3.6
|
41.0
|
1.0
|
CB
|
A:LEU224
|
3.7
|
31.7
|
1.0
|
CA
|
A:MSE225
|
3.8
|
30.5
|
1.0
|
C
|
A:LEU224
|
3.8
|
27.8
|
1.0
|
CA
|
A:ALA222
|
3.8
|
39.0
|
1.0
|
CA
|
A:LEU224
|
3.8
|
27.2
|
1.0
|
HD2
|
A:PRO226
|
3.9
|
39.8
|
1.0
|
HB2
|
A:LEU224
|
4.0
|
38.1
|
1.0
|
N
|
A:ASP223
|
4.1
|
35.9
|
1.0
|
C
|
A:ASP223
|
4.2
|
32.0
|
1.0
|
CD
|
A:PRO226
|
4.2
|
33.1
|
1.0
|
C
|
A:ASP221
|
4.2
|
39.2
|
1.0
|
HA
|
A:MSE225
|
4.3
|
36.6
|
1.0
|
HB1
|
A:ALA290
|
4.3
|
39.2
|
1.0
|
CE
|
A:MSE225
|
4.4
|
36.2
|
1.0
|
HA
|
A:ASP223
|
4.5
|
41.3
|
1.0
|
CA
|
A:ASP223
|
4.5
|
34.4
|
1.0
|
N
|
A:ALA222
|
4.5
|
36.0
|
1.0
|
H
|
A:ASP223
|
4.6
|
43.1
|
1.0
|
CG
|
A:MSE225
|
4.6
|
51.7
|
1.0
|
HA
|
A:LEU224
|
4.7
|
32.7
|
1.0
|
HD23
|
A:LEU224
|
4.8
|
51.1
|
1.0
|
HE3
|
A:MSE225
|
4.9
|
43.5
|
1.0
|
SE
|
A:MSE225
|
4.9
|
68.2
|
1.0
|
HB1
|
A:ALA222
|
4.9
|
46.1
|
1.0
|
C
|
A:MSE225
|
4.9
|
26.8
|
1.0
|
O
|
A:LEU224
|
4.9
|
25.4
|
1.0
|
HE1
|
A:MSE225
|
5.0
|
43.5
|
1.0
|
N
|
A:PRO226
|
5.0
|
26.4
|
1.0
|
HG3
|
A:MSE225
|
5.0
|
62.1
|
1.0
|
|
Magnesium binding site 2 out
of 15 in 6j7t
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Magnesium Binding Sites List in 6j7t
Magnesium binding site 2 out
of 15 in the Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant D82A From Mycobacterium Tuberculosis
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant D82A From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg302
b:35.2
occ:1.00
|
HH11
|
A:ARG138
|
2.6
|
61.9
|
1.0
|
H
|
A:ARG13
|
2.6
|
40.3
|
1.0
|
HD2
|
A:ARG138
|
2.8
|
56.2
|
1.0
|
HB3
|
A:LEU12
|
2.9
|
41.1
|
1.0
|
HB2
|
A:ASN11
|
2.9
|
39.1
|
1.0
|
H
|
A:LEU12
|
3.1
|
41.7
|
1.0
|
NH1
|
A:ARG138
|
3.4
|
51.6
|
1.0
|
N
|
A:ARG13
|
3.4
|
33.6
|
1.0
|
N
|
A:LEU12
|
3.5
|
34.7
|
1.0
|
CD
|
A:ARG138
|
3.7
|
46.8
|
1.0
|
CB
|
A:LEU12
|
3.7
|
34.2
|
1.0
|
HH12
|
A:ARG138
|
3.7
|
61.9
|
1.0
|
HB2
|
A:ARG13
|
3.8
|
50.1
|
1.0
|
CB
|
A:ASN11
|
3.8
|
32.5
|
1.0
|
HB3
|
A:ARG13
|
3.9
|
50.1
|
1.0
|
CA
|
A:LEU12
|
4.0
|
32.5
|
1.0
|
CG
|
A:ASN11
|
4.1
|
32.9
|
1.0
|
OD1
|
A:ASN11
|
4.1
|
37.2
|
1.0
|
HD3
|
A:ARG138
|
4.1
|
56.2
|
1.0
|
CB
|
A:ARG13
|
4.2
|
41.7
|
1.0
|
O
|
A:HOH453
|
4.2
|
31.2
