Zinc in PDB 4zum: Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Trifluoromethylketone Inhibitor

The structure of Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Trifluoromethylketone Inhibitor, PDB code: 4zum was solved by C.Decroos, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.89 / 1.42
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.119, 121.351, 64.295, 90.00, 96.76, 90.00
R / Rfree (%)	13.3 / 15.3

The structure of Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Trifluoromethylketone Inhibitor also contains other interesting chemical elements:

Fluorine	(F)	6 atoms
Potassium	(K)	2 atoms
Sodium	(Na)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Trifluoromethylketone Inhibitor (pdb code 4zum). 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 From Mycoplana Ramosa in Complex with A Trifluoromethylketone Inhibitor, PDB code: 4zum:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Trifluoromethylketone Inhibitor


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 From Mycoplana Ramosa in Complex with A Trifluoromethylketone Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:6.6 occ:1.00 OD2 A:ASP284 2.0 6.6 1.0 O13 A:FKS404 2.0 7.2 1.0 OD1 A:ASP195 2.0 5.9 1.0 ND1 A:HIS197 2.1 5.4 1.0 O14 A:FKS404 2.4 7.2 1.0 C11 A:FKS404 2.7 9.0 1.0 CG A:ASP195 2.8 7.1 1.0 OD2 A:ASP195 2.8 7.2 1.0 CE1 A:HIS197 2.9 6.3 1.0 CG A:ASP284 3.0 6.2 1.0 CG A:HIS197 3.2 4.5 1.0 OD1 A:ASP284 3.3 6.3 1.0 CB A:HIS197 3.6 5.8 1.0 F16 A:FKS404 3.6 10.9 1.0 N A:HIS197 3.8 5.0 1.0 C12 A:FKS404 3.8 10.7 1.0 C10 A:FKS404 3.8 10.3 1.0 C9 A:FKS404 3.9 9.6 1.0 NE2 A:HIS197 4.1 6.4 1.0 CB A:ASP195 4.2 5.6 1.0 CD2 A:HIS197 4.2 5.0 1.0 N A:PHE196 4.3 5.5 1.0 NE2 A:HIS158 4.3 6.9 1.0 CB A:ASP284 4.3 7.0 1.0 CA A:HIS197 4.3 5.6 1.0 CA A:GLY321 4.4 6.7 1.0 CE1 A:TYR323 4.4 7.1 1.0 OH A:TYR323 4.5 8.4 1.0 F17 A:FKS404 4.5 12.3 1.0 CB A:PHE196 4.7 6.4 1.0 CE1 A:HIS158 4.7 5.6 1.0 N A:GLY321 4.7 6.3 1.0 C A:PHE196 4.7 7.0 1.0 F15 A:FKS404 4.8 10.8 1.0 CA A:PHE196 4.8 6.2 1.0 C A:ASP195 4.8 6.2 1.0 NE2 A:HIS159 4.9 5.9 1.0 CA A:ASP195 4.9 5.2 1.0 CZ A:TYR323 5.0 7.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Trifluoromethylketone Inhibitor


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 From Mycoplana Ramosa in Complex with A Trifluoromethylketone Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:6.6 occ:1.00 OD1 B:ASP195 2.0 5.4 1.0 OD2 B:ASP284 2.0 6.8 1.0 O13 B:FKS404 2.0 6.7 1.0 ND1 B:HIS197 2.1 5.3 1.0 O14 B:FKS404 2.4 7.5 1.0 C11 B:FKS404 2.7 7.7 1.0 CG B:ASP195 2.7 6.7 1.0 OD2 B:ASP195 2.8 6.5 1.0 CE1 B:HIS197 2.9 6.0 1.0 CG B:ASP284 3.0 6.1 1.0 CG B:HIS197 3.2 5.0 1.0 OD1 B:ASP284 3.4 6.0 1.0 CB B:HIS197 3.6 4.8 1.0 F16 B:FKS404 3.6 10.2 1.0 N B:HIS197 3.8 5.4 1.0 C12 B:FKS404 3.8 9.6 1.0 C10 B:FKS404 3.8 8.8 1.0 C9 B:FKS404 3.9 9.4 1.0 NE2 B:HIS197 4.1 6.1 1.0 CB B:ASP195 4.2 5.6 1.0 CD2 B:HIS197 4.2 5.5 1.0 NE2 B:HIS158 4.3 6.0 1.0 CB B:ASP284 4.3 5.6 1.0 N B:PHE196 4.3 5.1 1.0 CA B:HIS197 4.3 5.2 1.0 CA B:GLY321 4.3 6.5 1.0 CE2 B:TYR323 4.4 7.7 1.0 OH B:TYR323 4.5 8.2 1.0 F17 B:FKS404 4.5 12.0 1.0 CB B:PHE196 4.7 4.9 1.0 CE1 B:HIS158 4.7 5.4 1.0 N B:GLY321 4.7 5.7 1.0 C B:PHE196 4.7 6.1 1.0 F15 B:FKS404 4.8 9.9 1.0 CA B:PHE196 4.8 6.0 1.0 C B:ASP195 4.8 5.8 1.0 NE2 B:HIS159 4.9 6.3 1.0 CA B:ASP195 4.9 4.4 1.0 CZ B:TYR323 4.9 7.3 1.0 C B:GLY321 5.0 6.1 1.0

C.Decroos, D.W.Christianson. Design, Synthesis, and Evaluation of Polyamine Deacetylase Inhibitors, and High-Resolution Crystal Structures of Their Complexes with Acetylpolyamine Amidohydrolase. Biochemistry V. 54 4692 2015.
ISSN: ISSN 0006-2960
PubMed: 26200446
DOI: 10.1021/ACS.BIOCHEM.5B00536