Zinc in PDB 4zup: 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: 4zup 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)	38.68 / 1.42
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.715, 120.903, 64.146, 90.00, 96.98, 90.00
R / Rfree (%)	13.1 / 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)

4 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 4zup). 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: 4zup:
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:Zn401 b:9.3 occ:1.00 OD2 A:ASP284 1.9 10.0 1.0 O8 A:5XA405 2.0 13.2 1.0 OD1 A:ASP195 2.0 7.7 1.0 ND1 A:HIS197 2.1 8.1 1.0 O9 A:5XA405 2.3 18.6 1.0 CG A:ASP195 2.7 8.6 1.0 OD2 A:ASP195 2.8 9.3 1.0 N7 A:5XA405 2.8 13.7 1.0 C6 A:5XA405 2.8 19.1 1.0 CG A:ASP284 2.9 9.2 1.0 CE1 A:HIS197 2.9 8.8 1.0 CG A:HIS197 3.2 7.8 1.0 OD1 A:ASP284 3.3 8.9 1.0 CB A:HIS197 3.6 7.8 1.0 N A:HIS197 3.8 7.8 1.0 NE2 A:HIS197 4.1 8.8 1.0 NE2 A:HIS158 4.1 9.0 1.0 CB A:ASP195 4.2 7.7 1.0 CB A:ASP284 4.2 8.7 1.0 C5 A:5XA405 4.2 22.9 1.0 CD2 A:HIS197 4.3 8.0 1.0 N A:PHE196 4.3 7.1 1.0 CA A:GLY321 4.3 10.1 1.0 CA A:HIS197 4.3 7.7 1.0 CE2 A:TYR323 4.5 10.5 1.0 CE1 A:HIS158 4.5 8.6 1.0 O A:HOH729 4.5 42.0 1.0 OH A:TYR323 4.6 14.6 1.0 N A:GLY321 4.7 8.3 1.0 CB A:PHE196 4.7 8.1 1.0 C A:PHE196 4.7 8.2 1.0 C A:ASP195 4.8 8.0 1.0 C4 A:5XA405 4.8 21.5 1.0 CA A:PHE196 4.8 8.2 1.0 CA A:ASP195 4.9 7.6 1.0 NE2 A:HIS159 4.9 9.5 1.0 C A:GLY321 4.9 9.7 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:Zn402 b:25.1 occ:0.46 O3 A:NO3408 2.1 42.0 0.5 O2 A:NO3408 2.1 42.4 0.5 ND1 A:HIS146 2.1 25.1 1.0 N A:NO3408 2.4 42.2 0.5 O2 A:NO3408 2.9 42.2 0.5 CE1 A:HIS146 3.0 25.6 1.0 CG A:HIS146 3.2 19.6 1.0 O3 A:NO3408 3.3 42.1 0.5 N A:NO3408 3.5 42.2 0.5 CB A:HIS146 3.6 15.7 1.0 O1 A:NO3408 3.6 42.2 0.5 CA A:HIS146 3.7 14.9 1.0 NE2 A:HIS146 4.2 24.6 1.0 CD2 A:HIS146 4.3 21.2 1.0 N A:LYS147 4.5 14.6 1.0 O A:HOH839 4.5 42.3 1.0 C A:HIS146 4.7 13.8 1.0 O A:HOH564 4.7 22.2 1.0 O1 A:NO3408 4.7 42.3 0.5 N A:HIS146 4.7 16.4 1.0 O A:HOH777 4.9 21.8 0.5

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:Zn401 b:8.7 occ:1.00 OD2 B:ASP284 1.9 7.7 1.0 O8 B:5XA405 2.0 13.1 1.0 OD1 B:ASP195 2.0 6.9 1.0 ND1 B:HIS197 2.1 9.3 1.0 OD2 B:ASP195 2.7 7.8 1.0 CG B:ASP195 2.7 9.1 1.0 N7 B:5XA405 2.8 12.8 1.0 O9 B:5XA405 2.8 23.8 1.0 CG B:ASP284 2.9 8.5 1.0 CE1 B:HIS197 3.0 8.9 1.0 C6 B:5XA405 3.1 18.2 1.0 CG B:HIS197 3.2 7.7 1.0 OD1 B:ASP284 3.3 9.0 1.0 CB B:HIS197 3.6 7.4 1.0 N B:HIS197 3.8 7.3 1.0 NE2 B:HIS158 4.1 9.7 1.0 NE2 B:HIS197 4.1 8.2 1.0 CB B:ASP195 4.2 7.7 1.0 CB B:ASP284 4.2 7.5 1.0 CD2 B:HIS197 4.2 7.6 1.0 N B:PHE196 4.3 6.7 1.0 CA B:HIS197 4.3 7.0 1.0 CA B:GLY321 4.3 9.9 1.0 CE1 B:HIS158 4.4 8.5 1.0 OH B:TYR323 4.5 10.2 1.0 C5 B:5XA405 4.5 19.3 1.0 CE2 B:TYR323 4.5 9.2 1.0 N B:GLY321 4.7 7.8 1.0 CB B:PHE196 4.7 7.5 1.0 O B:HOH751 4.7 17.4 0.6 C B:PHE196 4.7 8.0 1.0 CA B:PHE196 4.8 8.1 1.0 C B:ASP195 4.8 6.9 1.0 NE2 B:HIS159 4.8 9.6 1.0 CA B:ASP195 4.9 7.5 1.0 C B:GLY321 5.0 9.9 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:Zn402 b:17.8 occ:0.31 O3 B:NO3408 2.0 36.5 0.3 O2 B:NO3408 2.1 38.7 0.3 ND1 B:HIS146 2.2 33.8 1.0 N B:NO3408 2.4 38.0 0.3 O2 B:NO3408 2.5 38.6 0.7 CE1 B:HIS146 3.0 33.8 1.0 CG B:HIS146 3.2 27.2 1.0 N B:NO3408 3.4 38.5 0.7 O3 B:NO3408 3.5 37.4 0.7 O1 B:NO3408 3.6 38.5 0.3 CB B:HIS146 3.6 19.7 1.0 O B:HOH501 3.8 37.1 1.0 CA B:HIS146 3.8 18.0 1.0 NE2 B:HIS146 4.1 30.5 1.0 CD2 B:HIS146 4.2 29.2 1.0 N B:LYS147 4.6 14.1 1.0 O1 B:NO3408 4.6 38.8 0.7 O B:HOH568 4.6 20.4 1.0 C B:HIS146 4.7 15.7 1.0 N B:HIS146 4.8 18.3 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