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

The structure of Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Thiol Inhibitor, PDB code: 4zun 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)	41.78 / 1.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.859, 120.993, 64.710, 90.00, 97.03, 90.00
R / Rfree (%)	14.6 / 16.4

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

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 Thiol Inhibitor (pdb code 4zun). 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 of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Thiol Inhibitor, PDB code: 4zun:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Thiol 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 Thiol Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:9.9 occ:0.50 ZN A:ZN404 0.0 9.9 0.5 ZN A:ZN404 0.7 11.4 0.5 S11 A:SS9401 1.7 10.7 0.5 OD1 A:ASP195 2.0 10.4 1.0 OD2 A:ASP284 2.1 15.0 1.0 S11 A:SS9401 2.3 9.3 0.5 ND1 A:HIS197 2.3 13.0 1.0 CG A:ASP195 2.7 11.3 1.0 OD2 A:ASP195 2.7 11.1 1.0 CG A:ASP284 3.0 14.3 1.0 C10 A:SS9401 3.1 11.1 0.5 ZN A:ZN405 3.1 12.0 0.5 CE1 A:HIS197 3.2 14.4 1.0 CG A:HIS197 3.3 11.8 1.0 OD1 A:ASP284 3.4 13.0 1.0 C10 A:SS9401 3.5 10.5 0.5 CB A:HIS197 3.7 11.0 1.0 C9 A:SS9401 3.8 10.5 0.5 N A:HIS197 3.9 10.1 1.0 NE2 A:HIS158 4.0 11.3 1.0 CB A:ASP195 4.2 10.8 1.0 CA A:GLY321 4.3 12.7 1.0 CE2 A:TYR323 4.3 14.7 1.0 NE2 A:HIS197 4.3 13.8 1.0 CE1 A:HIS158 4.3 11.0 1.0 C9 A:SS9401 4.4 10.7 0.5 CB A:ASP284 4.4 11.6 1.0 N A:PHE196 4.4 10.2 1.0 CD2 A:HIS197 4.4 11.4 1.0 CA A:HIS197 4.5 10.6 1.0 NE2 A:HIS159 4.5 13.0 1.0 N A:GLY321 4.6 10.7 1.0 OH A:TYR323 4.6 14.9 1.0 O A:HOH793 4.8 6.3 0.5 CB A:PHE196 4.9 11.9 1.0 C A:ASP195 4.9 10.2 1.0 C A:PHE196 4.9 11.2 1.0 C A:GLY321 4.9 13.1 1.0 CA A:ASP195 4.9 10.1 1.0 N A:GLY322 5.0 15.7 1.0 CZ A:TYR323 5.0 13.6 1.0 CA A:PHE196 5.0 11.0 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Thiol 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 Thiol Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:11.4 occ:0.50 ZN A:ZN404 0.0 11.4 0.5 ZN A:ZN404 0.7 9.9 0.5 ND1 A:HIS197 1.8 13.0 1.0 OD2 A:ASP284 1.9 15.0 1.0 OD1 A:ASP195 2.0 10.4 1.0 S11 A:SS9401 2.2 10.7 0.5 CE1 A:HIS197 2.7 14.4 1.0 CG A:ASP284 2.8 14.3 1.0 CG A:ASP195 2.9 11.3 1.0 CG A:HIS197 2.9 11.8 1.0 S11 A:SS9401 2.9 9.3 0.5 OD2 A:ASP195 3.1 11.1 1.0 OD1 A:ASP284 3.1 13.0 1.0 C10 A:SS9401 3.3 11.1 0.5 CB A:HIS197 3.4 11.0 1.0 N A:HIS197 3.5 10.1 1.0 ZN A:ZN405 3.7 12.0 0.5 NE2 A:HIS197 3.8 13.8 1.0 C10 A:SS9401 3.9 10.5 0.5 CD2 A:HIS197 4.0 11.4 1.0 N A:PHE196 4.0 10.2 1.0 C9 A:SS9401 4.0 10.5 0.5 CA A:HIS197 4.1 10.6 