Calcium in PDB 2wy6: Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I

All present enzymatic activity of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I:
3.1.4.3;

The structure of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I, PDB code: 2wy6 was solved by S.G.Vachieri, C.E.Naylor, A.K.Basak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.91 / 3.20
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	107.238, 107.238, 225.087, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 28.1

The structure of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I also contains other interesting chemical elements:

Cadmium	(Cd)	15 atoms
Zinc	(Zn)	3 atoms

The binding sites of Calcium atom in the Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I (pdb code 2wy6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I, PDB code: 2wy6:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1375 b:0.9 occ:1.00 OD1 A:ASP293 2.8 0.1 1.0 O A:ASN294 3.2 0.9 1.0 CG A:ASP293 3.6 0.3 1.0 O B:GLU43 3.6 0.6 1.0 OD2 A:ASP293 3.7 0.9 1.0 OD1 B:ASN44 3.7 0.4 1.0 O A:PRO295 3.7 0.9 1.0 O A:GLY296 4.3 99.4 1.0 C A:ASN294 4.4 0.5 1.0 C A:PRO295 4.4 0.5 1.0 C B:GLU43 4.5 1.0 1.0 CG B:ASN44 4.6 0.3 1.0 CB B:GLU43 4.6 0.4 1.0 OD1 A:ASP298 4.6 0.8 1.0 CA A:PRO295 4.8 0.5 1.0 ND2 B:ASN44 5.0 99.4 1.0 CB A:ASP293 5.0 0.2 1.0

Calcium binding site 2 out of 4 in the Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1377 b:0.5 occ:1.00 OD1 B:ASP293 2.6 83.4 1.0 OD1 B:ASP298 2.6 63.1 1.0 O B:GLY296 2.9 83.2 1.0 O B:ASN294 3.1 81.3 1.0 CG B:ASP298 3.8 62.1 1.0 CG B:ASP293 3.8 73.2 1.0 C B:GLY296 4.0 85.7 1.0 C B:ASN294 4.3 78.6 1.0 N B:ASP298 4.4 75.3 1.0 O B:PRO295 4.4 87.8 1.0 N B:ASN294 4.4 81.2 1.0 OD2 B:ASP293 4.5 73.9 1.0 OD2 B:ASP298 4.6 66.3 1.0 C B:PRO295 4.7 82.6 1.0 CA B:ASP293 4.7 65.7 1.0 CB B:ASP298 4.7 59.1 1.0 CA B:ASN297 4.8 74.2 1.0 C B:ASP293 4.8 76.8 1.0 N B:ASN297 4.9 75.2 1.0 CB B:ASP293 4.9 67.5 1.0 CA B:GLY296 4.9 87.7 1.0 N B:GLY296 4.9 81.9 1.0

Calcium binding site 3 out of 4 in the Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1378 b:99.1 occ:1.00 O B:GLY271 2.6 85.6 1.0 O B:ALA337 2.9 78.7 1.0 O B:ASP269 3.0 0.5 1.0 OD1 B:ASP336 3.0 98.9 1.0 CA B:ASP336 3.3 0.7 1.0 N B:ALA337 3.5 98.0 1.0 C B:ASP336 3.6 0.8 1.0 C B:ASP269 3.7 99.7 1.0 CB B:ASP336 3.7 0.1 1.0 CG B:ASP336 3.7 96.9 1.0 C B:GLY271 3.8 71.5 1.0 C B:ALA337 3.9 85.2 1.0 CB B:ASP269 4.0 91.0 1.0 CA B:ASP269 4.1 0.1 1.0 O B:PRO335 4.3 0.6 1.0 CA B:ALA337 4.4 86.9 1.0 N B:GLY271 4.5 66.0 1.0 CA B:THR272 4.5 77.5 1.0 N B:ASP336 4.5 0.5 1.0 O B:ASP336 4.5 0.9 1.0 N B:THR272 4.6 81.2 1.0 N B:ALA270 4.6 70.0 1.0 C B:ALA270 4.7 72.3 1.0 CA B:GLY271 4.8 60.3 1.0 OD2 B:ASP336 4.9 90.3 1.0 C B:PRO335 4.9 0.9 1.0 CG B:ASP269 5.0 80.4 1.0

Calcium binding site 4 out of 4 in the Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1377 b:0.5 occ:1.00 OD1 C:ASP293 2.7 95.0 1.0 O C:GLY296 2.7 68.0 1.0 OD1 C:ASP298 2.7 93.4 1.0 O C:ASN294 3.0 95.2 1.0 C C:GLY296 3.9 71.1 1.0 CG C:ASP298 3.9 89.5 1.0 CG C:ASP293 3.9 87.7 1.0 O C:PRO295 4.1 0.4 1.0 C C:ASN294 4.2 93.2 1.0 N C:ASP298 4.4 96.4 1.0 C C:PRO295 4.4 97.6 1.0 N C:ASN294 4.4 94.3 1.0 OD2 C:ASP293 4.6 89.5 1.0 OD2 C:ASP298 4.6 87.7 1.0 CA C:ASN297 4.7 81.2 1.0 N C:GLY296 4.7 71.7 1.0 N C:ASN297 4.7 83.5 1.0 CA C:GLY296 4.7 70.8 1.0 CB C:ASP298 4.8 84.8 1.0 CA C:ASP293 4.8 72.3 1.0 C C:ASP293 4.8 87.1 1.0 CB C:ASP293 5.0 76.7 1.0 CA C:ASN294 5.0 88.8 1.0 C C:ASN297 5.0 87.3 1.0

S.G.Vachieri, G.C.Clark, A.Alape-Giron, M.Flores-Diaz, N.Justin, C.E.Naylor, R.W.Titball, A.K.Basak. Comparison of A Nontoxic Variant of Clostridium Perfringens [Alpha]-Toxin with the Toxic Wild-Type Strain Acta Crystallogr.,Sect.D V. 66 1067 2011.
ISSN: ISSN 0907-4449
PubMed: 20944240
DOI: 10.1107/S090744491003369X