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

The structure of Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Hydroxamate Inhibitor, PDB code: 4zuq 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)	41.80 / 1.22
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.917, 120.511, 64.408, 90.00, 96.89, 90.00
R / Rfree (%)	13.7 / 15.2

The structure of Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Hydroxamate 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 Hydroxamate Inhibitor (pdb code 4zuq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Hydroxamate Inhibitor, PDB code: 4zuq:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Hydroxamate 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 Hydroxamate Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:6.0 occ:1.00 O9 A:6XA403 2.0 5.1 0.2 OD2 A:ASP284 2.0 6.0 1.0 OD1 A:ASP195 2.0 5.6 1.0 O9 A:6XA403 2.0 7.3 0.8 ND1 A:HIS197 2.1 5.4 1.0 O10 A:6XA403 2.3 10.3 0.8 CG A:ASP195 2.7 5.5 1.0 OD2 A:ASP195 2.8 6.2 1.0 N8 A:6XA403 2.8 8.1 0.8 N8 A:6XA403 2.8 10.1 0.2 C7 A:6XA403 2.8 9.4 0.8 CG A:ASP284 3.0 5.7 1.0 CE1 A:HIS197 3.0 5.6 1.0 O10 A:6XA403 3.1 9.5 0.2 CG A:HIS197 3.2 4.7 1.0 C7 A:6XA403 3.3 10.6 0.2 OD1 A:ASP284 3.3 6.6 1.0 CB A:HIS197 3.6 5.7 1.0 N A:HIS197 3.8 5.1 1.0 NE2 A:HIS158 4.1 7.2 1.0 NE2 A:HIS197 4.2 5.6 1.0 CB A:ASP195 4.2 5.8 1.0 C6 A:6XA403 4.2 13.0 0.8 CB A:ASP284 4.3 6.0 1.0 CD2 A:HIS197 4.3 6.1 1.0 CA A:GLY321 4.3 6.4 1.0 N A:PHE196 4.3 5.0 1.0 CA A:HIS197 4.3 5.4 1.0 CE1 A:HIS158 4.5 6.3 1.0 CE1 A:TYR323 4.5 6.8 1.0 OH A:TYR323 4.6 7.6 1.0 C6 A:6XA403 4.6 8.0 0.2 N A:GLY321 4.6 5.6 1.0 O A:HOH597 4.7 13.2 0.6 CB A:PHE196 4.7 6.3 1.0 C A:PHE196 4.8 5.4 1.0 C A:ASP195 4.8 5.3 1.0 CA A:PHE196 4.8 5.4 1.0 NE2 A:HIS159 4.9 6.9 1.0 CA A:ASP195 4.9 5.0 1.0 C5 A:6XA403 4.9 17.9 0.8 C A:GLY321 5.0 6.0 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Hydroxamate 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 Hydroxamate Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:15.2 occ:0.45 ND1 A:HIS146 2.0 24.2 1.0 CE1 A:HIS146 2.9 25.5 1.0 CG A:HIS146 3.1 20.2 1.0 CB A:HIS146 3.5 15.2 1.0 CA A:HIS146 3.8 15.3 1.0 NE2 A:HIS146 4.0 23.4 1.0 O A:HOH828 4.1 41.2 1.0 CD2 A:HIS146 4.1 21.4 1.0 O A:HOH819 4.5 39.5 1.0 O A:HOH594 4.5 17.2 1.0 N A:LYS147 4.5 12.6 1.0 C A:HIS146 4.7 13.1 1.0 N A:HIS146 4.8 15.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Hydroxamate 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 Hydroxamate Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn404 b:6.0 occ:1.00 OD2 B:ASP284 1.9 6.0 1.0 O9 B:6XA403 2.0 6.5 0.6 O9 B:6XA403 2.0 6.7 0.4 OD1 B:ASP195 2.0 5.5 1.0 ND1 B:HIS197 2.1 5.6 1.0 O10 B:6XA403 2.3 7.9 0.6 CG B:ASP195 2.7 5.0 1.0 N8 B:6XA403 2.7 7.9 0.6 OD2 B:ASP195 2.8 6.5 1.0 N8 B:6XA403 2.8 8.7 0.4 C7 B:6XA403 2.8 8.6 0.6 CG B:ASP284 2.9 5.5 1.0 CE1 B:HIS197 3.0 5.4 1.0 O10 B:6XA403 3.1 10.0 0.4 CG B:HIS197 3.2 5.1 1.0 C7 B:6XA403 3.2 9.3 0.4 OD1 B:ASP284 3.3 6.4 1.0 CB B:HIS197 3.6 6.1 1.0 N B:HIS197 3.8 5.5 1.0 NE2 B:HIS158 4.1 7.2 1.0 NE2 B:HIS197 4.1 5.7 1.0 CB B:ASP195 4.2 6.4 1.0 CB B:ASP284 4.2 5.8 1.0 CD2 B:HIS197 4.3 5.8 1.0 C6 B:6XA403 4.3 10.8 0.6 N B:PHE196 4.3 5.0 1.0 CA B:GLY321 4.3 6.7 1.0 CA B:HIS197 4.3 5.6 1.0 CE1 B:HIS158 4.5 6.2 1.0 CE2 B:TYR323 4.5 6.5 1.0 OH B:TYR323 4.6 6.9 1.0 C6 B:6XA403 4.6 8.0 0.4 N B:GLY321 4.7 5.4 1.0 CB B:PHE196 4.7 6.4 1.0 O B:HOH626 4.7 10.5 0.5 C B:PHE196 4.7 5.5 1.0 C5 B:6XA403 4.8 18.0 0.6 C B:ASP195 4.8 4.8 1.0 CA B:PHE196 4.8 5.0 1.0 NE2 B:HIS159 4.8 6.9 1.0 CA B:ASP195 4.9 5.3 1.0 C B:GLY321 5.0 6.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Hydroxamate 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 Hydroxamate Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn405 b:16.2 occ:0.45 ND1 B:HIS146 2.1 31.0 1.0 CE1 B:HIS146 3.0 32.6 1.0 CG B:HIS146 3.1 25.1 1.0 CB B:HIS146 3.5 19.1 1.0 CA B:HIS146 3.9 16.4 1.0 O B:HOH819 3.9 39.6 1.0 NE2 B:HIS146 4.1 33.0 1.0 CD2 B:HIS146 4.2 27.1 1.0 O B:HOH560 4.4 17.0 1.0 O B:HOH814 4.5 35.5 1.0 N B:LYS147 4.5 13.6 1.0 C B:HIS146 4.7 13.5 1.0 N B:HIS146 5.0 16.8 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