|
1.0
|
C
|
A:LEU12
|
4.2
|
28.7
|
1.0
|
HG2
|
A:ARG138
|
4.2
|
53.9
|
1.0
|
HH21
|
A:ARG13
|
4.2
|
72.7
|
1.0
|
HB2
|
A:LEU12
|
4.2
|
41.1
|
1.0
|
NH2
|
A:ARG13
|
4.3
|
60.6
|
1.0
|
HD23
|
A:LEU12
|
4.3
|
48.7
|
1.0
|
HB3
|
A:ASN11
|
4.3
|
39.1
|
1.0
|
CZ
|
A:ARG138
|
4.4
|
47.8
|
1.0
|
CA
|
A:ARG13
|
4.4
|
34.9
|
1.0
|
C
|
A:ASN11
|
4.4
|
28.6
|
1.0
|
HH22
|
A:ARG13
|
4.4
|
72.7
|
1.0
|
CG
|
A:ARG138
|
4.5
|
44.9
|
1.0
|
NE
|
A:ARG138
|
4.5
|
50.9
|
1.0
|
O
|
A:HOH404
|
4.6
|
42.3
|
1.0
|
HB2
|
A:ARG138
|
4.6
|
41.6
|
1.0
|
CA
|
A:ASN11
|
4.6
|
38.2
|
1.0
|
HG
|
A:LEU12
|
4.7
|
47.7
|
1.0
|
HB3
|
A:ARG138
|
4.7
|
41.6
|
1.0
|
CG
|
A:LEU12
|
4.8
|
39.8
|
1.0
|
CZ
|
A:ARG13
|
4.8
|
67.9
|
1.0
|
HA
|
A:ARG13
|
4.8
|
41.8
|
1.0
|
CB
|
A:ARG138
|
4.9
|
34.6
|
1.0
|
HA
|
A:ASN11
|
4.9
|
45.9
|
1.0
|
ND2
|
A:ASN11
|
4.9
|
44.8
|
1.0
|
HA
|
A:LEU12
|
4.9
|
39.0
|
1.0
|
HE
|
A:ARG13
|
5.0
|
72.5
|
1.0
|
|
Magnesium binding site 3 out
of 15 in 6j7t
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Magnesium Binding Sites List in 6j7t
Magnesium binding site 3 out
of 15 in the Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant D82A From Mycobacterium Tuberculosis
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant D82A From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg303
b:33.7
occ:1.00
|
H
|
A:PHE158
|
2.3
|
26.6
|
1.0
|
HB3
|
A:GLN157
|
2.8
|
39.7
|
1.0
|
O
|
A:HOH567
|
2.9
|
48.5
|
1.0
|
HA
|
A:GLN157
|
3.0
|
31.3
|
1.0
|
N
|
A:PHE158
|
3.1
|
22.2
|
1.0
|
O
|
A:PHE158
|
3.4
|
21.6
|
1.0
|
CB
|
A:GLN157
|
3.5
|
33.0
|
1.0
|
CA
|
A:GLN157
|
3.6
|
26.1
|
1.0
|
CD1
|
A:PHE158
|
3.8
|
25.6
|
1.0
|
HD1
|
A:PHE158
|
3.8
|
30.7
|
1.0
|
C
|
A:GLN157
|
3.9
|
22.6
|
1.0
|
CE1
|
A:PHE158
|
3.9
|
25.3
|
1.0
|
HG2
|
A:GLN157
|
4.0
|
49.7
|
1.0
|
HE1
|
A:PHE158
|
4.1
|
30.4
|
1.0
|
HG3
|
A:GLN157
|
4.1
|
49.7
|
1.0
|
CG
|
A:GLN157
|
4.1
|
41.4
|
1.0
|
CA
|
A:PHE158
|
4.2
|
20.2
|
1.0
|
C
|
A:PHE158
|
4.2
|
20.3
|
1.0
|
CG
|
A:PHE158
|
4.2
|
20.6
|
1.0
|
HB2
|
A:GLN157
|
4.3
|
39.7
|
1.0
|
CZ
|
A:PHE158
|
4.5
|
23.9
|
1.0
|
H31
|
A:GOL316
|
4.6
|
48.0
|
1.0
|
O
|
A:HOH480
|
4.7
|
22.8
|
1.0
|
CD2
|
A:PHE158
|
4.8
|
21.9
|
1.0
|
