Zinc in PDB 1olp: Alpha Toxin From Clostridium Absonum

All present enzymatic activity of Alpha Toxin From Clostridium Absonum:
3.1.4.3;

The structure of Alpha Toxin From Clostridium Absonum, PDB code: 1olp was solved by D.C.Briggs, A.K.Basak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.75 / 2.5
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	92.956, 193.592, 92.686, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 23.7

The structure of Alpha Toxin From Clostridium Absonum also contains other interesting chemical elements:

Calcium

(Ca)

8 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Alpha Toxin From Clostridium Absonum (pdb code 1olp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Alpha Toxin From Clostridium Absonum, PDB code: 1olp:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the Alpha Toxin From Clostridium Absonum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Alpha Toxin From Clostridium Absonum within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1373 b:24.6 occ:1.00 NE2 A:HIS11 2.0 21.1 1.0 OD1 A:ASP130 2.1 20.4 1.0 N A:TRP1 2.2 25.3 1.0 O A:TRP1 2.2 26.6 1.0 CE1 A:HIS11 2.9 21.6 1.0 C A:TRP1 2.9 26.2 1.0 CD2 A:HIS11 3.0 22.2 1.0 CA A:TRP1 3.0 25.4 1.0 CG A:ASP130 3.1 18.1 1.0 ZN A:ZN1375 3.4 23.6 1.0 OD2 A:ASP130 3.4 17.6 1.0 CB A:TRP1 3.7 25.2 1.0 CE1 A:HIS126 3.9 18.8 1.0 NE2 A:HIS126 3.9 18.0 1.0 OD2 A:ASP56 3.9 19.8 1.0 ND1 A:HIS11 4.0 20.4 1.0 CG A:HIS11 4.1 21.7 1.0 N A:ASP2 4.2 26.7 1.0 CB A:ASP130 4.5 17.7 1.0 CG A:TRP1 4.5 23.9 1.0 OD1 A:ASP56 4.7 22.8 1.0 CA A:ASP130 4.7 17.7 1.0 CD1 A:TRP1 4.7 22.6 1.0 OE1 A:GLU152 4.7 34.9 1.0 ND1 A:HIS126 4.7 18.2 1.0 CG A:ASP56 4.8 20.4 1.0 CD2 A:HIS126 4.8 18.7 1.0 OE2 A:GLU152 4.9 35.2 1.0 CE1 A:HIS136 4.9 24.4 1.0 OG1 A:THR133 4.9 21.5 1.0 NE2 A:HIS136 4.9 23.7 1.0

Zinc binding site 2 out of 12 in the Alpha Toxin From Clostridium Absonum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Alpha Toxin From Clostridium Absonum within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1374 b:43.7 occ:1.00 NE2 A:HIS148 2.1 36.7 1.0 NE2 A:HIS136 2.3 23.7 1.0 OE2 A:GLU152 2.3 35.2 1.0 OE1 A:GLU152 2.8 34.9 1.0 CD A:GLU152 2.8 32.7 1.0 CE1 A:HIS148 3.1 37.4 1.0 CD2 A:HIS148 3.2 37.7 1.0 CE1 A:HIS136 3.2 24.4 1.0 CD2 A:HIS136 3.2 25.9 1.0 O A:HOH2027 3.7 34.3 1.0 CG A:GLU152 4.2 31.6 1.0 ND1 A:HIS148 4.2 38.0 1.0 CG A:HIS148 4.3 39.0 1.0 ND1 A:HIS136 4.3 24.9 1.0 CG A:HIS136 4.4 24.6 1.0 N A:TRP1 4.7 25.3 1.0 CZ A:PHE69 4.9 17.6 1.0

