Zinc in PDB 1kho: Crystal Structure Analysis of Clostridium Perfringens Alpha- Toxin Isolated From Avian Strain Swcp

The structure of Crystal Structure Analysis of Clostridium Perfringens Alpha- Toxin Isolated From Avian Strain Swcp, PDB code: 1kho was solved by N.Justin, D.S.Moss, 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 / 2.40
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	117.230, 117.230, 220.590, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 23.6

The binding sites of Zinc atom in the Crystal Structure Analysis of Clostridium Perfringens Alpha- Toxin Isolated From Avian Strain Swcp (pdb code 1kho). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure Analysis of Clostridium Perfringens Alpha- Toxin Isolated From Avian Strain Swcp, PDB code: 1kho:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure Analysis of Clostridium Perfringens Alpha- Toxin Isolated From Avian Strain Swcp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure Analysis of Clostridium Perfringens Alpha- Toxin Isolated From Avian Strain Swcp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn371 b:28.4 occ:1.00 NE2 A:HIS11 2.2 23.6 1.0 N A:TRP1 2.3 20.8 1.0 OD2 A:ASP130 2.3 26.2 1.0 O A:HOH421 2.4 40.8 1.0 O A:TRP1 2.4 23.5 1.0 CD2 A:HIS11 3.1 25.7 1.0 CA A:TRP1 3.1 23.1 1.0 C A:TRP1 3.1 23.9 1.0 CE1 A:HIS11 3.2 24.9 1.0 ZN A:ZN372 3.3 27.3 1.0 CG A:ASP130 3.3 25.5 1.0 CB A:TRP1 3.6 18.9 1.0 OD1 A:ASP130 3.6 25.8 1.0 NE2 A:HIS126 3.9 18.2 1.0 OD2 A:ASP56 4.0 29.5 1.0 CE1 A:HIS126 4.0 16.3 1.0 CG A:HIS11 4.3 24.4 1.0 ND1 A:HIS11 4.3 25.4 1.0 N A:ASP2 4.4 25.2 1.0 CG A:TRP1 4.6 19.3 1.0 CB A:ASP130 4.6 25.3 1.0 OD1 A:ASP56 4.7 30.9 1.0 CE1 A:HIS136 4.8 22.5 1.0 OG1 A:THR133 4.8 23.4 1.0 CA A:ASP130 4.8 24.1 1.0 CG A:ASP56 4.8 29.5 1.0 NE2 A:HIS136 4.9 24.2 1.0 OE1 A:GLU152 4.9 29.7 1.0 CD2 A:HIS126 4.9 18.7 1.0 CD1 A:TRP1 4.9 18.8 1.0 ND1 A:HIS126 5.0 20.6 1.0

Zinc binding site 2 out of 6 in the Crystal Structure Analysis of Clostridium Perfringens Alpha- Toxin Isolated From Avian Strain Swcp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure Analysis of Clostridium Perfringens Alpha- Toxin Isolated From Avian Strain Swcp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn372 b:27.3 occ:1.00 NE2 A:HIS126 2.3 18.2 1.0 OD1 A:ASP130 2.3 25.8 1.0 O A:HOH421 2.3 40.8 1.0 CD2 A:HIS68 2.4 20.0 1.0 OD1 A:ASP56 2.5 30.9 1.0 CE1 A:HIS126 3.2 16.3 1.0 CG A:ASP130 3.2 25.5 1.0 CD2 A:HIS126 3.3 18.7 1.0 ZN A:ZN371 3.3 28.4 1.0 CG A:HIS68 3.3 20.4 1.0 CG A:ASP56 3.4 29.5 1.0 NE2 A:HIS68 3.4 21.1 1.0 OD2 A:ASP130 3.4 26.2 1.0 OD2 A:ASP56 3.5 29.5 1.0 CB A:HIS68 3.7 20.0 1.0 NE2 A:HIS11 4.2 23.6 1.0 ND1 A:HIS126 4.3 20.6 1.0 CG A:HIS126 4.4 21.6 1.0 ND1 A:HIS68 4.5 23.4 1.0 CE1 A:HIS68 4.5 21.6 1.0 O A:HOH423 4.5 40.6 1.0 CB A:ASP130 4.6 25.3 1.0 CB A:ASP56 4.8 29.1 1.0 CE1 A:HIS136 4.8 22.5 1.0 CA A:HIS68 4.9 20.4 1.0 CE1 A:HIS11 4.9 24.9 1.0 O A:TRP1 5.0 23.5 1.0 CD2 A:HIS11 5.0 25.7 1.0

Zinc binding site 3 out of 6 in the Crystal Structure Analysis of Clostridium Perfringens Alpha- Toxin Isolated From Avian Strain Swcp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure Analysis of Clostridium Perfringens Alpha- Toxin Isolated From Avian Strain Swcp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn373 b:31.1 occ:1.00 OE1 A:GLU152 2.3 29.7 1.0 NE2 A:HIS148 2.3 33.7 1.0 NE2 A:HIS136 2.3 24.2 1.0 O A:HOH374 2.5 61.9 1.0 OE2 A:GLU152 2.5 32.8 1.0 CD A:GLU152 2.7 30.7 1.0 CD2 A:HIS148 3.2 32.8 1.0 CD2 A:HIS136 3.3 25.0 1.0 CE1 A:HIS136 3.3 22.5 1.0 CE1 A:HIS148 3.3 31.5 1.0 O A:HOH423 3.9 40.6 1.0 CG A:GLU152 4.2 28.3 1.0 O A:HOH421 4.4 40.8 1.0 N A:TRP1 4.4 20.8 1.0 CG A:HIS148 4.4 32.3 1.0 ND1 A:HIS148 4.4 32.4 1.0 ND1 A:HIS136 4.4 27.6 1.0 CG A:HIS136 4.4 26.6 1.0

