Zinc in PDB 9gkz: Crystal Structure of Acetylpolyamine Amidohydrolase (Apah) From Pseudomonas Sp. M30-35

The structure of Crystal Structure of Acetylpolyamine Amidohydrolase (Apah) From Pseudomonas Sp. M30-35, PDB code: 9gkz was solved by L.G.Graf, S.Schulze, G.J.Palm, M.Lammers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	73.67 / 2.72
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	147.342, 48.858, 82.249, 90, 90, 90
R / Rfree (%)	15.6 / 23.3

The structure of Crystal Structure of Acetylpolyamine Amidohydrolase (Apah) From Pseudomonas Sp. M30-35 also contains other interesting chemical elements:

Potassium	(K)	6 atoms
Chlorine	(Cl)	1 atom

The binding sites of Zinc atom in the Crystal Structure of Acetylpolyamine Amidohydrolase (Apah) From Pseudomonas Sp. M30-35 (pdb code 9gkz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Acetylpolyamine Amidohydrolase (Apah) From Pseudomonas Sp. M30-35, PDB code: 9gkz:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Acetylpolyamine Amidohydrolase (Apah) From Pseudomonas Sp. M30-35


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Acetylpolyamine Amidohydrolase (Apah) From Pseudomonas Sp. M30-35 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:30.6 occ:1.00 OD1 A:ASP195 2.0 32.2 1.0 OD2 A:ASP284 2.1 32.0 1.0 ND1 A:HIS197 2.3 33.6 1.0 CL A:CL406 2.7 50.0 1.0 CG A:ASP195 3.0 29.6 1.0 CG A:ASP284 3.2 29.3 1.0 CE1 A:HIS197 3.2 31.4 1.0 CG A:HIS197 3.2 28.6 1.0 OD2 A:ASP195 3.3 31.5 1.0 CB A:HIS197 3.5 26.5 1.0 OD1 A:ASP284 3.6 29.4 1.0 N A:HIS197 3.9 26.4 1.0 CA A:GLY321 4.2 30.6 1.0 NE2 A:HIS158 4.2 33.7 1.0 NE2 A:HIS197 4.3 30.4 1.0 CD2 A:HIS197 4.3 31.3 1.0 CA A:HIS197 4.3 26.7 1.0 CB A:ASP195 4.3 22.8 1.0 N A:TYR196 4.4 24.2 1.0 NE2 A:HIS159 4.4 31.8 1.0 CB A:ASP284 4.5 26.1 1.0 CE1 A:HIS158 4.6 27.1 1.0 N A:GLY321 4.6 31.7 1.0 O A:HOH553 4.6 39.1 1.0 O A:HOH560 4.7 31.3 1.0 C A:TYR196 4.7 27.5 1.0 CB A:TYR196 4.8 24.3 1.0 CA A:TYR196 4.8 26.4 1.0 C A:GLY321 4.9 32.9 1.0 C A:ASP195 5.0 29.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Acetylpolyamine Amidohydrolase (Apah) From Pseudomonas Sp. M30-35


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Acetylpolyamine Amidohydrolase (Apah) From Pseudomonas Sp. M30-35 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn406 b:31.9 occ:1.00 OD2 B:ASP195 1.9 27.8 1.0 OD2 B:ASP284 2.0 32.2 1.0 O B:ACT401 2.2 34.9 1.0 ND1 B:HIS197 2.3 28.6 1.0 C B:ACT401 2.8 37.4 1.0 CG B:ASP195 2.8 31.3 1.0 OXT B:ACT401 2.8 36.4 1.0 OD1 B:ASP195 3.0 32.5 1.0 CG B:ASP284 3.1 31.4 1.0 CE1 B:HIS197 3.2 29.6 1.0 CG B:HIS197 3.3 24.3 1.0 OD1 B:ASP284 3.5 28.6 1.0 CB B:HIS197 3.6 24.7 1.0 N B:HIS197 3.9 29.0 1.0 CA B:GLY321 4.1 33.1 1.0 CB B:ASP195 4.2 26.1 1.0 NE2 B:HIS197 4.3 29.4 1.0 CH3 B:ACT401 4.3 31.0 1.0 CB B:ASP284 4.3 28.3 1.0 CD2 B:HIS197 4.3 28.5 1.0 O B:HOH549 4.4 33.3 1.0 CA B:HIS197 4.4 25.3 1.0 N B:TYR196 4.4 29.0 1.0 NE2 B:HIS158 4.4 36.8 1.0 O B:HOH554 4.4 27.3 1.0 N B:GLY321 4.5 35.1 1.0 CE1 B:HIS158 4.6 33.4 1.0 CB B:TYR196 4.8 22.0 1.0 C B:TYR196 4.8 28.5 1.0 NE2 B:HIS159 4.9 34.0 1.0 C B:GLY321 4.9 33.8 1.0 CA B:TYR196 4.9 23.6 1.0 C B:ASP195 5.0 27.7 1.0

L.G.Graf, C.Moreno-Yruela, C.Qin, S.Schulze, G.J.Palm, O.Schmoeker, N.Wang, D.Hocking, L.Jebeli, B.Girbardt, L.Berndt, D.M.Weis, M.Janetzky, D.Zuehlke, S.Sievers, R.A.Strugnell, C.A.Olsen, K.Hofmann, M.Lammers. Distribution and Diversity of Classical Deacylases in Bacteria Nature Communications 2024.