Magnesium in PDB 8bo1: Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin, Bound to Latrunculin-B-Atp-Mg-Actin, and 3'-Deoxyadenosine-5'- Triphosphate and 2 Mg Ions
Enzymatic activity of Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin, Bound to Latrunculin-B-Atp-Mg-Actin, and 3'-Deoxyadenosine-5'- Triphosphate and 2 Mg Ions
All present enzymatic activity of Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin, Bound to Latrunculin-B-Atp-Mg-Actin, and 3'-Deoxyadenosine-5'- Triphosphate and 2 Mg Ions:
4.6.1.1;
Protein crystallography data
The structure of Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin, Bound to Latrunculin-B-Atp-Mg-Actin, and 3'-Deoxyadenosine-5'- Triphosphate and 2 Mg Ions, PDB code: 8bo1
was solved by
M.Teixeira-Nunes,
L.Renault,
P.Retailleau,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.24 /
2.50
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
75.5,
132.169,
96.027,
90,
110.8,
90
|
R / Rfree (%)
|
19.1 /
23.1
|
Other elements in 8bo1:
The structure of Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin, Bound to Latrunculin-B-Atp-Mg-Actin, and 3'-Deoxyadenosine-5'- Triphosphate and 2 Mg Ions also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin, Bound to Latrunculin-B-Atp-Mg-Actin, and 3'-Deoxyadenosine-5'- Triphosphate and 2 Mg Ions
(pdb code 8bo1). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the
Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin, Bound to Latrunculin-B-Atp-Mg-Actin, and 3'-Deoxyadenosine-5'- Triphosphate and 2 Mg Ions, PDB code: 8bo1:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 8bo1
Go back to
Magnesium Binding Sites List in 8bo1
Magnesium binding site 1 out
of 6 in the Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin, Bound to Latrunculin-B-Atp-Mg-Actin, and 3'-Deoxyadenosine-5'- Triphosphate and 2 Mg Ions
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin, Bound to Latrunculin-B-Atp-Mg-Actin, and 3'-Deoxyadenosine-5'- Triphosphate and 2 Mg Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg403
b:54.6
occ:1.00
|
O
|
A:HOH516
|
1.9
|
41.8
|
1.0
|
O3G
|
A:ATP402
|
1.9
|
72.7
|
1.0
|
O
|
A:HOH524
|
2.0
|
54.3
|
1.0
|
O1B
|
A:ATP402
|
2.1
|
67.5
|
1.0
|
O
|
A:HOH509
|
2.5
|
78.0
|
1.0
|
O
|
A:HOH523
|
2.8
|
63.6
|
1.0
|
PG
|
A:ATP402
|
3.0
|
72.5
|
1.0
|
PB
|
A:ATP402
|
3.2
|
67.6
|
1.0
|
O3B
|
