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Manganese 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 (Mg) 6 atoms
Chlorine (Cl) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total 8 binding sites of Manganese 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 Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 8bo1

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Manganese binding site 1 out of 8 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 Manganese with other atoms in the Mn 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
B:Mn1102

b:64.1
occ:0.30
 MG B:MG1103 0.0 64.1 0.7
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

Manganese binding site 2 out of 8 in 8bo1

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Manganese binding site 2 out of 8 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 Manganese with other atoms in the Mn 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:Mn1104

b:62.8
occ:0.23
 MG B:MG1105 0.0 62.8 0.8
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

Manganese binding site 3 out of 8 in 8bo1

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Manganese binding site 3 out of 8 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 Manganese with other atoms in the Mn 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
C:Mn404

b:81.1
occ:0.20
 MG C:MG403 0.0 81.1 0.8
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

Manganese binding site 4 out of 8 in 8bo1

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Manganese binding site 4 out of 8 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 Manganese with other atoms in the Mn 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
D:Mn1102

b:66.7
occ:0.32
 MG D:MG1103 0.0 66.7 0.7
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

Manganese binding site 5 out of 8 in 8bo1

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Manganese binding site 5 out of 8 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 Manganese with other atoms in the Mn 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:Mn1104

b:67.5
occ:0.28
 MG D:MG1105 0.0 67.5 0.7
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

Manganese binding site 6 out of 8 in 8bo1

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Manganese binding site 6 out of 8 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 Manganese with other atoms in the Mn 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:Mn1107

b:87.8
occ:1.00
 N3 D:AZI1111 2.1 61.0 1.0
N1 D:AZI1110 2.3 67.5 1.0
OE1 D:GLU569 2.7 72.1 1.0
CL D:CL1117 2.8 77.9 1.0
N2 D:AZI1111 2.9 61.9 1.0
MN D:MN1108 3.1 80.1 1.0
N2 D:AZI1110 3.3 67.6 1.0
OE2 D:GLU569 3.5 73.5 1.0
CD D:GLU569 3.5 70.6 1.0
N2 D:AZI1114 3.5 71.5 1.0
N1 D:AZI1114 3.6 71.3 1.0
N3 D:AZI1114 3.8 71.6 1.0
N1 D:AZI1111 3.9 62.0 1.0
N3 D:AZI1110 4.4 67.0 1.0
CG D:GLU569 4.9 65.1 1.0

Manganese binding site 7 out of 8 in 8bo1

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Manganese binding site 7 out of 8 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 Manganese with other atoms in the Mn binding site number 7 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:Mn1108

b:80.1
occ:1.00
 OE2 D:GLU569 2.5 73.5 1.0
N1 D:AZI1115 2.7 65.2 1.0
N3 D:AZI1111 2.8 61.0 1.0
N3 D:AZI1112 2.8 73.6 1.0
MN D:MN1107 3.1 87.8 1.0
MN D:MN1109 3.3 87.5 1.0
N1 D:AZI1110 3.4 67.5 1.0
CD D:GLU569 3.5 70.6 1.0
N2 D:AZI1115 3.8 65.3 1.0
OE1 D:GLU569 3.9 72.1 1.0
N2 D:AZI1111 3.9 61.9 1.0
N2 D:AZI1112 4.0 73.7 1.0
N2 D:AZI1110 4.4 67.6 1.0
N1 D:AZI1113 4.8 66.5 1.0
CG D:GLU569 4.8 65.1 1.0
N1 D:AZI1114 4.9 71.3 1.0
N3 D:AZI1115 5.0 65.2 1.0

Manganese binding site 8 out of 8 in 8bo1

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Manganese binding site 8 out of 8 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 Manganese with other atoms in the Mn binding site number 8 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:Mn1109

b:87.5
occ:1.00
 N1 D:AZI1115 2.1 65.2 1.0
N3 D:AZI1112 2.4 73.6 1.0
N2 D:AZI1112 2.6 73.7 1.0
N2 D:AZI1115 2.7 65.3 1.0
CL D:CL1116 3.0 80.6 1.0
N1 D:AZI1112 3.2 73.5 1.0
MN D:MN1108 3.3 80.1 1.0
N1 D:AZI1113 3.5 66.5 1.0
N2 D:AZI1113 3.5 66.7 1.0
N3 D:AZI1115 3.5 65.2 1.0
N3 D:AZI1113 3.9 66.7 1.0
OE2 D:GLU569 4.9 73.5 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 Dec 28 11:04:17 2023

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