Zinc binding site 3 out of 12 in the Alpha Toxin From Clostridium Absonum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Alpha Toxin From Clostridium Absonum within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1375 b:23.6 occ:1.00 OD2 A:ASP130 2.0 17.6 1.0 ND1 A:HIS68 2.1 19.2 1.0 NE2 A:HIS126 2.2 18.0 1.0 OD1 A:ASP56 2.6 22.8 1.0 CE1 A:HIS68 2.8 20.7 1.0 CE1 A:HIS126 3.1 18.8 1.0 CG A:ASP130 3.1 18.1 1.0 CD2 A:HIS126 3.2 18.7 1.0 CG A:HIS68 3.3 18.9 1.0 ZN A:ZN1373 3.4 24.6 1.0 OD1 A:ASP130 3.4 20.4 1.0 CG A:ASP56 3.5 20.4 1.0 OD2 A:ASP56 3.6 19.8 1.0 CB A:HIS68 3.8 19.2 1.0 NE2 A:HIS68 4.0 18.6 1.0 O A:HOH2027 4.0 34.3 1.0 ND1 A:HIS126 4.2 18.2 1.0 CD2 A:HIS68 4.2 18.8 1.0 CG A:HIS126 4.3 18.1 1.0 NE2 A:HIS11 4.4 21.1 1.0 CB A:ASP130 4.4 17.7 1.0 CE1 A:HIS136 4.6 24.4 1.0 CE1 A:HIS11 4.7 21.6 1.0 CB A:ASP56 4.8 20.5 1.0 O A:TRP1 4.9 26.6 1.0 N A:ASP56 5.0 20.5 1.0

Zinc binding site 4 out of 12 in the Alpha Toxin From Clostridium Absonum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Alpha Toxin From Clostridium Absonum within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1373 b:23.1 occ:1.00 NE2 B:HIS11 2.1 14.2 1.0 OD1 B:ASP130 2.2 24.0 1.0 O B:TRP1 2.2 28.0 1.0 N B:TRP1 2.3 27.4 1.0 C B:TRP1 2.9 28.1 1.0 CE1 B:HIS11 3.0 16.5 1.0 CA B:TRP1 3.0 27.8 1.0 CD2 B:HIS11 3.1 16.4 1.0 CG B:ASP130 3.2 23.5 1.0 ZN B:ZN1375 3.3 26.0 1.0 OD2 B:ASP130 3.5 22.4 1.0 CB B:TRP1 3.7 27.7 1.0 CE1 B:HIS126 3.9 21.6 1.0 OD2 B:ASP56 4.0 24.1 1.0 NE2 B:HIS126 4.1 21.9 1.0 ND1 B:HIS11 4.1 13.4 1.0 CG B:HIS11 4.2 16.9 1.0 N B:ASP2 4.2 28.7 1.0 OE2 B:GLU152 4.3 39.7 1.0 CG B:TRP1 4.4 28.3 1.0 CB B:ASP130 4.5 23.5 1.0 CD1 B:TRP1 4.6 27.4 1.0 OD1 B:ASP56 4.7 26.3 1.0 CE1 B:HIS136 4.7 28.4 1.0 CA B:ASP130 4.7 23.3 1.0 ND1 B:HIS126 4.8 21.4 1.0 CG B:ASP56 4.8 24.4 1.0 OG1 B:THR133 4.9 21.0 1.0 O B:HOH2001 4.9 31.6 1.0 NE2 B:HIS136 5.0 28.8 1.0

Zinc binding site 5 out of 12 in the Alpha Toxin From Clostridium Absonum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Alpha Toxin From Clostridium Absonum within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1374 b:46.4 occ:1.00 NE2 B:HIS148 2.0 42.2 1.0 NE2 B:HIS136 2.1 28.8 1.0 OE2 B:GLU152 2.4 39.7 1.0 OE1 B:GLU152 2.8 40.5 1.0 CD B:GLU152 2.8 37.9 1.0 CE1 B:HIS148 2.8 43.2 1.0 CE1 B:HIS136 3.0 28.4 1.0 CD2 B:HIS148 3.1 42.8 1.0 CD2 B:HIS136 3.1 28.1 1.0 O B:HOH2020 3.9 32.0 1.0 ND1 B:HIS148 4.0 42.9 1.0 ND1 B:HIS136 4.1 28.9 1.0 CG B:HIS148 4.1 41.6 1.0 CG B:GLU152 4.2 35.1 1.0 CG B:HIS136 4.2 29.3 1.0 O B:HOH2047 4.2 28.8 1.0 O B:HOH2001 4.3 31.6 1.0 N B:TRP1 4.7 27.4 1.0 CZ B:PHE69 4.8 23.2 1.0

