Zinc in PDB 1qm6: Closed Form of Clostridium Perfringens Alpha-Toxin Strain NCTC8237

All present enzymatic activity of Closed Form of Clostridium Perfringens Alpha-Toxin Strain NCTC8237:
3.1.4.3;

The structure of Closed Form of Clostridium Perfringens Alpha-Toxin Strain NCTC8237, PDB code: 1qm6 was solved by C.E.Naylor, J.Miller, R.W.Titball, A.K.Basak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.50
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	149.540, 149.540, 193.830, 90.00, 90.00, 120.00
R / Rfree (%)	22 / 24.7

The binding sites of Zinc atom in the Closed Form of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 (pdb code 1qm6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Closed Form of Clostridium Perfringens Alpha-Toxin Strain NCTC8237, PDB code: 1qm6:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Closed Form of Clostridium Perfringens Alpha-Toxin Strain NCTC8237


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Closed Form of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn400 b:13.3 occ:1.00 OD1 A:ASP130 2.3 12.7 1.0 O A:TRP1 2.3 8.1 1.0 NE2 A:HIS11 2.3 9.6 1.0 N A:TRP1 2.4 6.4 1.0 C A:TRP1 3.1 8.5 1.0 CA A:TRP1 3.1 7.9 1.0 CD2 A:HIS11 3.2 8.7 1.0 ZN A:ZN401 3.2 15.9 1.0 CE1 A:HIS11 3.4 9.7 1.0 CG A:ASP130 3.4 12.2 1.0 CB A:TRP1 3.7 7.2 1.0 OE2 A:GLU152 3.8 8.6 1.0 CE1 A:HIS126 3.9 9.9 1.0 OD2 A:ASP130 3.9 14.3 1.0 OD2 A:ASP56 4.0 11.1 1.0 NE2 A:HIS126 4.2 10.5 1.0 N A:ASP2 4.3 9.6 1.0 CG A:HIS11 4.4 9.5 1.0 ND1 A:HIS11 4.5 9.2 1.0 CG A:TRP1 4.6 7.7 1.0 ND1 A:HIS126 4.6 10.9 1.0 CB A:ASP130 4.6 12.4 1.0 CA A:ASP130 4.7 11.3 1.0 CD A:GLU152 4.8 9.8 1.0 OD1 A:ASP56 4.8 12.2 1.0 CG A:ASP56 4.8 11.7 1.0 O A:HIS126 4.9 10.9 1.0 CE1 A:HIS148 4.9 9.6 1.0 N A:ASP130 4.9 11.6 1.0 OG1 A:THR133 4.9 11.1 1.0 CD1 A:TRP1 5.0 7.9 1.0

Zinc binding site 2 out of 4 in the Closed Form of Clostridium Perfringens Alpha-Toxin Strain NCTC8237


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Closed Form of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:15.9 occ:1.00 ND1 A:HIS68 2.3 15.6 1.0 NE2 A:HIS126 2.3 10.5 1.0 OD2 A:ASP130 2.4 14.3 1.0 OD1 A:ASP56 2.5 12.2 1.0 CE1 A:HIS126 3.0 9.9 1.0 OD1 A:ASP130 3.1 12.7 1.0 CG A:ASP130 3.1 12.2 1.0 CE1 A:HIS68 3.2 15.9 1.0 ZN A:ZN400 3.2 13.3 1.0 CG A:HIS68 3.3 15.8 1.0 CG A:ASP56 3.3 11.7 1.0 OD2 A:ASP56 3.4 11.1 1.0 CD2 A:HIS126 3.5 10.5 1.0 CB A:HIS68 3.6 16.1 1.0 ND1 A:HIS126 4.2 10.9 1.0 NE2 A:HIS11 4.3 9.6 1.0 NE2 A:HIS68 4.3 17.2 1.0 CD2 A:HIS68 4.4 16.7 1.0 CG A:HIS126 4.4 9.9 1.0 CB A:ASP130 4.5 12.4 1.0 CB A:ASP56 4.8 11.2 1.0 O A:TRP1 4.8 8.1 1.0 O A:HIS126 5.0 10.9 1.0