A:ATP402
|
3.3
|
70.0
|
1.0
|
O1G
|
A:ATP402
|
3.6
|
73.3
|
1.0
|
O
|
A:HOH538
|
3.9
|
77.3
|
1.0
|
OE1
|
A:GLN137
|
3.9
|
72.1
|
1.0
|
O3A
|
A:ATP402
|
4.0
|
67.0
|
1.0
|
O2A
|
A:ATP402
|
4.2
|
66.1
|
1.0
|
O2G
|
A:ATP402
|
4.3
|
73.4
|
1.0
|
CA
|
A:GLY13
|
4.3
|
60.4
|
1.0
|
O2B
|
A:ATP402
|
4.4
|
67.7
|
1.0
|
CD
|
A:GLN137
|
4.5
|
70.9
|
1.0
|
NZ
|
A:LYS18
|
4.6
|
54.0
|
1.0
|
OD1
|
A:ASP11
|
4.6
|
66.5
|
1.0
|
OD2
|
A:ASP11
|
4.6
|
73.5
|
1.0
|
PA
|
A:ATP402
|
4.6
|
66.3
|
1.0
|
CA
|
A:GLY156
|
4.7
|
57.8
|
1.0
|
OD2
|
A:ASP154
|
4.7
|
73.2
|
1.0
|
O1A
|
A:ATP402
|
4.9
|
67.2
|
1.0
|
NE2
|
A:GLN137
|
4.9
|
69.9
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 8bo1
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Magnesium Binding Sites List in 8bo1
Magnesium binding site 2 out
of 6 in the Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin, Bound to Latrunculin-B-Atp-Mg-Actin, and 3'-Deoxyadenosine-5'- Triphosphate and 2 Mg Ions
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin, Bound to Latrunculin-B-Atp-Mg-Actin, and 3'-Deoxyadenosine-5'- Triphosphate and 2 Mg Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1103
b:64.1
occ:0.70
|
MN
|
B:MN1102
|
0.0
|
64.1
|
0.3
|
OD2
|
B:ASP665
|
2.1
|
72.4
|
1.0
|
NE2
|
B:HIS753
|
2.1
|
57.4
|
1.0
|
O
|
B:HOH1218
|
2.1
|
78.6
|
1.0
|
OD1
|
B:ASP667
|
2.3
|
58.1
|
1.0
|
O1A
|
B:3AT1101
|
2.4
|
66.3
|
1.0
|
CG
|
B:ASP665
|
3.0
|
70.2
|
1.0
|
CE1
|
B:HIS753
|
3.0
|
57.7
|
1.0
|
OD1
|
B:ASP665
|
3.2
|
70.6
|
1.0
|
CD2
|
B:HIS753
|
3.2
|
56.5
|
1.0
|
CG
|
B:ASP667
|
3.2
|
58.9
|
1.0
|
PA
|
B:3AT1101
|
3.5
|
66.5
|
1.0
|
OD2
|
B:ASP667
|
3.6
|
62.4
|
1.0
|
C5'
|
B:3AT1101
|
3.6
|
67.4
|
1.0
|
O5'
|
B:3AT1101
|
4.0
|
66.7
|
1.0
|
MN
|
B:MN1104
|
4.0
|
62.8
|
0.2
|
MG
|
B:MG1105
|
4.0
|
62.8
|
0.8
|
O2A
|
B:3AT1101
|
4.1
|
66.1
|
1.0
|
ND1
|
B:HIS753
|
4.1
|
57.9
|
1.0
|
O
|
B:LYS528
|
4.2
|
61.1
|
1.0
|
CG
|
B:HIS753
|
4.3
|
56.6
|
1.0
|
CB
|
B:ASP665
|
4.4
|
66.2
|
1.0
|
CB
|
B:ASP667
|
4.5
|
57.3
|
1.0
|
C3'
|
B:3AT1101
|
4.6
|
68.9
|
1.0
|
C4'
|
B:3AT1101
|
4.7
|
68.5
|
1.0
|
O3A
|
B:3AT1101
|
4.9
|
67.3
|
1.0
|
O2B
|
B:3AT1101
|
4.9
|
67.7
|
1.0
|
CD1
|
B:LEU530
|
4.9
|
61.8
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 8bo1
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Magnesium Binding Sites List in 8bo1
Magnesium binding site 3 out
