Zinc 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
Calcium	(Ca)	4 atoms

The binding sites of Zinc 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 Zinc atom.
In total 3 binding sites of Zinc where determined in the Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I, PDB code: 2wy6:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn1371 b:61.4 occ:1.00 O A:TRP1 2.1 87.3 1.0 NE2 A:HIS11 2.2 65.7 1.0 N A:TRP1 2.2 82.9 1.0 OD1 A:ASP130 2.3 51.7 1.0 C A:TRP1 2.9 83.5 1.0 CD2 A:HIS11 2.9 66.4 1.0 CA A:TRP1 3.0 80.8 1.0 CG A:ASP130 3.2 53.3 1.0 CE1 A:HIS11 3.3 66.8 1.0 CD A:CD1372 3.3 68.7 1.0 OD2 A:ASP130 3.4 58.3 1.0 CB A:TRP1 3.6 68.8 1.0 CE1 A:HIS126 3.8 68.3 1.0 NE2 A:HIS126 4.0 58.1 1.0 OD2 A:ASP56 4.1 85.3 1.0 CG A:HIS11 4.1 63.2 1.0 N A:ASP2 4.1 83.3 1.0 ND1 A:HIS11 4.3 59.6 1.0 CG A:TRP1 4.5 73.0 1.0 ND1 A:HIS126 4.6 71.1 1.0 OD1 A:ASP56 4.6 78.7 1.0 CB A:ASP130 4.6 54.7 1.0 CD A:CD1373 4.7 80.4 1.0 CG A:ASP56 4.7 82.2 1.0 OE2 A:GLU152 4.8 70.5 1.0 CD1 A:TRP1 4.8 76.5 1.0 CA A:ASP2 4.8 82.6 1.0 C A:ASP2 5.0 88.1 1.0 CD2 A:HIS126 5.0 74.2 1.0

Zinc binding site 2 out of 3 in the Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn1372 b:74.5 occ:1.00 NE2 B:HIS11 2.0 55.9 1.0 O B:TRP1 2.1 98.2 1.0 OD1 B:ASP130 2.4 73.1 1.0 N B:TRP1 2.4 96.1 1.0 CD2 B:HIS11 2.7 61.0 1.0 C B:TRP1 2.9 98.0 1.0 CA B:TRP1 3.0 97.9 1.0 CE1 B:HIS11 3.2 59.0 1.0 CG B:ASP130 3.3 70.9 1.0 OD2 B:ASP130 3.4 76.7 1.0 CD B:CD1373 3.6 70.2 1.0 CB B:TRP1 3.6 81.0 1.0 CE1 B:HIS126 3.7 49.4 1.0 NE2 B:HIS126 3.9 39.7 1.0 CG B:HIS11 3.9 61.4 1.0 OD2 B:ASP56 4.0 79.5 1.0 ND1 B:HIS11 4.1 50.3 1.0 N B:ASP2 4.1 72.1 1.0 ND1 B:HIS126 4.4 46.9 1.0 CG B:TRP1 4.5 82.5 1.0 OD1 B:ASP56 4.6 67.7 1.0 CB B:ASP130 4.7 67.9 1.0 CD B:CD1374 4.7 81.2 1.0 CG B:ASP56 4.7 73.9 1.0 CD1 B:TRP1 4.8 87.9 1.0 CD2 B:HIS126 4.8 47.4 1.0 CA B:ASP2 4.8 66.5 1.0 O B:ASP2 4.8 67.3 1.0 C B:ASP2 4.9 70.7 1.0 OE2 B:GLU152 4.9 94.9 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 Mutant T74I within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1372 b:66.5 occ:1.00 O C:TRP1 2.0 78.4 1.0 N C:TRP1 2.1 76.0 1.0 NE2 C:HIS11 2.2 78.1 1.0 OD1 C:ASP130 2.4 68.4 1.0 C C:TRP1 2.7 73.7 1.0 CA C:TRP1 2.8 75.7 1.0 CD2 C:HIS11 2.9 87.5 1.0 CG C:ASP130 3.4 67.9 1.0 CE1 C:HIS11 3.4 84.8 1.0 CB C:TRP1 3.4 70.9 1.0 CD C:CD1373 3.6 76.1 1.0 OD2 C:ASP130 3.6 77.9 1.0 CE1 C:HIS126 4.0 59.8 1.0 N C:ASP2 4.0 76.2 1.0 CG C:HIS11 4.2 92.3 1.0 OD2 C:ASP56 4.2 71.5 1.0 NE2 C:HIS126 4.3 56.7 1.0 CG C:TRP1 4.3 70.3 1.0 ND1 C:HIS11 4.4 84.5 1.0 CD C:CD1374 4.6 88.2 1.0 OE2 C:GLU152 4.6 88.4 1.0 CD1 C:TRP1 4.7 69.8 1.0 CA C:ASP2 4.7 74.6 1.0 CB C:ASP130 4.7 66.1 1.0 OD1 C:ASP56 4.7 67.6 1.0 ND1 C:HIS126 4.7 58.5 1.0 C C:ASP2 4.8 82.6 1.0 O C:ASP2 4.8 77.0 1.0 CG C:ASP56 4.9 69.1 1.0 CD C:GLU152 4.9 91.3 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