Zinc binding site 3 out of 4 in the Closed Form of Clostridium Perfringens Alpha-Toxin Strain NCTC8237


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Closed Form of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn400 b:21.6 occ:1.00 OD1 B:ASP130 2.3 9.5 1.0 NE2 B:HIS11 2.3 8.6 1.0 O B:TRP1 2.4 6.4 1.0 N B:TRP1 2.4 6.8 1.0 C B:TRP1 3.0 7.6 1.0 CA B:TRP1 3.1 7.6 1.0 CD2 B:HIS11 3.1 8.9 1.0 ZN B:ZN401 3.3 22.7 1.0 CE1 B:HIS11 3.4 9.1 1.0 CG B:ASP130 3.4 11.3 1.0 CB B:TRP1 3.6 7.1 1.0 OE2 B:GLU152 3.7 8.0 1.0 OD2 B:ASP130 3.9 12.4 1.0 CE1 B:HIS126 3.9 8.5 1.0 OD2 B:ASP56 4.0 10.7 1.0 NE2 B:HIS126 4.2 9.8 1.0 N B:ASP2 4.3 8.4 1.0 CG B:HIS11 4.4 9.5 1.0 ND1 B:HIS11 4.5 9.2 1.0 CG B:TRP1 4.6 8.2 1.0 CB B:ASP130 4.7 11.7 1.0 ND1 B:HIS126 4.7 9.0 1.0 CA B:ASP130 4.7 11.6 1.0 CD B:GLU152 4.8 9.8 1.0 OD1 B:ASP56 4.8 13.8 1.0 CG B:ASP56 4.9 11.7 1.0 OG1 B:THR133 4.9 10.1 1.0 O B:HIS126 4.9 10.8 1.0 CE1 B:HIS148 4.9 10.8 1.0 N B:ASP130 4.9 12.2 1.0 CD1 B:TRP1 4.9 7.4 1.0

Zinc binding site 4 out of 4 in the Closed Form of Clostridium Perfringens Alpha-Toxin Strain NCTC8237


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Closed Form of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:22.7 occ:1.00 ND1 B:HIS68 2.3 14.6 1.0 NE2 B:HIS126 2.3 9.8 1.0 OD2 B:ASP130 2.4 12.4 1.0 OD1 B:ASP56 2.5 13.8 1.0 CE1 B:HIS126 3.0 8.5 1.0 OD1 B:ASP130 3.1 9.5 1.0 CG B:ASP130 3.1 11.3 1.0 CE1 B:HIS68 3.2 16.2 1.0 CG B:HIS68 3.3 14.4 1.0 ZN B:ZN400 3.3 21.6 1.0 CG B:ASP56 3.3 11.7 1.0 OD2 B:ASP56 3.4 10.7 1.0 CD2 B:HIS126 3.4 9.7 1.0 CB B:HIS68 3.6 14.8 1.0 ND1 B:HIS126 4.1 9.0 1.0 NE2 B:HIS68 4.3 14.7 1.0 NE2 B:HIS11 4.3 8.6 1.0 CD2 B:HIS68 4.4 15.4 1.0 CG B:HIS126 4.4 9.5 1.0 CB B:ASP130 4.6 11.7 1.0 CB B:ASP56 4.7 12.3 1.0 O B:TRP1 4.9 6.4 1.0 O B:HIS126 4.9 10.8 1.0

C.E.Naylor, M.Jepson, D.T.Crane, R.W.Titball, J.Miller, A.K.Basak, B.Bolgiano. Characterisation of the Calcium-Binding C-Terminal Domain of Clostridium Perfringens Alpha-Toxin J.Mol.Biol. V. 294 757 1999.
ISSN: ISSN 0022-2836
PubMed: 10610794
DOI: 10.1006/JMBI.1999.3279