Zinc in PDB 1qmd: Calcium Bound Closed Form Alpha-Toxin From Clostridium Perfringens

All present enzymatic activity of Calcium Bound Closed Form Alpha-Toxin From Clostridium Perfringens:
3.1.4.3;

The structure of Calcium Bound Closed Form Alpha-Toxin From Clostridium Perfringens, PDB code: 1qmd 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)	50.00 / 2.20
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	149.890, 149.890, 192.930, 90.00, 90.00, 120.00
R / Rfree (%)	19.8 / 23.5

The structure of Calcium Bound Closed Form Alpha-Toxin From Clostridium Perfringens also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

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

Zinc binding site 1 out of 4 in the Calcium Bound Closed Form Alpha-Toxin From Clostridium Perfringens


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Calcium Bound Closed Form Alpha-Toxin From Clostridium Perfringens within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:21.6 occ:1.00 OD1 A:ASP130 2.3 6.9 1.0 O A:TRP1 2.4 14.3 1.0 CE1 A:HIS11 2.4 13.7 1.0 N A:TRP1 2.4 11.7 1.0 O A:HOH2023 2.7 34.8 1.0 C A:TRP1 3.1 14.5 1.0 CA A:TRP1 3.2 13.6 1.0 ZN A:ZN402 3.3 17.4 1.0 NE2 A:HIS11 3.3 16.6 1.0 ND1 A:HIS11 3.3 15.8 1.0 CG A:ASP130 3.4 13.9 1.0 O A:HOH2088 3.5 16.1 1.0 CB A:TRP1 3.8 11.8 1.0 OD2 A:ASP130 3.9 16.1 1.0 CE1 A:HIS126 3.9 16.2 1.0 OE2 A:GLU152 4.0 11.0 1.0 NE2 A:HIS126 4.0 15.9 1.0 OD2 A:ASP56 4.1 14.7 1.0 N A:ASP2 4.4 15.5 1.0 CD2 A:HIS11 4.5 14.5 1.0 CG A:HIS11 4.5 15.2 1.0 CB A:ASP130 4.6 10.2 1.0 CA A:ASP130 4.6 12.3 1.0 CG A:TRP1 4.7 15.0 1.0 OD1 A:ASP56 4.7 15.3 1.0 ND1 A:HIS126 4.7 20.5 1.0 N A:ASP130 4.8 13.7 1.0 OG1 A:THR133 4.8 14.6 1.0 O A:HIS126 4.8 16.7 1.0 CG A:ASP56 4.8 17.7 1.0 CD2 A:HIS126 4.9 16.9 1.0 CD1 A:TRP1 5.0 11.7 1.0 CD A:GLU152 5.0 14.8 1.0

Zinc binding site 2 out of 4 in the Calcium Bound Closed Form Alpha-Toxin From Clostridium Perfringens


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Calcium Bound Closed Form Alpha-Toxin From Clostridium Perfringens within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:17.4 occ:1.00 NE2 A:HIS126 2.3 15.9 1.0 ND1 A:HIS68 2.3 19.9 1.0 OD2 A:ASP130 2.4 16.1 1.0 OD1 A:ASP56 2.6 15.3 1.0 O A:HOH2023 2.7 34.8 1.0 CE1 A:HIS126 3.1 16.2 1.0 CG A:ASP130 3.1 13.9 1.0 OD1 A:ASP130 3.1 6.9 1.0 CE1 A:HIS68 3.2 21.2 1.0 CG A:HIS68 3.2 20.6 1.0 ZN A:ZN401 3.3 21.6 1.0 CD2 A:HIS126 3.3 16.9 1.0 CG A:ASP56 3.5 17.7 1.0 CB A:HIS68 3.5 16.2 1.0 OD2 A:ASP56 3.7 14.7 1.0 O A:HOH2024 3.9 19.5 1.0 O A:HOH2088 3.9 16.1 1.0 ND1 A:HIS126 4.2 20.5 1.0 NE2 A:HIS68 4.2 22.9 1.0 CD2 A:HIS68 4.3 20.1 1.0 CE1 A:HIS11 4.3 13.7 1.0 CG A:HIS126 4.3 18.0 1.0 CB A:ASP130 4.5 10.2 1.0 CB A:ASP56 4.8 14.2 1.0 O A:TRP1 5.0 14.3 1.0