CB
|
A:PHE158
|
4.8
|
19.4
|
1.0
|
CE2
|
A:PHE158
|
4.9
|
24.9
|
1.0
|
N
|
A:GLN157
|
4.9
|
28.9
|
1.0
|
HZ
|
A:PHE158
|
5.0
|
28.7
|
1.0
|
HA
|
A:PHE158
|
5.0
|
24.3
|
1.0
|
O
|
A:ASP156
|
5.0
|
35.1
|
1.0
|
|
Magnesium binding site 4 out
of 15 in 6j7t
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Magnesium Binding Sites List in 6j7t
Magnesium binding site 4 out
of 15 in the Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant D82A From Mycobacterium Tuberculosis
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant D82A From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg304
b:43.8
occ:1.00
|
HH11
|
A:ARG286
|
2.4
|
55.4
|
1.0
|
HD3
|
A:ARG286
|
2.5
|
45.9
|
1.0
|
HA
|
A:PHE283
|
2.9
|
22.3
|
1.0
|
OE2
|
A:GLU216
|
3.0
|
65.2
|
1.0
|
NH1
|
A:ARG286
|
3.2
|
46.2
|
1.0
|
CD
|
A:ARG286
|
3.4
|
38.2
|
1.0
|
HD1
|
A:PHE283
|
3.4
|
30.6
|
1.0
|
HB2
|
A:ARG286
|
3.5
|
30.3
|
1.0
|
O
|
A:HOH425
|
3.5
|
24.3
|
1.0
|
HD2
|
A:ARG286
|
3.5
|
45.9
|
1.0
|
HH12
|
A:ARG286
|
3.6
|
55.4
|
1.0
|
CA
|
A:PHE283
|
3.7
|
18.5
|
1.0
|
HB3
|
A:ARG286
|
3.7
|
30.3
|
1.0
|
O
|
A:ARG282
|
3.8
|
17.7
|
1.0
|
N
|
A:PHE283
|
3.9
|
19.0
|
1.0
|
HB2
|
A:PHE283
|
3.9
|
25.8
|
1.0
|
HB3
|
A:ARG282
|
3.9
|
27.1
|
1.0
|
C
|
A:ARG282
|
4.0
|
20.1
|
1.0
|
CB
|
A:ARG286
|
4.0
|
25.2
|
1.0
|
CZ
|
A:ARG286
|
4.1
|
50.9
|
1.0
|
CD1
|
A:PHE283
|
4.1
|
25.5
|
1.0
|
NE
|
A:ARG286
|
4.2
|
50.3
|
1.0
|
CD
|
A:GLU216
|
4.2
|
44.2
|
1.0
|
CB
|
A:PHE283
|
4.3
|
21.5
|
1.0
|
H
|
A:PHE283
|
4.3
|
22.8
|
1.0
|
CG
|
A:ARG286
|
4.3
|
36.2
|
1.0
|
HB2
|
A:ARG282
|
4.5
|
27.1
|
1.0
|
HG3
|
A:GLU216
|
4.6
|
32.5
|
1.0
|
CB
|
A:ARG282
|
4.6
|
22.6
|
1.0
|
CG
|
A:PHE283
|
4.6
|
23.6
|
1.0
|
O
|
A:HOH462
|
4.8
|
26.2
|
1.0
|
C
|
A:PHE283
|
4.9
|
18.1
|
1.0
|
HG2
|
A:ARG286
|
4.9
|
43.4
|
1.0
|
H
|
A:ARG286
|
4.9
|
27.8
|
1.0
|
CA
|
A:ARG282
|
5.0
|
18.8
|
1.0
|
CG
|
A:GLU216
|
5.0
|
27.1
|
1.0
|
HE
|
A:ARG286
|
5.0
|
60.4
|
1.0
|
HG3
|
A:ARG286
|
5.0
|
43.4
|
1.0
|
|
Magnesium binding site 5 out
of 15 in 6j7t
Go back to
Magnesium Binding Sites List in 6j7t
Magnesium binding site 5 out
of 15 in the Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant D82A From Mycobacterium Tuberculosis
