Zinc in PDB 6phr: Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 5-[(3-Aminopropyl) Amino]Pentane-1-Thiol

The structure of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 5-[(3-Aminopropyl) Amino]Pentane-1-Thiol, PDB code: 6phr 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)	61.77 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.874, 120.680, 65.360, 90.00, 109.09, 90.00
R / Rfree (%)	17.9 / 20.8

The structure of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 5-[(3-Aminopropyl) Amino]Pentane-1-Thiol also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Potassium	(K)	4 atoms

The binding sites of Zinc atom in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 5-[(3-Aminopropyl) Amino]Pentane-1-Thiol (pdb code 6phr). 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 5-[(3-Aminopropyl) Amino]Pentane-1-Thiol, PDB code: 6phr:
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 5-[(3-Aminopropyl) Amino]Pentane-1-Thiol


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 5-[(3-Aminopropyl) Amino]Pentane-1-Thiol within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:5.8 occ:1.00 OD2 A:ASP284 2.0 11.8 1.0 OD1 A:ASP195 2.1 9.7 1.0 ND1 A:HIS197 2.2 11.0 1.0 S11 A:SS9502 2.4 16.0 1.0 OD2 A:ASP195 2.7 11.2 1.0 CG A:ASP195 2.8 10.5 1.0 CG A:ASP284 3.0 10.7 1.0 CE1 A:HIS197 3.1 8.9 1.0 CG A:HIS197 3.3 9.8 1.0 OD1 A:ASP284 3.4 11.8 1.0 C9 A:SS9502 3.6 16.2 1.0 C10 A:SS9502 3.6 16.1 1.0 CB A:HIS197 3.7 8.3 1.0 N A:HIS197 3.9 7.7 1.0 NE2 A:HIS158 4.1 10.6 1.0 CA A:GLY321 4.2 13.9 1.0 NE2 A:HIS197 4.2 12.3 1.0 CB A:ASP195 4.3 9.1 1.0 N A:PHE196 4.3 8.6 1.0 CD2 A:HIS197 4.4 10.4 1.0 CE1 A:TYR323 4.4 14.1 1.0 CE1 A:HIS158 4.4 10.9 1.0 CB A:ASP284 4.4 11.4 1.0 CA A:HIS197 4.4 8.4 1.0 N A:GLY321 4.5 11.7 1.0 NE2 A:HIS159 4.6 10.2 1.0 OH A:TYR323 4.7 15.0 1.0 CB A:PHE196 4.8 10.1 1.0 C A:PHE196 4.8 9.0 1.0 CA A:PHE196 4.9 8.0 1.0 C A:ASP195 4.9 9.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 5-[(3-Aminopropyl) Amino]Pentane-1-Thiol


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 5-[(3-Aminopropyl) Amino]Pentane-1-Thiol within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:4.5 occ:1.00 OD2 B:ASP284 2.0 11.1 1.0 OD1 B:ASP195 2.1 8.7 1.0 ND1 B:HIS197 2.3 11.7 1.0 S11 B:SS9502 2.4 18.9 1.0 OD2 B:ASP195 2.7 9.3 1.0 CG B:ASP195 2.7 8.7 1.0 CG B:ASP284 3.1 12.2 1.0 CE1 B:HIS197 3.2 10.4 1.0 C10 B:SS9502 3.3 11.8 1.0 OD1 B:ASP284 3.4 10.8 1.0 CG B:HIS197 3.4 7.7 1.0 C9 B:SS9502 3.5 13.3 1.0 CB B:HIS197 3.7 9.2 1.0 N B:HIS197 3.9 8.6 1.0 NE2 B:HIS158 4.1 11.3 1.0 CA B:GLY321 4.2 14.1 1.0 CB B:ASP195 4.2 8.6 1.0 N B:PHE196 4.4 8.7 1.0 CE2 B:TYR323 4.4 14.2 1.0 NE2 B:HIS197 4.4 10.6 1.0 CE1 B:HIS158 4.4 9.7 1.0 CB B:ASP284 4.4 11.3 1.0 CA B:HIS197 4.4 8.1 1.0 CD2 B:HIS197 4.5 11.1 1.0 NE2 B:HIS159 4.5 9.8 1.0 N B:GLY321 4.5 12.5 1.0 OH B:TYR323 4.7 14.5 1.0 CB B:PHE196 4.8 10.3 1.0 C B:PHE196 4.8 10.4 1.0 CA B:PHE196 4.9 9.4 1.0 C B:ASP195 4.9 7.7 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