of 6 in the Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin, Bound to Latrunculin-B-Atp-Mg-Actin, and 3'-Deoxyadenosine-5'- Triphosphate and 2 Mg Ions
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin, Bound to Latrunculin-B-Atp-Mg-Actin, and 3'-Deoxyadenosine-5'- Triphosphate and 2 Mg Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1105
b:62.8
occ:0.77
|
MN
|
B:MN1104
|
0.0
|
62.8
|
0.2
|
OD2
|
B:ASP667
|
2.0
|
62.4
|
1.0
|
O2G
|
B:3AT1101
|
2.1
|
70.4
|
1.0
|
OD1
|
B:ASP665
|
2.1
|
70.6
|
1.0
|
O2B
|
B:3AT1101
|
2.2
|
67.7
|
1.0
|
O1A
|
B:3AT1101
|
2.6
|
66.3
|
1.0
|
CG
|
B:ASP667
|
3.2
|
58.9
|
1.0
|
PB
|
B:3AT1101
|
3.2
|
67.8
|
1.0
|
PG
|
B:3AT1101
|
3.3
|
69.7
|
1.0
|
CG
|
B:ASP665
|
3.4
|
70.2
|
1.0
|
O3B
|
B:3AT1101
|
3.4
|
68.3
|
1.0
|
O3A
|
B:3AT1101
|
3.6
|
67.3
|
1.0
|
PA
|
B:3AT1101
|
3.6
|
66.5
|
1.0
|
OD1
|
B:ASP667
|
3.7
|
58.1
|
1.0
|
O1G
|
B:3AT1101
|
3.8
|
70.3
|
1.0
|
O
|
B:ASP665
|
4.0
|
62.7
|
1.0
|
MN
|
B:MN1102
|
4.0
|
64.1
|
0.3
|
MG
|
B:MG1103
|
4.0
|
64.1
|
0.7
|
OD2
|
B:ASP665
|
4.0
|
72.4
|
1.0
|
N
|
B:ASP665
|
4.0
|
66.3
|
1.0
|
CB
|
B:ASP667
|
4.4
|
57.3
|
1.0
|
C
|
B:ASP665
|
4.4
|
62.9
|
1.0
|
O5'
|
B:3AT1101
|
4.5
|
66.7
|
1.0
|
CB
|
B:ASP665
|
4.5
|
66.2
|
1.0
|
O3G
|
B:3AT1101
|
4.5
|
69.5
|
1.0
|
CA
|
B:ASP665
|
4.5
|
64.7
|
1.0
|
NH1
|
B:ARG510
|
4.6
|
56.8
|
1.0
|
O1B
|
B:3AT1101
|
4.6
|
67.5
|
1.0
|
O2A
|
B:3AT1101
|
4.8
|
66.1
|
1.0
|
CE
|
B:LYS528
|
4.8
|
54.7
|
1.0
|
CB
|
B:ALA664
|
4.8
|
68.2
|
1.0
|
N
|
B:ASP667
|
4.9
|
59.4
|
1.0
|
O
|
B:HOH1218
|
5.0
|
78.6
|
1.0
|
NZ
|
B:LYS528
|
5.0
|
54.3
|
1.0
|
C
|
B:ALA664
|
5.0
|
67.8
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 8bo1
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Magnesium Binding Sites List in 8bo1
Magnesium binding site 4 out
of 6 in the Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin, Bound to Latrunculin-B-Atp-Mg-Actin, and 3'-Deoxyadenosine-5'- Triphosphate and 2 Mg Ions
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin, Bound to Latrunculin-B-Atp-Mg-Actin, and 3'-Deoxyadenosine-5'- Triphosphate and 2 Mg Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg403
b:81.1
occ:0.80
|
MN
|
C:MN404
|
0.0
|
81.1
|
0.2
|
O
|
C:HOH507
|
1.9
|
74.3
|
1.0
|
O1B
|
C:ATP402
|
2.2
|
83.9
|
1.0
|
O3G
|
C:ATP402
|
2.2
|
87.0
|
1.0
|
PB
|
C:ATP402
|
3.3
|
84.1
|
1.0
|
PG
|
C:ATP402