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant D82A From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg305
b:54.3
occ:1.00
|
HH11
|
A:ARG246
|
2.2
|
89.6
|
1.0
|
NH1
|
A:ARG246
|
2.3
|
74.7
|
1.0
|
HH12
|
A:ARG246
|
2.5
|
89.6
|
1.0
|
CZ
|
A:ARG246
|
3.1
|
72.8
|
1.0
|
HD2
|
A:ARG246
|
3.2
|
81.7
|
1.0
|
NE
|
A:ARG246
|
3.7
|
71.5
|
1.0
|
CD
|
A:ARG246
|
3.8
|
68.0
|
1.0
|
NH2
|
A:ARG246
|
3.9
|
68.6
|
1.0
|
HD3
|
A:ARG246
|
4.0
|
81.7
|
1.0
|
HH22
|
A:ARG246
|
4.0
|
82.4
|
1.0
|
HE
|
A:ARG246
|
4.4
|
85.9
|
1.0
|
HH21
|
A:ARG246
|
4.6
|
82.4
|
1.0
|
|
Magnesium binding site 6 out
of 15 in 6j7t
Go back to
Magnesium Binding Sites List in 6j7t
Magnesium binding site 6 out
of 15 in the Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant D82A From Mycobacterium Tuberculosis
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant D82A From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg306
b:43.4
occ:1.00
|
H
|
A:ALA248
|
2.2
|
33.1
|
1.0
|
O
|
A:ALA248
|
2.5
|
34.6
|
1.0
|
N
|
A:ALA248
|
2.7
|
27.5
|
1.0
|
HA
|
A:THR194
|
2.7
|
28.0
|
1.0
|
O
|
A:VAL193
|
2.8
|
18.8
|
1.0
|
HA
|
A:VAL247
|
3.0
|
32.7
|
1.0
|
HG22
|
A:THR194
|
3.0
|
26.2
|
1.0
|
C
|
A:ALA248
|
3.3
|
31.5
|
1.0
|
HB3
|
A:ALA248
|
3.4
|
37.5
|
1.0
|
CA
|
A:ALA248
|
3.4
|
28.6
|
1.0
|
C
|
A:VAL247
|
3.5
|
30.5
|
1.0
|
HG13
|
A:VAL247
|
3.5
|
34.1
|
1.0
|
HH2
|
A:TRP253
|
3.6
|
24.0
|
1.0
|
CA
|
A:THR194
|
3.6
|
23.4
|
1.0
|
CA
|
A:VAL247
|
3.7
|
27.2
|
1.0
|
C
|
A:VAL193
|
3.7
|
18.8
|
1.0
|
HZ3
|
A:TRP253
|
3.8
|
21.7
|
1.0
|
HG22
|
A:VAL193
|
3.8
|
24.9
|
1.0
|
CG2
|
A:THR194
|
3.9
|
21.8
|
1.0
|
CB
|
A:ALA248
|
3.9
|
31.2
|
1.0
|
HG13
|
A:VAL193
|
4.0
|
20.8
|
1.0
|
O
|
A:ARG246
|
4.0
|
26.5
|
1.0
|
HG12
|
A:VAL247
|
4.1
|
34.1
|
1.0
|
N
|
A:THR194
|
4.1
|
19.1
|
1.0
|
CH2
|
A:TRP253
|
4.1
|
20.0
|
1.0
|
CG1
|
A:VAL247
|
4.2
|
28.4
|
1.0
|
CZ3
|
A:TRP253
|
4.2
|
18.1
|
1.0
|
CB
|
A:THR194
|
4.2
|
20.3
|
1.0
|
HG23
|
A:THR194
|
4.3
|
26.2
|
1.0
|
HA
|
A:ALA248
|
4.3
|
34.3
|
1.0
|
HB
|
A:THR194
|
4.3
|
24.4
|
1.0
|
HB2
|
A:ALA248
|
4.4
|
37.5
|
1.0
|
O
|
A:VAL247
|
4.5
|
35.5
|
1.0
|
CB
|
A:VAL247
|
4.6
|
28.4
|
1.0
|