1.0 CB A:ASP284 4.1 11.6 1.0 CB A:PHE196 4.3 11.9 1.0 CB A:ASP195 4.3 10.8 1.0 C A:PHE196 4.4 11.2 1.0 CA A:PHE196 4.4 11.0 1.0 NE2 A:HIS158 4.5 11.3 1.0 CE2 A:TYR323 4.6 14.7 1.0 C A:ASP195 4.6 10.2 1.0 CE1 A:HIS158 4.7 11.0 1.0 C9 A:SS9401 4.7 10.7 0.5 CA A:GLY321 4.8 12.7 1.0 CD2 A:PHE196 4.8 12.7 1.0 NE2 A:HIS159 4.8 13.0 1.0 CA A:ASP195 4.9 10.1 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Thiol Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Thiol Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:12.0 occ:0.50 S11 A:SS9401 1.7 9.3 0.5 NE2 A:HIS158 2.0 11.3 1.0 C10 A:SS9401 2.2 10.5 0.5 O A:HOH793 2.3 6.3 0.5 S11 A:SS9401 2.3 10.7 0.5 NE2 A:HIS159 2.4 13.0 1.0 CD2 A:HIS158 2.8 10.7 1.0 CD2 A:HIS159 2.9 11.0 1.0 CE1 A:HIS158 3.1 11.0 1.0 ZN A:ZN404 3.1 9.9 0.5 C10 A:SS9401 3.1 11.1 0.5 CE1 A:HIS159 3.5 14.4 1.0 C9 A:SS9401 3.6 10.7 0.5 C9 A:SS9401 3.6 10.5 0.5 ZN A:ZN404 3.7 11.4 0.5 OD2 A:ASP195 3.8 11.1 1.0 OD1 A:ASP195 3.8 10.4 1.0 CG A:ASP195 4.0 11.3 1.0 CG A:HIS158 4.0 9.7 1.0 CG A:HIS159 4.1 9.0 1.0 ND1 A:HIS158 4.1 10.2 1.0 ND1 A:HIS159 4.3 11.4 1.0 O A:GLY167 4.4 11.7 1.0 ND1 A:HIS197 4.5 13.0 1.0 OH A:TYR323 4.5 14.9 1.0 CB A:HIS197 4.5 11.0 1.0 C8 A:SS9401 4.6 11.6 0.5 N A:GLY321 4.7 10.7 1.0 C8 A:SS9401 4.8 11.3 0.5 SG A:CYS169 4.8 10.8 1.0 CG A:HIS197 4.8 11.8 1.0 CA A:GLY321 4.9 12.7 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Thiol Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Thiol Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:10.8 occ:0.50 ZN B:ZN403 0.0 10.8 0.5 ZN B:ZN403 0.7 10.7 0.5 S11 B:SS9405 1.8 9.8 0.5 OD1 B:ASP195 1.9 10.6 1.0 OD2 B:ASP284 2.2 14.8 1.0 S11 B:SS9405 2.3 10.1 0.5 ND1 B:HIS197 2.3 13.3 1.0 CG B:ASP195 2.6 11.7 1.0 OD2 B:ASP195 2.6 12.2 1.0 ZN B:ZN404 3.1 11.0 0.5 CG B:ASP284 3.1 12.2 1.0 C10 B:SS9405 3.1 10.3 0.5 CE1 B:HIS197 3.3 13.3 1.0 CG B:HIS197 3.3 11.7 1.0 OD1 B:ASP284 3.4 12.2 1.0 C10 B:SS9405 3.5 10.5 0.5 CB B:HIS197 3.6 11.6 1.0 C9 B:SS9405 3.8 10.6 0.5 N B:HIS197 3.9 10.3 1.0 NE2 B:HIS158 4.0 11.3 1.0 CB B:ASP195 4.1 10.5 1.0 CA B:GLY321 4.3 11.6 0.3 CE1 B:HIS158 4.3 12.1 1.0 CE2 B:TYR323 4.3 11.7 0.7 CA B:GLY321 4.3 12.3 0.7 CA B:HIS197 4.4 10.7 1.0 NE2 B:HIS197 4.4 14.7 1.0 N B:PHE196 4.4 9.5 1.0 CD2 B:HIS197 4.4 11.5 1.0 C9 B:SS9405 4.4 9.9 0.5 CB B:ASP284 4.5 12.0 1.0 NE2 B:HIS159 4.5 13.6 1.0 N B:GLY321 4.6 11.1 0.3 N B:GLY321 4.7 10.6 0.7 OH B:TYR323 4.7 13.9 0.7 C B:GLY321 4.7 12.5 0.3 O B:HOH804 4.8 6.6 0.5 C B:ASP195 4.8 10.1 1.0 C B:PHE196 4.9 10.8 1.0 CA B:ASP195 4.9 10.0 1.0 N B:GLY322 4.9 13.3 0.3 CB B:PHE196 4.9 12.0 1.0 CA B:PHE196 5.0 10.4 1.0 C B:GLY321 5.0 11.6 0.7