|
3.4
|
86.3
|
1.0
|
O3B
|
C:ATP402
|
3.6
|
85.3
|
1.0
|
O2A
|
C:ATP402
|
3.8
|
83.7
|
1.0
|
O3A
|
C:ATP402
|
3.9
|
83.6
|
1.0
|
O1G
|
C:ATP402
|
4.1
|
85.9
|
1.0
|
OE1
|
C:GLN137
|
4.2
|
80.7
|
1.0
|
PA
|
C:ATP402
|
4.4
|
83.6
|
1.0
|
O
|
C:HOH504
|
4.4
|
91.0
|
1.0
|
OD2
|
C:ASP11
|
4.5
|
92.3
|
1.0
|
NZ
|
C:LYS18
|
4.5
|
77.3
|
1.0
|
OD2
|
C:ASP154
|
4.5
|
84.0
|
1.0
|
CA
|
C:GLY156
|
4.6
|
76.4
|
1.0
|
O2B
|
C:ATP402
|
4.6
|
84.3
|
1.0
|
O2G
|
C:ATP402
|
4.6
|
86.1
|
1.0
|
OD1
|
C:ASP11
|
4.6
|
90.9
|
1.0
|
CA
|
C:GLY13
|
4.7
|
81.6
|
1.0
|
O1A
|
C:ATP402
|
4.7
|
84.3
|
1.0
|
CD
|
C:GLN137
|
4.8
|
79.4
|
1.0
|
OD1
|
C:ASP154
|
4.8
|
82.6
|
1.0
|
CG2
|
C:VAL339
|
5.0
|
79.9
|
1.0
|
CG
|
C:ASP154
|
5.0
|
82.0
|
1.0
|
CG
|
C:ASP11
|
5.0
|
90.4
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 8bo1
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Magnesium Binding Sites List in 8bo1
Magnesium binding site 5 out
of 6 in the Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin, Bound to Latrunculin-B-Atp-Mg-Actin, and 3'-Deoxyadenosine-5'- Triphosphate and 2 Mg Ions
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin, Bound to Latrunculin-B-Atp-Mg-Actin, and 3'-Deoxyadenosine-5'- Triphosphate and 2 Mg Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg1103
b:66.7
occ:0.68
|
MN
|
D:MN1102
|
0.0
|
66.7
|
0.3
|
O3G
|
D:3AT1101
|
1.9
|
57.1
|
1.0
|
OD2
|
D:ASP667
|
2.1
|
63.0
|
1.0
|
OD1
|
D:ASP665
|
2.2
|
65.1
|
1.0
|
O2B
|
D:3AT1101
|
2.2
|
60.1
|
1.0
|
O
|
D:HOH1327
|
2.4
|
53.8
|
1.0
|
O1A
|
D:3AT1101
|
2.5
|
62.1
|
1.0
|
PG
|
D:3AT1101
|
3.2
|
56.8
|
1.0
|
PB
|
D:3AT1101
|
3.3
|
58.9
|
1.0
|
CG
|
D:ASP667
|
3.3
|
61.0
|
1.0
|
O3B
|
D:3AT1101
|
3.4
|
57.9
|
1.0
|
CG
|
D:ASP665
|
3.4
|
64.6
|
1.0
|
O3A
|
D:3AT1101
|
3.6
|
60.0
|
1.0
|
PA
|
D:3AT1101
|
3.7
|
61.9
|
1.0
|
MN
|
D:MN1104
|
3.8
|
67.5
|
0.3
|
MG
|
D:MG1105
|
3.8
|
67.5
|
0.7
|
OD1
|
D:ASP667
|
3.9
|
61.1
|
1.0
|
O2G
|
D:3AT1101
|
3.9
|
56.7
|
1.0
|
N
|
D:ASP665
|
4.0
|
57.3
|
1.0
|
O
|
D:ASP665
|
4.0
|
55.8
|
1.0
|
OD2
|
D:ASP665
|
4.1
|
69.4
|
1.0
|
O1G
|
D:3AT1101
|
4.4
|
55.2
|
1.0
|
C
|
D:ASP665
|
4.4
|
55.5
|
1.0
|
CB
|
D:ASP667
|
4.5
|
56.9
|
1.0
|
CB
|
D:ASP665
|
4.5
|
57.6
|
1.0
|
CA
|
D:ASP665
|
4.5
|
56.1
|
1.0
|
O1B
|
D:3AT1101
|
4.6
|
58.4
|
1.0
|
O5'
|
D:3AT1101
|
4.6
|
62.6
|
1.0
|
CE
|
D:LYS528
|
4.6
|
53.8
|
1.0
|
O
