Zinc in PDB 4zuo: 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: 4zuo 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)	38.84 / 1.33
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.998, 121.076, 64.417, 90.00, 96.75, 90.00
R / Rfree (%)	13.3 / 14.7

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

The binding sites of Zinc atom in the Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Hydroxamate Inhibitor (pdb code 4zuo). 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 Hydroxamate Inhibitor, PDB code: 4zuo:
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 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:Zn401 b:8.9 occ:1.00 OD2 A:ASP284 1.9 9.6 1.0 O14 A:XS6404 1.9 9.9 0.8 OD1 A:ASP195 2.0 8.3 1.0 ND1 A:HIS197 2.1 8.7 1.0 O A:HOH511 2.1 14.8 0.1 O A:HOH557 2.2 14.8 0.1 CG A:ASP195 2.7 7.7 1.0 N13 A:XS6404 2.8 8.5 0.8 OD2 A:ASP195 2.8 8.4 1.0 CG A:ASP284 2.9 9.3 1.0 CE1 A:HIS197 3.0 8.8 1.0 O12 A:XS6404 3.1 12.2 0.8 CG A:HIS197 3.2 8.2 1.0 C11 A:XS6404 3.2 11.0 0.8 OD1 A:ASP284 3.3 10.4 1.0 CB A:HIS197 3.6 8.9 1.0 N A:HIS197 3.8 8.5 1.0 NE2 A:HIS158 4.0 8.5 1.0 NE2 A:HIS197 4.1 8.6 1.0 CB A:ASP195 4.2 8.9 1.0 CB A:ASP284 4.2 8.2 1.0 CD2 A:HIS197 4.2 8.3 1.0 N A:PHE196 4.3 8.2 1.0 CA A:HIS197 4.3 8.5 1.0 CE1 A:HIS158 4.4 9.1 1.0 CA A:GLY321 4.4 10.5 1.0 OH A:TYR323 4.5 10.4 1.0 CE1 A:TYR323 4.6 9.5 1.0 C10 A:XS6404 4.6 11.3 0.8 CB A:PHE196 4.7 9.5 1.0 N A:GLY321 4.7 9.5 1.0 C A:PHE196 4.7 8.7 1.0 O A:HOH756 4.8 12.7 0.7 NE2 A:HIS159 4.8 9.6 1.0 CA A:PHE196 4.8 8.3 1.0 C A:ASP195 4.8 8.3 1.0 CA A:ASP195 4.9 8.3 1.0

Zinc binding site 2 out of 2 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 B:Zn401 b:9.2 occ:1.00 O14 B:XS6404 1.9 10.2 0.8 OD1 B:ASP195 2.0 8.2 1.0 OD2 B:ASP284 2.0 10.1 1.0 O B:HOH539 2.0 7.1 0.1 ND1 B:HIS197 2.1 8.4 1.0 O B:HOH541 2.1 11.1 0.1 CG B:ASP195 2.7 9.1 1.0 OD2 B:ASP195 2.8 8.9 1.0 N13 B:XS6404 2.8 8.7 0.8 CG B:ASP284 3.0 8.6 1.0 CE1 B:HIS197 3.0 8.8 1.0 O12 B:XS6404 3.0 15.1 0.8 CG B:HIS197 3.2 8.5 1.0 C11 B:XS6404 3.2 12.5 0.8 OD1 B:ASP284 3.3 9.8 1.0 CB B:HIS197 3.6 8.0 1.0 N B:HIS197 3.8 7.7 1.0 NE2 B:HIS158 4.0 9.0 1.0 NE2 B:HIS197 4.1 8.9 1.0 CB B:ASP195 4.2 8.2 1.0 CD2 B:HIS197 4.2 8.4 1.0 CB B:ASP284 4.3 8.5 1.0 N B:PHE196 4.3 8.0 1.0 CA B:HIS197 4.3 7.5 1.0 CA B:GLY321 4.4 9.9 1.0 CE1 B:HIS158 4.4 9.1 1.0 OH B:TYR323 4.5 11.1 1.0 CE2 B:TYR323 4.5 10.5 1.0 C10 B:XS6404 4.6 12.1 0.8 N B:GLY321 4.7 9.2 1.0 CB B:PHE196 4.7 8.5 1.0 C B:PHE196 4.7 8.3 1.0 O B:HOH795 4.8 12.2 0.6 C B:ASP195 4.8 8.4 1.0 NE2 B:HIS159 4.8 10.4 1.0 CA B:PHE196 4.8 7.8 1.0 CA B:ASP195 4.9 7.7 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