Zinc in PDB 6phz: Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 7-[(3-Aminopropyl)Amino]-1,1, 1-Trifluoroheptan-2-One

The structure of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 7-[(3-Aminopropyl)Amino]-1,1, 1-Trifluoroheptan-2-One, PDB code: 6phz 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)	60.69 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.370, 82.360, 90.720, 90.00, 98.22, 90.00
R / Rfree (%)	16.1 / 21.2

The structure of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 7-[(3-Aminopropyl)Amino]-1,1, 1-Trifluoroheptan-2-One also contains other interesting chemical elements:

Fluorine	(F)	6 atoms
Magnesium	(Mg)	4 atoms
Potassium	(K)	4 atoms

The binding sites of Zinc atom in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 7-[(3-Aminopropyl)Amino]-1,1, 1-Trifluoroheptan-2-One (pdb code 6phz). 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 7-[(3-Aminopropyl)Amino]-1,1, 1-Trifluoroheptan-2-One, PDB code: 6phz:
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 7-[(3-Aminopropyl)Amino]-1,1, 1-Trifluoroheptan-2-One


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 7-[(3-Aminopropyl)Amino]-1,1, 1-Trifluoroheptan-2-One within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:13.4 occ:0.41 OD2 A:ASP284 2.1 7.8 1.0 O13 A:FKS406 2.1 13.2 1.0 OD1 A:ASP195 2.2 5.8 1.0 O14 A:FKS406 2.3 12.0 1.0 ND1 A:HIS197 2.4 9.7 1.0 OD2 A:ASP195 2.6 5.0 1.0 C11 A:FKS406 2.7 18.4 1.0 CG A:ASP195 2.7 7.9 1.0 CG A:ASP284 3.1 10.0 1.0 CE1 A:HIS197 3.3 9.3 1.0 CG A:HIS197 3.5 10.3 1.0 OD1 A:ASP284 3.6 8.7 1.0 F17 A:FKS406 3.8 28.4 1.0 C12 A:FKS406 3.8 21.8 1.0 N A:HIS197 3.8 3.7 1.0 C10 A:FKS406 3.9 17.7 1.0 CB A:HIS197 3.9 6.1 1.0 C9 A:FKS406 4.0 18.0 1.0 CA A:GLY321 4.1 8.1 1.0 N A:PHE196 4.1 3.8 1.0 CB A:ASP195 4.2 3.5 1.0 NE2 A:HIS158 4.2 6.2 1.0 CB A:ASP284 4.4 4.8 1.0 NE2 A:HIS197 4.5 12.9 1.0 CE1 A:HIS158 4.5 7.0 1.0 CA A:HIS197 4.5 4.3 1.0 O A:HOH669 4.5 25.8 1.0 N A:GLY321 4.6 8.0 1.0 CB A:PHE196 4.6 6.5 1.0 CD2 A:HIS197 4.6 4.1 1.0 F15 A:FKS406 4.6 27.1 1.0 NE2 A:HIS159 4.6 9.0 1.0 CA A:PHE196 4.7 3.5 1.0 C A:PHE196 4.7 6.8 1.0 C A:ASP195 4.8 4.6 1.0 F16 A:FKS406 4.8 24.2 1.0 C A:GLY321 4.9 9.4 1.0 CA A:ASP195 4.9 6.3 1.0 N A:GLY322 5.0 11.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 7-[(3-Aminopropyl)Amino]-1,1, 1-Trifluoroheptan-2-One


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 7-[(3-Aminopropyl)Amino]-1,1, 1-Trifluoroheptan-2-One within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:38.3 occ:0.37 OD2 B:ASP284 2.0 22.7 1.0 OD2 B:ASP195 2.2 5.7 1.0 O13 B:FKS406 2.2 17.5 1.0 ND1 B:HIS197 2.3 8.1 1.0 O14 B:FKS406 2.3 16.7 1.0 C11 B:FKS406 2.7 19.3 1.0 OD1 B:ASP195 2.8 8.2 1.0 CG B:ASP195 2.8 15.4 1.0 CG B:ASP284 3.1 19.2 1.0 CE1 B:HIS197 3.2 13.8 1.0 CG B:HIS197 3.3 14.8 1.0 OD1 B:ASP284 3.6 15.8 1.0 CB B:HIS197 3.7 5.2 1.0 N B:HIS197 3.7 8.6 1.0 C10 B:FKS406 3.8 24.6 1.0 C9 B:FKS406 3.8 13.3 1.0 C12 B:FKS406 4.1 25.3 1.0 F17 B:FKS406 4.2 28.8 1.0 N B:PHE196 4.2 10.0 1.0 CA B:GLY321 4.2 10.9 1.0 NE2 B:HIS158 4.2 9.3 1.0 CB B:ASP195 4.3 9.9 1.0 CA B:HIS197 4.3 6.3 1.0 CB B:ASP284 4.3 12.4 1.0 NE2 B:HIS197 4.4 12.7 1.0 CD2 B:HIS197 4.5 10.2 1.0 CE1 B:HIS158 4.5 5.3 1.0 CE2 B:TYR323 4.5 18.4 1.0 N B:GLY321 4.6 9.8 1.0 OH B:TYR323 4.6 15.6 1.0 NE2 B:HIS159 4.6 6.2 1.0 C B:PHE196 4.6 10.4 1.0 CB B:PHE196 4.7 11.5 1.0 CA B:PHE196 4.7 10.2 1.0 C B:ASP195 4.8 10.3 1.0 F16 B:FKS406 4.9 20.9 1.0 C B:GLY321 4.9 12.2 1.0 F15 B:FKS406 4.9 28.2 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