Zinc in PDB 1gyg: R32 Closed Form of Alpha-Toxin From Clostridium Perfringens Strain CER89L43

All present enzymatic activity of R32 Closed Form of Alpha-Toxin From Clostridium Perfringens Strain CER89L43:
3.1.4.3;

The structure of R32 Closed Form of Alpha-Toxin From Clostridium Perfringens Strain CER89L43, PDB code: 1gyg was solved by A.K.Basak, J.T.Eaton, R.W.Titball, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 1.90
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	151.400, 151.400, 195.500, 90.00, 90.00, 120.00
R / Rfree (%)	20.8 / 25.4

The binding sites of Zinc atom in the R32 Closed Form of Alpha-Toxin From Clostridium Perfringens Strain CER89L43 (pdb code 1gyg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the R32 Closed Form of Alpha-Toxin From Clostridium Perfringens Strain CER89L43, PDB code: 1gyg:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the R32 Closed Form of Alpha-Toxin From Clostridium Perfringens Strain CER89L43


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of R32 Closed Form of Alpha-Toxin From Clostridium Perfringens Strain CER89L43 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1371 b:18.5 occ:1.00 OD2 A:ASP130 2.1 13.9 1.0 ND1 A:HIS68 2.2 22.1 1.0 NE2 A:HIS126 2.2 18.8 1.0 OD1 A:ASP56 2.4 16.2 1.0 CG A:ASP130 3.0 18.7 1.0 CE1 A:HIS68 3.1 21.1 1.0 CD2 A:HIS126 3.2 14.9 1.0 CE1 A:HIS126 3.2 20.3 1.0 CG A:HIS68 3.2 23.1 1.0 OD1 A:ASP130 3.4 11.6 1.0 CG A:ASP56 3.4 15.5 1.0 ZN A:ZN1372 3.4 18.4 1.0 CB A:HIS68 3.6 19.8 1.0 OD2 A:ASP56 3.6 16.2 1.0 O A:HOH2059 4.0 25.8 1.0 O A:HOH2061 4.0 16.3 1.0 NE2 A:HIS68 4.2 22.5 1.0 ND1 A:HIS126 4.3 17.4 1.0 CG A:HIS126 4.3 15.1 1.0 CD2 A:HIS68 4.3 23.4 1.0 NE2 A:HIS11 4.4 17.7 1.0 CB A:ASP130 4.4 12.9 1.0 CB A:ASP56 4.7 13.1 1.0 O A:HOH2014 4.8 16.3 1.0 N A:ASP56 4.9 18.5 1.0 O A:TRP1 5.0 11.1 1.0 CA A:ASP56 5.0 19.6 1.0 CE1 A:HIS11 5.0 13.5 1.0

Zinc binding site 2 out of 4 in the R32 Closed Form of Alpha-Toxin From Clostridium Perfringens Strain CER89L43


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of R32 Closed Form of Alpha-Toxin From Clostridium Perfringens Strain CER89L43 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1372 b:18.4 occ:1.00 OD1 A:ASP130 2.1 11.6 1.0 NE2 A:HIS11 2.3 17.7 1.0 N A:TRP1 2.3 14.5 1.0 O A:TRP1 2.3 11.1 1.0 C A:TRP1 3.0 16.7 1.0 CG A:ASP130 3.1 18.7 1.0 CA A:TRP1 3.1 15.8 1.0 CE1 A:HIS11 3.1 13.5 1.0 CD2 A:HIS11 3.3 17.5 1.0 ZN A:ZN1371 3.4 18.5 1.0 OD2 A:ASP130 3.4 13.9 1.0 O A:HOH2061 3.5 16.3 1.0 CB A:TRP1 3.7 16.6 1.0 OE2 A:GLU152 4.0 15.5 1.0 NE2 A:HIS126 4.0 18.8 1.0 CE1 A:HIS126 4.0 20.3 1.0 OD2 A:ASP56 4.1 16.2 1.0 ND1 A:HIS11 4.2 16.5 1.0 N A:ASP2 4.3 15.8 1.0 CG A:HIS11 4.3 17.6 1.0 CB A:ASP130 4.4 12.9 1.0 CA A:ASP130 4.5 18.8 1.0 CG A:TRP1 4.6 20.3 1.0 OD1 A:ASP56 4.7 16.2 1.0 N A:ASP130 4.8 16.7 1.0 CD2 A:HIS126 4.8 14.9 1.0 ND1 A:HIS126 4.8 17.4 1.0 CG A:ASP56 4.8 15.5 1.0 CD1 A:TRP1 4.9 16.3 1.0 CD A:GLU152 4.9 16.6 1.0 OG1 A:THR133 4.9 17.1 1.0 O A:HIS126 5.0 16.3 1.0 CA A:ASP2 5.0 18.2 1.0

