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Chlorine 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:

Manganese (Mn) 8 atoms
Magnesium (Mg) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine 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 Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 8bo1

Go back to Chlorine Binding Sites List in 8bo1
Chlorine binding site 1 out of 2 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 Chlorine with other atoms in the Cl 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
D:Cl1116

b:80.6
occ:1.00
 MN D:MN1109 3.0 87.5 1.0
N3 D:AZI1113 3.1 66.7 1.0
N3 D:AZI1115 3.2 65.2 1.0
N2 D:AZI1115 3.3 65.3 1.0
N2 D:AZI1113 3.4 66.7 1.0
N1 D:AZI1115 3.8 65.2 1.0
N1 D:AZI1113 4.0 66.5 1.0
N1 D:AZI1112 5.0 73.5 1.0
N2 D:AZI1112 5.0 73.7 1.0

Chlorine binding site 2 out of 2 in 8bo1

Go back to Chlorine Binding Sites List in 8bo1
Chlorine binding site 2 out of 2 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 Chlorine with other atoms in the Cl 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
D:Cl1117

b:77.9
occ:1.00
 MN D:MN1107 2.8 87.8 1.0
O D:HOH1385 2.9 53.5 1.0
N3 D:AZI1114 3.1 71.6 1.0
N2 D:AZI1114 3.6 71.5 1.0
N2 D:AZI1111 3.8 61.9 1.0
N3 D:AZI1111 3.9 61.0 1.0
OE1 D:GLU569 4.0 72.1 1.0
N1 D:AZI1111 4.2 62.0 1.0
N1 D:AZI1110 4.3 67.5 1.0
N1 D:AZI1114 4.4 71.3 1.0
N2 D:AZI1110 4.9 67.6 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 03:03:16 2023

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