Zinc in PDB 6pid: Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 8-Amino-N-Hydroxyoctanamide

The structure of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 8-Amino-N-Hydroxyoctanamide, PDB code: 6pid was solved by J.D.Osko, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.53 / 1.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.330, 119.060, 66.220, 90.00, 109.24, 90.00
R / Rfree (%)	24.4 / 28.1

The structure of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 8-Amino-N-Hydroxyoctanamide also contains other interesting chemical elements:

Magnesium	(Mg)	3 atoms
Potassium	(K)	4 atoms

The binding sites of Zinc atom in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 8-Amino-N-Hydroxyoctanamide (pdb code 6pid). 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 Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 8-Amino-N-Hydroxyoctanamide, PDB code: 6pid:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 8-Amino-N-Hydroxyoctanamide


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 Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 8-Amino-N-Hydroxyoctanamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:8.8 occ:1.00 O11 A:OKS406 1.9 8.0 1.0 OD2 A:ASP284 2.0 9.2 1.0 OD1 A:ASP195 2.1 8.6 1.0 ND1 A:HIS197 2.2 10.3 1.0 O12 A:OKS406 2.7 16.8 1.0 OD2 A:ASP195 2.7 11.0 1.0 CG A:ASP195 2.7 9.1 1.0 N10 A:OKS406 2.8 12.1 1.0 CG A:ASP284 3.0 11.3 1.0 C09 A:OKS406 3.1 14.2 1.0 CE1 A:HIS197 3.1 10.8 1.0 OD1 A:ASP284 3.3 5.1 1.0 CG A:HIS197 3.3 7.2 1.0 CB A:HIS197 3.7 8.4 1.0 N A:HIS197 3.8 7.8 1.0 NE2 A:HIS158 4.1 10.2 1.0 CA A:GLY321 4.2 13.0 1.0 CB A:ASP195 4.2 6.9 1.0 N A:PHE196 4.2 4.7 1.0 NE2 A:HIS197 4.2 10.8 1.0 CB A:ASP284 4.3 9.1 1.0 CA A:HIS197 4.3 9.4 1.0 CD2 A:HIS197 4.4 6.6 1.0 CE1 A:HIS158 4.4 10.6 1.0 C08 A:OKS406 4.5 16.4 1.0 CE2 A:TYR323 4.5 11.6 1.0 OH A:TYR323 4.5 15.9 1.0 N A:GLY321 4.6 8.5 1.0 CB A:PHE196 4.6 8.4 1.0 C A:PHE196 4.7 11.1 1.0 CA A:PHE196 4.7 11.3 1.0 C A:ASP195 4.8 7.6 1.0 NE2 A:HIS159 4.8 9.8 1.0 CA A:ASP195 4.9 5.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 8-Amino-N-Hydroxyoctanamide


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 Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 8-Amino-N-Hydroxyoctanamide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:9.4 occ:1.00 OD1 B:ASP195 1.9 14.7 1.0 OD2 B:ASP284 2.0 9.0 1.0 O11 B:OKS405 2.1 12.6 1.0 ND1 B:HIS197 2.1 5.6 1.0 O12 B:OKS405 2.4 19.4 1.0 N10 B:OKS405 2.4 12.9 1.0 C09 B:OKS405 2.6 16.8 1.0 CG B:ASP195 2.7 6.3 1.0 OD2 B:ASP195 2.8 11.0 1.0 CE1 B:HIS197 2.9 4.2 1.0 CG B:ASP284 3.0 11.1 1.0 CG B:HIS197 3.2 6.8 1.0 OD1 B:ASP284 3.4 10.7 1.0 CB B:HIS197 3.7 3.2 1.0 N B:HIS197 3.7 3.0 1.0 C08 B:OKS405 3.8 19.7 1.0 N B:PHE196 4.1 9.5 1.0 NE2 B:HIS197 4.1 5.8 1.0 CB B:ASP195 4.1 8.7 1.0 CB B:ASP284 4.2 7.7 1.0 NE2 B:HIS158 4.2 12.3 1.0 CD2 B:HIS197 4.3 4.8 1.0 CA B:GLY321 4.3 9.7 1.0 CA B:HIS197 4.3 4.6 1.0 CE1 B:HIS158 4.4 10.8 1.0 CB B:PHE196 4.5 6.3 1.0 C B:PHE196 4.6 9.2 1.0 CA B:PHE196 4.6 7.3 1.0 N B:GLY321 4.6 9.5 1.0 O B:HOH514 4.6 19.1 1.0 OH B:TYR323 4.7 9.9 1.0 CE1 B:TYR323 4.7 13.1 1.0 C B:ASP195 4.7 7.3 1.0 C07 B:OKS405 4.7 17.6 1.0 NE2 B:HIS159 4.7 9.6 1.0 CA B:ASP195 4.8 9.6 1.0

J.D.Osko, B.W.Roose, S.A.Shinsky, D.W.Christianson. Structure and Function of the Acetylpolyamine Amidohydrolase From the Deep Earth Halophilemarinobacter Subterrani. Biochemistry V. 58 3755 2019.
ISSN: ISSN 0006-2960
PubMed: 31436969
DOI: 10.1021/ACS.BIOCHEM.9B00582