Zinc binding site 3 out of 4 in the R32 Closed Form of Alpha-Toxin From Clostridium Perfringens Strain CER89L43


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of R32 Closed Form of Alpha-Toxin From Clostridium Perfringens Strain CER89L43 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1371 b:17.7 occ:1.00 OD2 B:ASP130 2.1 12.6 1.0 ND1 B:HIS68 2.2 22.1 1.0 NE2 B:HIS126 2.2 14.7 1.0 OD1 B:ASP56 2.5 16.2 1.0 CE1 B:HIS68 3.1 23.1 1.0 CG B:ASP130 3.1 19.6 1.0 CE1 B:HIS126 3.1 20.9 1.0 CG B:HIS68 3.2 23.9 1.0 CD2 B:HIS126 3.2 14.2 1.0 ZN B:ZN1372 3.3 19.0 1.0 OD1 B:ASP130 3.4 14.1 1.0 CG B:ASP56 3.4 13.3 1.0 CB B:HIS68 3.5 19.9 1.0 OD2 B:ASP56 3.6 16.7 1.0 O B:HOH2009 3.7 31.5 1.0 O B:HOH2066 4.0 19.7 1.0 NE2 B:HIS68 4.2 23.0 1.0 ND1 B:HIS126 4.2 14.0 1.0 CD2 B:HIS68 4.3 21.5 1.0 CG B:HIS126 4.3 13.0 1.0 CB B:ASP130 4.5 11.6 1.0 NE2 B:HIS11 4.6 15.3 1.0 CB B:ASP56 4.7 15.8 1.0 N B:ASP56 4.9 17.8 1.0 O B:HOH2016 4.9 17.4 1.0 CA B:ASP56 5.0 19.3 1.0

Zinc binding site 4 out of 4 in the R32 Closed Form of Alpha-Toxin From Clostridium Perfringens Strain CER89L43


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of R32 Closed Form of Alpha-Toxin From Clostridium Perfringens Strain CER89L43 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1372 b:19.0 occ:1.00 OD1 B:ASP130 2.3 14.1 1.0 NE2 B:HIS11 2.4 15.3 1.0 O B:TRP1 2.5 14.3 1.0 N B:TRP1 2.6 16.4 1.0 C B:TRP1 3.3 16.6 1.0 CG B:ASP130 3.3 19.6 1.0 CD2 B:HIS11 3.3 16.7 1.0 CA B:TRP1 3.3 16.7 1.0 ZN B:ZN1371 3.3 17.7 1.0 CE1 B:HIS11 3.4 14.9 1.0 OD2 B:ASP130 3.5 12.6 1.0 O B:HOH2066 3.5 19.7 1.0 CB B:TRP1 3.9 14.4 1.0 CE1 B:HIS126 3.9 20.9 1.0 NE2 B:HIS126 3.9 14.7 1.0 OE2 B:GLU152 4.0 16.6 1.0 OD2 B:ASP56 4.0 16.7 1.0 CG B:HIS11 4.4 17.6 1.0 ND1 B:HIS11 4.5 18.9 1.0 N B:ASP2 4.5 14.8 1.0 CA B:ASP130 4.6 16.3 1.0 CB B:ASP130 4.6 11.6 1.0 CG B:TRP1 4.6 17.1 1.0 OD1 B:ASP56 4.7 16.2 1.0 ND1 B:HIS126 4.7 14.0 1.0 N B:ASP130 4.7 14.5 1.0 CD2 B:HIS126 4.8 14.2 1.0 CG B:ASP56 4.8 13.3 1.0 CD1 B:TRP1 4.9 15.0 1.0 OG1 B:THR133 4.9 18.1 1.0 O B:HIS126 4.9 16.9 1.0 CD B:GLU152 4.9 14.9 1.0

J.T.Eaton, C.Naylor, A.Howells, D.Moss, R.W.Titball, A.K.Basak. Crystal Structure of the C. Perfringens Alpha-Toxin with the Active Site Closed By A Flexible Loop Region J.Mol.Biol. V. 319 275 2002.
ISSN: ISSN 0022-2836
PubMed: 12051905
DOI: 10.1016/S0022-2836(02)00290-5