Zinc binding site 6 out of 12 in the Alpha Toxin From Clostridium Absonum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Alpha Toxin From Clostridium Absonum within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1375 b:26.0 occ:1.00 OD2 B:ASP130 2.1 22.4 1.0 ND1 B:HIS68 2.2 22.6 1.0 NE2 B:HIS126 2.2 21.9 1.0 OD1 B:ASP56 2.6 26.3 1.0 CE1 B:HIS68 2.9 23.0 1.0 CG B:ASP130 3.1 23.5 1.0 CE1 B:HIS126 3.1 21.6 1.0 CD2 B:HIS126 3.2 21.6 1.0 CG B:HIS68 3.3 24.6 1.0 OD1 B:ASP130 3.3 24.0 1.0 ZN B:ZN1373 3.3 23.1 1.0 CG B:ASP56 3.5 24.4 1.0 OD2 B:ASP56 3.6 24.1 1.0 CB B:HIS68 3.8 25.1 1.0 NE2 B:HIS68 4.0 21.1 1.0 ND1 B:HIS126 4.2 21.4 1.0 CD2 B:HIS68 4.2 23.5 1.0 NE2 B:HIS11 4.3 14.2 1.0 O B:HOH2020 4.3 32.0 1.0 CG B:HIS126 4.3 21.0 1.0 CB B:ASP130 4.4 23.5 1.0 CE1 B:HIS11 4.6 16.5 1.0 CE1 B:HIS136 4.7 28.4 1.0 O B:TRP1 4.9 28.0 1.0 CB B:ASP56 4.9 23.6 1.0 CA B:HIS68 5.0 25.3 1.0

Zinc binding site 7 out of 12 in the Alpha Toxin From Clostridium Absonum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Alpha Toxin From Clostridium Absonum within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1373 b:29.3 occ:1.00 N C:TRP1 2.0 30.9 1.0 OD1 C:ASP130 2.0 25.3 1.0 NE2 C:HIS11 2.0 26.7 1.0 O C:TRP1 2.3 31.9 1.0 CA C:TRP1 3.0 31.3 1.0 C C:TRP1 3.0 31.9 1.0 CE1 C:HIS11 3.0 26.8 1.0 CG C:ASP130 3.0 26.0 1.0 CD2 C:HIS11 3.1 27.2 1.0 OD2 C:ASP130 3.2 25.2 1.0 ZN C:ZN1375 3.4 32.2 1.0 CB C:TRP1 3.8 31.1 1.0 OD2 C:ASP56 3.9 31.4 1.0 CE1 C:HIS126 3.9 28.6 1.0 NE2 C:HIS126 4.1 28.4 1.0 ND1 C:HIS11 4.1 25.2 1.0 CG C:HIS11 4.2 27.0 1.0 N C:ASP2 4.3 32.8 1.0 CB C:ASP130 4.4 26.2 1.0 OE1 C:GLU152 4.5 40.3 1.0 CG C:TRP1 4.5 29.9 1.0 OD1 C:ASP56 4.5 32.5 1.0 CG C:ASP56 4.7 31.3 1.0 ND1 C:HIS126 4.7 27.4 1.0 CD1 C:TRP1 4.7 28.6 1.0 CA C:ASP130 4.7 26.1 1.0 CE1 C:HIS136 4.8 30.2 1.0 OG1 C:THR133 4.8 28.0 1.0 O C:HOH2052 5.0 34.3 1.0

Zinc binding site 8 out of 12 in the Alpha Toxin From Clostridium Absonum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Alpha Toxin From Clostridium Absonum within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1374 b:36.7 occ:1.00 OE2 C:GLU152 1.9 33.1 1.0 NE2 C:HIS136 2.0 28.7 1.0 NE2 C:HIS148 2.1 40.7 1.0 CD C:GLU152 2.8 36.5 1.0 CE1 C:HIS136 2.9 30.2 1.0 CE1 C:HIS148 3.1 41.1 1.0 O C:HOH2052 3.1 34.3 1.0 CD2 C:HIS136 3.1 28.6 1.0 CD2 C:HIS148 3.1 42.7 1.0 OE1 C:GLU152 3.2 40.3 1.0 ND1 C:HIS136 4.0 29.5 1.0 CG C:HIS136 4.2 28.9 1.0 ND1 C:HIS148 4.2 41.6 1.0 CG C:GLU152 4.2 37.0 1.0 CG C:HIS148 4.3 42.9 1.0 N C:TRP1 4.8 30.9 1.0 CZ C:PHE69 4.9 26.6 1.0