HG21
|
A:THR194
|
4.6
|
26.2
|
1.0
|
N
|
A:THR249
|
4.6
|
23.0
|
1.0
|
C
|
A:THR194
|
4.7
|
24.1
|
1.0
|
HB1
|
A:ALA248
|
4.7
|
37.5
|
1.0
|
N
|
A:VAL247
|
4.7
|
25.6
|
1.0
|
CG2
|
A:VAL193
|
4.8
|
20.7
|
1.0
|
C
|
A:ARG246
|
4.8
|
25.9
|
1.0
|
HA
|
A:THR249
|
4.8
|
29.8
|
1.0
|
H
|
A:THR194
|
4.9
|
23.0
|
1.0
|
CG1
|
A:VAL193
|
4.9
|
17.3
|
1.0
|
HG22
|
A:VAL247
|
5.0
|
36.8
|
1.0
|
CA
|
A:VAL193
|
5.0
|
18.6
|
1.0
|
HD21
|
A:LEU209
|
5.0
|
20.2
|
1.0
|
|
Magnesium binding site 7 out
of 15 in 6j7t
Go back to
Magnesium Binding Sites List in 6j7t
Magnesium binding site 7 out
of 15 in the Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant D82A From Mycobacterium Tuberculosis
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant D82A From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg307
b:40.6
occ:1.00
|
HG1
|
A:THR112
|
2.1
|
27.9
|
1.0
|
O
|
A:ALA113
|
2.5
|
26.5
|
1.0
|
HA
|
A:PHE129
|
2.8
|
26.7
|
1.0
|
OG1
|
A:THR112
|
2.8
|
23.3
|
1.0
|
HB
|
A:THR112
|
3.1
|
28.0
|
1.0
|
H
|
A:ALA113
|
3.2
|
27.9
|
1.0
|
N
|
A:ALA113
|
3.4
|
23.2
|
1.0
|
HB2
|
A:PHE129
|
3.5
|
27.1
|
1.0
|
HB3
|
A:PHE129
|
3.5
|
27.1
|
1.0
|
C
|
A:ALA113
|
3.5
|
25.3
|
1.0
|
CB
|
A:THR112
|
3.5
|
23.3
|
1.0
|
CA
|
A:PHE129
|
3.7
|
22.2
|
1.0
|
CB
|
A:PHE129
|
3.7
|
22.6
|
1.0
|
HB3
|
A:ALA113
|
3.9
|
30.6
|
1.0
|
C
|
A:THR112
|
3.9
|
21.2
|
1.0
|
CA
|
A:ALA113
|
4.0
|
24.9
|
1.0
|
H
|
A:THR130
|
4.1
|
25.2
|
1.0
|
O
|
A:ARG128
|
4.1
|
23.8
|
1.0
|
O
|
A:HOH466
|
4.3
|
25.8
|
1.0
|
CA
|
A:THR112
|
4.3
|
22.9
|
1.0
|
N
|
A:THR130
|
4.5
|
21.0
|
1.0
|
CB
|
A:ALA113
|
4.5
|
25.5
|
1.0
|
C
|
A:PHE129
|
4.5
|
21.6
|
1.0
|
HA
|
A:PRO114
|
4.5
|
32.9
|
1.0
|
O
|
A:THR112
|
4.6
|
23.8
|
1.0
|
HB2
|
A:GLU115
|
4.6
|
42.7
|
1.0
|
HB
|
A:THR130
|
4.6
|
33.1
|
1.0
|
N
|
A:PRO114
|
4.6
|
26.8
|
1.0
|
HG21
|
A:THR112
|
4.6
|
33.0
|
1.0
|
N
|
A:PHE129
|
4.7
|
21.4
|
1.0
|
CG2
|
A:THR112
|
4.7
|
27.4
|
1.0
|
C
|
A:ARG128
|
4.8
|
22.7
|
1.0
|
H
|
A:GLU115
|
4.8
|
32.7
|
1.0
|
HA
|
A:ALA113
|
4.8
|
29.9
|
1.0
|
CA
|
A:PRO114
|
5.0
|
27.4
|
1.0
|
HA
|
A:THR112
|
5.0
|
27.5
|
1.0
|
|
Magnesium binding site 8 out
of 15 in 6j7t
Go back to
Magnesium Binding Sites List in 6j7t