|
D:HOH1336
|
4.7
|
56.8
|
1.0
|
CB
|
D:ALA664
|
4.9
|
58.3
|
1.0
|
NZ
|
D:LYS528
|
4.9
|
55.1
|
1.0
|
O2A
|
D:3AT1101
|
4.9
|
62.1
|
1.0
|
C
|
D:ALA664
|
5.0
|
58.9
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 8bo1
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Magnesium Binding Sites List in 8bo1
Magnesium binding site 6 out
of 6 in the Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin, Bound to Latrunculin-B-Atp-Mg-Actin, and 3'-Deoxyadenosine-5'- Triphosphate and 2 Mg Ions
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A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Exoy Nucleotidyl Cyclase Domain From Vibrio Nigripulchritudo Martx Toxin, Bound to Latrunculin-B-Atp-Mg-Actin, and 3'-Deoxyadenosine-5'- Triphosphate and 2 Mg Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg1105
b:67.5
occ:0.72
|
MN
|
D:MN1104
|
0.0
|
67.5
|
0.3
|
OD2
|
D:ASP665
|
2.0
|
69.4
|
1.0
|
OD1
|
D:ASP667
|
2.2
|
61.1
|
1.0
|
NE2
|
D:HIS753
|
2.4
|
59.4
|
1.0
|
O1A
|
D:3AT1101
|
2.5
|
62.1
|
1.0
|
CG
|
D:ASP665
|
2.8
|
64.6
|
1.0
|
OD1
|
D:ASP665
|
2.9
|
65.1
|
1.0
|
CG
|
D:ASP667
|
3.1
|
61.0
|
1.0
|
OD2
|
D:ASP667
|
3.3
|
63.0
|
1.0
|
CD2
|
D:HIS753
|
3.4
|
59.0
|
1.0
|
CE1
|
D:HIS753
|
3.4
|
59.3
|
1.0
|
PA
|
D:3AT1101
|
3.6
|
61.9
|
1.0
|
C5'
|
D:3AT1101
|
3.6
|
63.6
|
1.0
|
MN
|
D:MN1102
|
3.8
|
66.7
|
0.3
|
MG
|
D:MG1103
|
3.8
|
66.7
|
0.7
|
O
|
D:HOH1302
|
3.8
|
48.2
|
1.0
|
O5'
|
D:3AT1101
|
4.0
|
62.6
|
1.0
|
O
|
D:LYS528
|
4.1
|
55.8
|
1.0
|
O2A
|
D:3AT1101
|
4.1
|
62.1
|
1.0
|
CB
|
D:ASP665
|
4.2
|
57.6
|
1.0
|
CB
|
D:ASP667
|
4.4
|
56.9
|
1.0
|
CG
|
D:HIS753
|
4.5
|
58.6
|
1.0
|
ND1
|
D:HIS753
|
4.5
|
59.6
|
1.0
|
C3'
|
D:3AT1101
|
4.6
|
68.1
|
1.0
|
C4'
|
D:3AT1101
|
4.7
|
66.5
|
1.0
|
O2B
|
D:3AT1101
|
4.7
|
60.1
|
1.0
|
CE
|
D:LYS528
|
4.8
|
53.8
|
1.0
|
O3A
|
D:3AT1101
|
4.9
|
60.0
|
1.0
|
CA
|
D:ASP667
|
5.0
|
57.0
|
1.0
|
|
Reference:
M.Teixeira-Nunes,
P.Retailleau,
D.Raoux-Barbot,
M.Comisso,
A.A.Missinou,
C.Velours,
S.Plancqueel,
D.Ladant,
U.Mechold,
L.Renault.
Functional and Structural Insights Into the Multi-Step Activation and Catalytic Mechanism of Bacterial Exoy Nucleotidyl Cyclase Toxins Bound to Actin-Profilin Plos Pathog. 2023.
ISSN: ESSN 1553-7374
DOI: 10.1371/JOURNAL.PPAT.1011654
Page generated: Thu Oct 3 19:48:11 2024
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