Zinc binding site 4 out of 6 in the Crystal Structure Analysis of Clostridium Perfringens Alpha- Toxin Isolated From Avian Strain Swcp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure Analysis of Clostridium Perfringens Alpha- Toxin Isolated From Avian Strain Swcp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn374 b:26.5 occ:1.00 NE2 B:HIS11 2.2 22.4 1.0 O B:TRP1 2.3 30.4 1.0 OD2 B:ASP130 2.3 26.8 1.0 N B:TRP1 2.4 27.8 1.0 O B:HOH424 2.6 62.4 1.0 C B:TRP1 3.1 29.9 1.0 CA B:TRP1 3.1 28.9 1.0 CE1 B:HIS11 3.1 24.6 1.0 CD2 B:HIS11 3.2 23.0 1.0 ZN B:ZN375 3.3 27.1 1.0 CG B:ASP130 3.4 27.3 1.0 CB B:TRP1 3.6 25.6 1.0 OD1 B:ASP130 3.7 31.3 1.0 CE1 B:HIS126 3.9 18.8 1.0 OD2 B:ASP56 4.0 32.6 1.0 NE2 B:HIS126 4.0 21.5 1.0 ND1 B:HIS11 4.3 25.5 1.0 CG B:HIS11 4.3 25.5 1.0 N B:ASP2 4.4 31.9 1.0 CG B:TRP1 4.5 25.8 1.0 OE1 B:GLU152 4.6 33.2 1.0 CB B:ASP130 4.6 27.5 1.0 CE1 B:HIS136 4.6 26.1 1.0 CA B:ASP130 4.7 25.0 1.0 NE2 B:HIS136 4.8 25.5 1.0 OG1 B:THR133 4.8 26.1 1.0 ND1 B:HIS126 4.8 22.6 1.0 OD1 B:ASP56 4.8 34.3 1.0 CG B:ASP56 4.8 31.8 1.0 CD1 B:TRP1 4.9 25.6 1.0 O B:HOH425 4.9 43.9 1.0 ZN B:ZN376 5.0 32.8 1.0

Zinc binding site 5 out of 6 in the Crystal Structure Analysis of Clostridium Perfringens Alpha- Toxin Isolated From Avian Strain Swcp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure Analysis of Clostridium Perfringens Alpha- Toxin Isolated From Avian Strain Swcp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn375 b:27.1 occ:1.00 NE2 B:HIS126 2.2 21.5 1.0 CD2 B:HIS68 2.4 25.4 1.0 OD1 B:ASP130 2.4 31.3 1.0 OD1 B:ASP56 2.5 34.3 1.0 O B:HOH424 2.5 62.4 1.0 CE1 B:HIS126 2.9 18.8 1.0 CG B:ASP130 3.2 27.3 1.0 ZN B:ZN374 3.3 26.5 1.0 OD2 B:ASP130 3.3 26.8 1.0 CG B:HIS68 3.3 27.0 1.0 NE2 B:HIS68 3.3 27.1 1.0 CG B:ASP56 3.4 31.8 1.0 CD2 B:HIS126 3.4 22.7 1.0 OD2 B:ASP56 3.5 32.6 1.0 CB B:HIS68 3.8 24.4 1.0 ND1 B:HIS126 4.1 22.6 1.0 NE2 B:HIS11 4.2 22.4 1.0 CG B:HIS126 4.4 22.9 1.0 CE1 B:HIS68 4.4 28.7 1.0 ND1 B:HIS68 4.4 27.9 1.0 CE1 B:HIS136 4.5 26.1 1.0 CB B:ASP130 4.6 27.5 1.0 O B:HOH377 4.7 35.8 1.0 CB B:ASP56 4.8 30.3 1.0 CE1 B:HIS11 4.8 24.6 1.0 O B:TRP1 4.9 30.4 1.0 CA B:HIS68 5.0 22.6 1.0

Zinc binding site 6 out of 6 in the Crystal Structure Analysis of Clostridium Perfringens Alpha- Toxin Isolated From Avian Strain Swcp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure Analysis of Clostridium Perfringens Alpha- Toxin Isolated From Avian Strain Swcp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn376 b:32.8 occ:1.00 NE2 B:HIS136 2.3 25.5 1.0 NE2 B:HIS148 2.3 26.4 1.0 OE1 B:GLU152 2.4 33.2 1.0 OE2 B:GLU152 2.5 33.3 1.0 CD B:GLU152 2.7 33.2 1.0 O B:HOH377 3.1 35.8 1.0 CD2 B:HIS136 3.2 29.0 1.0 CE1 B:HIS148 3.2 26.0 1.0 CE1 B:HIS136 3.3 26.1 1.0 CD2 B:HIS148 3.3 26.3 1.0 O B:HOH425 3.7 43.9 1.0 O B:HOH424 3.8 62.4 1.0 CG B:GLU152 4.2 32.3 1.0 ND1 B:HIS148 4.4 28.1 1.0 N B:TRP1 4.4 27.8 1.0 CG B:HIS136 4.4 29.2 1.0 ND1 B:HIS136 4.4 29.2 1.0 CG B:HIS148 4.4 27.9 1.0 ZN B:ZN374 5.0 26.5 1.0

N.Justin, N.Walker, H.L.Bullifent, G.Songer, D.M.Bueschel, H.Jost, C.Naylor, J.Miller, D.S.Moss, R.W.Titball, A.K.Basak. The First Strain of Clostridium Perfringens Isolated From An Avian Source Has An Alpha-Toxin with Divergent Structural and Kinetic Properties. Biochemistry V. 41 6253 2002.
ISSN: ISSN 0006-2960
PubMed: 12009886
DOI: 10.1021/BI012015V