Zinc binding site 5 out of 6 in the Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Thiol Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Thiol Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:10.7 occ:0.50 ZN B:ZN403 0.0 10.7 0.5 ZN B:ZN403 0.7 10.8 0.5 OD2 B:ASP284 1.8 14.8 1.0 ND1 B:HIS197 1.8 13.3 1.0 OD1 B:ASP195 2.1 10.6 1.0 S11 B:SS9405 2.2 9.8 0.5 CE1 B:HIS197 2.7 13.3 1.0 CG B:ASP284 2.8 12.2 1.0 S11 B:SS9405 2.9 10.1 0.5 CG B:ASP195 2.9 11.7 1.0 CG B:HIS197 3.0 11.7 1.0 OD2 B:ASP195 3.1 12.2 1.0 OD1 B:ASP284 3.2 12.2 1.0 C10 B:SS9405 3.3 10.3 0.5 CB B:HIS197 3.5 11.6 1.0 N B:HIS197 3.5 10.3 1.0 ZN B:ZN404 3.7 11.0 0.5 C10 B:SS9405 3.9 10.5 0.5 NE2 B:HIS197 3.9 14.7 1.0 C9 B:SS9405 3.9 10.6 0.5 CD2 B:HIS197 4.0 11.5 1.0 CB B:ASP284 4.1 12.0 1.0 N B:PHE196 4.1 9.5 1.0 CA B:HIS197 4.1 10.7 1.0 CB B:PHE196 4.4 12.0 1.0 CB B:ASP195 4.4 10.5 1.0 CE2 B:TYR323 4.4 11.7 0.7 C B:PHE196 4.5 10.8 1.0 CA B:PHE196 4.5 10.4 1.0 NE2 B:HIS158 4.6 11.3 1.0 C9 B:SS9405 4.7 9.9 0.5 CA B:GLY321 4.7 11.6 0.3 C B:ASP195 4.7 10.1 1.0 CE1 B:HIS158 4.8 12.1 1.0 CA B:GLY321 4.8 12.3 0.7 NE2 B:HIS159 4.9 13.6 1.0 CD2 B:PHE196 4.9 12.4 1.0 CA B:ASP195 4.9 10.0 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Thiol Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Thiol Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn404 b:11.0 occ:0.50 S11 B:SS9405 1.5 10.1 0.5 C10 B:SS9405 2.1 10.5 0.5 NE2 B:HIS158 2.1 11.3 1.0 O B:HOH804 2.2 6.6 0.5 S11 B:SS9405 2.3 9.8 0.5 NE2 B:HIS159 2.4 13.6 1.0 CD2 B:HIS159 2.9 12.1 1.0 CD2 B:HIS158 2.9 10.0 1.0 C10 B:SS9405 3.1 10.3 0.5 ZN B:ZN403 3.1 10.8 0.5 CE1 B:HIS158 3.2 12.1 1.0 CE1 B:HIS159 3.5 12.9 1.0 C9 B:SS9405 3.5 9.9 0.5 C9 B:SS9405 3.5 10.6 0.5 ZN B:ZN403 3.7 10.7 0.5 OD2 B:ASP195 3.8 12.2 1.0 OD1 B:ASP195 3.9 10.6 1.0 CG B:ASP195 4.1 11.7 1.0 CG B:HIS159 4.1 9.6 1.0 CG B:HIS158 4.1 10.3 1.0 ND1 B:HIS158 4.3 10.4 1.0 OH B:TYR323 4.3 13.9 0.7 ND1 B:HIS159 4.4 11.7 1.0 O B:GLY167 4.4 11.4 1.0 ND1 B:HIS197 4.5 13.3 1.0 C8 B:SS9405 4.5 11.7 0.5 CB B:HIS197 4.5 11.6 1.0 N B:GLY321 4.5 11.1 0.3 CA B:GLY321 4.6 11.6 0.3 N B:GLY321 4.7 10.6 0.7 C8 B:SS9405 4.7 11.2 0.5 SG B:CYS169 4.8 11.1 1.0 CG B:HIS197 4.8 11.7 1.0 CA B:GLY321 4.9 12.3 0.7

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