Magnesium binding site 8 out
of 15 in the Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant D82A From Mycobacterium Tuberculosis
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant D82A From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg308
b:37.5
occ:1.00
|
HH2
|
A:TRP184
|
2.6
|
27.3
|
1.0
|
H
|
A:GLY153
|
2.8
|
30.5
|
1.0
|
HB1
|
A:ALA152
|
3.0
|
32.9
|
1.0
|
HZ2
|
A:TRP184
|
3.2
|
28.7
|
1.0
|
HA3
|
A:GLY153
|
3.3
|
33.0
|
1.0
|
N
|
A:GLY153
|
3.4
|
25.4
|
1.0
|
CH2
|
A:TRP184
|
3.4
|
22.7
|
1.0
|
CZ2
|
A:TRP184
|
3.7
|
23.9
|
1.0
|
HB2
|
A:ALA233
|
3.7
|
26.6
|
1.0
|
HB1
|
A:ALA233
|
3.8
|
26.6
|
1.0
|
CA
|
A:GLY153
|
3.9
|
27.5
|
1.0
|
CB
|
A:ALA152
|
3.9
|
27.4
|
1.0
|
CB
|
A:ALA233
|
4.1
|
22.1
|
1.0
|
HB3
|
A:ALA152
|
4.2
|
32.9
|
1.0
|
C
|
A:ALA152
|
4.2
|
28.0
|
1.0
|
HB3
|
A:ALA233
|
4.3
|
26.6
|
1.0
|
CA
|
A:ALA152
|
4.5
|
27.0
|
1.0
|
HA2
|
A:GLY153
|
4.5
|
33.0
|
1.0
|
HB2
|
A:ALA152
|
4.5
|
32.9
|
1.0
|
HA
|
A:ALA152
|
4.6
|
32.4
|
1.0
|
CZ3
|
A:TRP184
|
4.6
|
22.6
|
1.0
|
HZ3
|
A:TRP184
|
4.8
|
27.1
|
1.0
|
C
|
A:GLY153
|
4.9
|
25.1
|
1.0
|
|
Magnesium binding site 9 out
of 15 in 6j7t
Go back to
Magnesium Binding Sites List in 6j7t
Magnesium binding site 9 out
of 15 in the Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant D82A From Mycobacterium Tuberculosis
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant D82A From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg309
b:51.5
occ:1.00
|
O
|
A:HOH475
|
2.9
|
40.0
|
1.0
|
O
|
A:HOH421
|
2.9
|
38.8
|
1.0
|
HB1
|
A:ALA258
|
3.1
|
20.8
|
1.0
|
HB2
|
A:ALA258
|
3.5
|
20.8
|
1.0
|
CB
|
A:ALA258
|
3.8
|
17.3
|
1.0
|
HB3
|
A:ALA258
|
4.4
|
20.8
|
1.0
|
MG
|
A:MG313
|
4.5
|
34.4
|
1.0
|
O
|
A:ARG271
|
4.5
|
18.8
|
1.0
|
HA
|
A:ALA258
|
4.6
|
18.9
|
1.0
|
CA
|
A:ALA258
|
4.8
|
15.7
|
1.0
|
|
Magnesium binding site 10 out
of 15 in 6j7t
Go back to
Magnesium Binding Sites List in 6j7t
Magnesium binding site 10 out
of 15 in the Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant D82A From Mycobacterium Tuberculosis