Zinc binding site 3 out of 4 in the Calcium Bound Closed Form Alpha-Toxin From Clostridium Perfringens


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Calcium Bound Closed Form Alpha-Toxin From Clostridium Perfringens within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:16.8 occ:1.00 O B:HOH2152 2.2 11.4 1.0 OD1 B:ASP130 2.3 11.4 1.0 NE2 B:HIS11 2.3 17.3 1.0 N B:TRP1 2.3 11.0 1.0 O B:TRP1 2.3 10.4 1.0 C B:TRP1 3.0 11.1 1.0 CD2 B:HIS11 3.0 15.9 1.0 CA B:TRP1 3.1 11.1 1.0 ZN B:ZN402 3.3 22.7 1.0 CG B:ASP130 3.3 16.2 1.0 O B:HOH2086 3.4 10.8 1.0 CE1 B:HIS11 3.5 17.2 1.0 CB B:TRP1 3.7 9.0 1.0 OD2 B:ASP130 3.8 14.5 1.0 OE2 B:GLU152 3.9 13.2 1.0 OD2 B:ASP56 3.9 16.7 1.0 CE1 B:HIS126 4.0 12.9 1.0 NE2 B:HIS126 4.0 12.8 1.0 CG B:HIS11 4.3 18.8 1.0 N B:ASP2 4.3 10.9 1.0 ND1 B:HIS11 4.4 18.9 1.0 CB B:ASP130 4.5 11.0 1.0 CG B:TRP1 4.6 12.1 1.0 CA B:ASP130 4.7 13.4 1.0 OD1 B:ASP56 4.8 12.8 1.0 ND1 B:HIS126 4.8 15.2 1.0 CG B:ASP56 4.8 18.3 1.0 CD2 B:HIS126 4.8 14.4 1.0 CD B:GLU152 4.9 13.4 1.0 N B:ASP130 4.9 15.2 1.0 OG1 B:THR133 4.9 14.0 1.0 CD1 B:TRP1 4.9 11.9 1.0 O B:HIS126 4.9 16.2 1.0 CD2 B:HIS148 4.9 14.8 1.0

Zinc binding site 4 out of 4 in the Calcium Bound Closed Form Alpha-Toxin From Clostridium Perfringens


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Calcium Bound Closed Form Alpha-Toxin From Clostridium Perfringens within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:22.7 occ:1.00 O B:HOH2152 2.1 11.4 1.0 ND1 B:HIS68 2.3 18.5 1.0 NE2 B:HIS126 2.3 12.8 1.0 OD2 B:ASP130 2.3 14.5 1.0 OD1 B:ASP56 2.5 12.8 1.0 CG B:ASP130 3.1 16.2 1.0 CE1 B:HIS68 3.2 20.2 1.0 CD2 B:HIS126 3.2 14.4 1.0 OD1 B:ASP130 3.2 11.4 1.0 CE1 B:HIS126 3.2 12.9 1.0 CG B:HIS68 3.3 19.4 1.0 CG B:ASP56 3.3 18.3 1.0 ZN B:ZN401 3.3 16.8 1.0 OD2 B:ASP56 3.4 16.7 1.0 CB B:HIS68 3.6 16.1 1.0 O B:HOH2022 3.8 19.6 1.0 O B:HOH2086 3.8 10.8 1.0 ND1 B:HIS126 4.3 15.2 1.0 CG B:HIS126 4.3 14.4 1.0 NE2 B:HIS68 4.3 21.2 1.0 NE2 B:HIS11 4.4 17.3 1.0 CD2 B:HIS68 4.4 17.9 1.0 CB B:ASP130 4.5 11.0 1.0 CB B:ASP56 4.7 15.7 1.0 O B:HOH2032 4.8 9.8 1.0 O B:TRP1 4.9 10.4 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