Zinc binding site 9 out of 12 in the Alpha Toxin From Clostridium Absonum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Alpha Toxin From Clostridium Absonum within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1375 b:32.2 occ:1.00 OD2 C:ASP130 2.0 25.2 1.0 NE2 C:HIS126 2.1 28.4 1.0 ND1 C:HIS68 2.2 24.6 1.0 OD1 C:ASP56 2.4 32.5 1.0 CE1 C:HIS126 2.9 28.6 1.0 CE1 C:HIS68 3.0 25.0 1.0 CG C:ASP130 3.0 26.0 1.0 CD2 C:HIS126 3.2 27.9 1.0 CG C:HIS68 3.3 25.4 1.0 ZN C:ZN1373 3.4 29.3 1.0 CG C:ASP56 3.4 31.3 1.0 OD1 C:ASP130 3.4 25.3 1.0 OD2 C:ASP56 3.6 31.4 1.0 CB C:HIS68 3.7 25.8 1.0 ND1 C:HIS126 4.0 27.4 1.0 NE2 C:HIS68 4.2 23.2 1.0 CG C:HIS126 4.2 27.0 1.0 NE2 C:HIS11 4.3 26.7 1.0 O C:HOH2052 4.3 34.3 1.0 CD2 C:HIS68 4.3 25.3 1.0 CB C:ASP130 4.4 26.2 1.0 CE1 C:HIS136 4.7 30.2 1.0 CE1 C:HIS11 4.7 26.8 1.0 CB C:ASP56 4.7 30.4 1.0 N C:ASP56 4.9 29.5 1.0 O C:TRP1 5.0 31.9 1.0

Zinc binding site 10 out of 12 in the Alpha Toxin From Clostridium Absonum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Alpha Toxin From Clostridium Absonum within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1373 b:27.2 occ:1.00 NE2 D:HIS11 2.0 22.6 1.0 O D:TRP1 2.1 29.0 1.0 OD1 D:ASP130 2.1 25.7 1.0 N D:TRP1 2.2 29.3 1.0 C D:TRP1 2.9 29.4 1.0 CE1 D:HIS11 2.9 25.9 1.0 CA D:TRP1 3.0 29.3 1.0 CD2 D:HIS11 3.1 24.0 1.0 CG D:ASP130 3.2 27.2 1.0 ZN D:ZN1375 3.3 28.6 1.0 OD2 D:ASP130 3.5 28.8 1.0 CB D:TRP1 3.7 29.3 1.0 OD2 D:ASP56 3.8 31.0 1.0 CE1 D:HIS126 3.8 23.9 1.0 NE2 D:HIS126 4.0 22.8 1.0 ND1 D:HIS11 4.0 24.2 1.0 N D:ASP2 4.1 29.5 1.0 NZ A:LYS83 4.2 32.4 1.0 CG D:HIS11 4.2 25.4 1.0 CE1 D:HIS136 4.4 30.7 1.0 NE2 D:HIS136 4.5 30.3 1.0 CB D:ASP130 4.5 28.0 1.0 CG D:TRP1 4.5 29.1 1.0 OE2 D:GLU152 4.6 32.2 1.0 OD1 D:ASP56 4.6 27.0 1.0 CG D:ASP56 4.7 27.4 1.0 ND1 D:HIS126 4.7 23.5 1.0 CA D:ASP130 4.8 28.2 1.0 ZN D:ZN1374 4.8 29.6 1.0 CD1 D:TRP1 4.9 28.0 1.0 CA D:ASP2 4.9 30.0 1.0 CD2 D:HIS126 4.9 22.9 1.0 OG1 D:THR133 5.0 32.2 1.0

G.Clark, D.C.Briggs, T.Karasawa, X.Wang, A.Cole, T.Maegawa, P.Jayasekera, C.Naylor, J.Miller, D.Moss, S.Nakamura, A.K.Basak, R.Titball. Clostridium Absonum Alpha-Toxin: New Insights Into Clostridial Phospholipase C Substrate Binding and Specificity J.Mol.Biol. V. 333 759 2003.
ISSN: ISSN 0022-2836
PubMed: 14568535
DOI: 10.1016/J.JMB.2003.07.016