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Crystal Structure of Toxin Tglt (Unusual Type Guanylyltransferase-Like Toxin, RV1045) Mutant D82A From Mycobacterium Tuberculosis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg310
b:65.2
occ:1.00
|
OH
|
A:TYR5
|
2.1
|
55.4
|
1.0
|
HH12
|
A:ARG25
|
2.3
|
78.3
|
1.0
|
HG23
|
A:VAL22
|
2.5
|
48.7
|
1.0
|
HH
|
A:TYR5
|
2.7
|
66.5
|
1.0
|
HE2
|
A:TYR5
|
2.7
|
48.4
|
1.0
|
HB3
|
A:GLN21
|
2.7
|
61.8
|
1.0
|
NH1
|
A:ARG25
|
2.8
|
65.2
|
1.0
|
HG22
|
A:VAL22
|
2.9
|
48.7
|
1.0
|
CZ
|
A:TYR5
|
3.0
|
47.2
|
1.0
|
HH11
|
A:ARG25
|
3.0
|
78.3
|
1.0
|
CG2
|
A:VAL22
|
3.1
|
40.5
|
1.0
|
CE2
|
A:TYR5
|
3.2
|
40.3
|
1.0
|
HB2
|
A:GLN21
|
3.2
|
61.8
|
1.0
|
CB
|
A:GLN21
|
3.4
|
51.5
|
1.0
|
H
|
A:VAL22
|
3.5
|
53.9
|
1.0
|
HH22
|
A:ARG25
|
3.5
|
90.8
|
1.0
|
N
|
A:VAL22
|
3.6
|
44.9
|
1.0
|
CZ
|
A:ARG25
|
3.6
|
86.0
|
1.0
|
O
|
A:ARG18
|
3.7
|
35.0
|
1.0
|
HG21
|
A:VAL22
|
3.7
|
48.7
|
1.0
|
OE1
|
A:GLN21
|
3.8
|
66.4
|
1.0
|
HA
|
A:VAL22
|
3.8
|
54.5
|
1.0
|
NH2
|
A:ARG25
|
3.9
|
75.6
|
1.0
|
C
|
A:GLN21
|
3.9
|
48.2
|
1.0
|
HA
|
A:ARG18
|
4.0
|
40.3
|
1.0
|
CA
|
A:VAL22
|
4.1
|
45.4
|
1.0
|
CB
|
A:VAL22
|
4.2
|
43.0
|
1.0
|
CE1
|
A:TYR5
|
4.3
|
45.3
|
1.0
|
HB3
|
A:ARG18
|
4.3
|
35.6
|
1.0
|
CA
|
A:GLN21
|
4.3
|
48.8
|
1.0
|
O
|
A:GLN21
|
4.5
|
46.9
|
1.0
|
CD2
|
A:TYR5
|
4.5
|
41.3
|
1.0
|
CG
|
A:GLN21
|
4.5
|
57.5
|
1.0
|
CD
|
A:GLN21
|
4.5
|
68.7
|
1.0
|
HD2
|
A:ARG25
|
4.5
|
88.2
|
1.0
|
O
|
A:LEU168
|
4.6
|
40.9
|
1.0
|
HE1
|
A:TYR5
|
4.6
|
54.4
|
1.0
|
C
|
A:ARG18
|
4.6
|
33.9
|
1.0
|
HB
|
A:VAL22
|
4.6
|
51.6
|
1.0
|
HH21
|
A:ARG25
|
4.6
|
90.8
|
1.0
|
NE
|
A:ARG25
|
4.7
|
91.2
|
1.0
|
CA
|
A:ARG18
|
4.7
|
33.6
|
1.0
|
HG2
|
A:ARG18
|
4.7
|
40.4
|
1.0
|
HG2
|
A:GLN21
|
4.9
|
69.0
|
1.0
|
CB
|
A:ARG18
|
4.9
|
29.7
|
1.0
|
HG12
|
A:VAL169
|
4.9
|
41.0
|
1.0
|
HD2
|
A:TYR5
|
4.9
|
49.6
|
1.0
|
HA
|
A:VAL169
|
4.9
|
35.4
|
1.0
|
HA
|
A:GLN21
|
5.0
|
58.6
|
1.0
|
|
Reference:
X.Yu,
X.Gao,
K.Zhu,
H.Yin,
X.Mao,
J.A.Wojdyla,
B.Qin,
H.Huang,
M.Wang,
Y.Sun,
S.Cui.
Characterization of A Toxin-Antitoxin System in Mycobacterium Tuberculosis Suggests Neutralization By Phosphorylation As the Antitoxicity Mechanism Commun Biol 2020.
ISSN: ESSN 2399-3642
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