Zinc in PDB 6pi1: Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide

The structure of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide, PDB code: 6pi1 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)	60.71 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.624, 163.013, 65.624, 90.00, 94.51, 90.00
R / Rfree (%)	16.3 / 19.9

The structure of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide also contains other interesting chemical elements:

Magnesium	(Mg)	5 atoms
Potassium	(K)	8 atoms

The binding sites of Zinc atom in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide (pdb code 6pi1). 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 Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide, PDB code: 6pi1:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide


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 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:12.1 occ:0.46 O4 A:B3N405 1.9 12.4 1.0 OD2 A:ASP284 1.9 11.1 1.0 OD1 A:ASP195 2.1 9.3 1.0 O2 A:B3N405 2.1 14.9 1.0 ND1 A:HIS197 2.2 6.5 1.0 OD2 A:ASP195 2.5 8.6 1.0 CG A:ASP195 2.6 9.8 1.0 N3 A:B3N405 2.7 13.5 1.0 C1 A:B3N405 2.8 20.2 1.0 CG A:ASP284 3.0 10.0 1.0 CE1 A:HIS197 3.0 8.2 1.0 CG A:HIS197 3.4 8.3 1.0 OD1 A:ASP284 3.4 10.7 1.0 CB A:HIS197 3.8 7.0 1.0 N A:HIS197 3.9 7.9 1.0 CA A:GLY321 4.0 13.3 1.0 CB A:ASP195 4.1 10.9 1.0 C5 A:B3N405 4.2 23.2 1.0 NE2 A:HIS158 4.2 11.8 1.0 NE2 A:HIS197 4.2 8.6 1.0 N A:PHE196 4.3 6.9 1.0 CB A:ASP284 4.3 10.0 1.0 N A:GLY321 4.4 12.1 1.0 CD2 A:HIS197 4.4 9.4 1.0 CE2 A:TYR323 4.5 13.5 1.0 CA A:HIS197 4.5 8.0 1.0 OH A:TYR323 4.5 13.9 1.0 CE1 A:HIS158 4.6 7.6 1.0 CB A:PHE196 4.7 7.9 1.0 C6 A:B3N405 4.7 15.6 1.0 C A:GLY321 4.8 16.9 1.0 CA A:PHE196 4.8 9.4 1.0 C A:ASP195 4.8 8.6 1.0 C A:PHE196 4.8 6.3 1.0 CA A:ASP195 4.9 9.2 1.0 C7 A:B3N405 4.9 13.3 1.0 NE2 A:HIS159 4.9 7.4 1.0 N A:GLY322 4.9 12.6 1.0 CZ A:TYR323 5.0 11.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide


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 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:11.7 occ:0.38 O4 B:B3N406 1.9 21.1 1.0 OD2 B:ASP284 2.0 8.8 1.0 OD1 B:ASP195 2.0 8.7 1.0 O2 B:B3N406 2.1 18.6 1.0 ND1 B:HIS197 2.2 10.0 1.0 OD2 B:ASP195 2.4 9.1 1.0 CG B:ASP195 2.5 10.8 1.0 N3 B:B3N406 2.6 17.7 1.0 C1 B:B3N406 2.7 21.9 1.0 CE1 B:HIS197 3.0 7.5 1.0 CG B:ASP284 3.0 9.8 1.0 CG B:HIS197 3.3 8.7 1.0 OD1 B:ASP284 3.5 10.5 1.0 CB B:HIS197 3.8 7.8 1.0 N B:HIS197 3.9 7.6 1.0 CB B:ASP195 4.0 10.3 1.0 CA B:GLY321 4.0 12.1 1.0 C5 B:B3N406 4.1 19.8 1.0 NE2 B:HIS158 4.1 12.2 1.0 N B:PHE196 4.2 6.5 1.0 NE2 B:HIS197 4.2 7.2 1.0 CB B:ASP284 4.3 10.1 1.0 N B:GLY321 4.3 9.4 1.0 CD2 B:HIS197 4.4 6.3 1.0 CA B:HIS197 4.5 9.2 1.0 CE1 B:HIS158 4.5 12.3 1.0 OH B:TYR323 4.5 10.2 1.0 CE2 B:TYR323 4.5 9.8 1.0 C6 B:B3N406 4.6 20.3 1.0 CB B:PHE196 4.7 9.3 1.0 C B:ASP195 4.7 8.1 1.0 C7 B:B3N406 4.7 21.1 1.0 C B:PHE196 4.8 11.6 1.0 CA B:PHE196 4.8 8.9 1.0 CA B:ASP195 4.8 9.1 1.0 NE2 B:HIS159 4.8 7.1 1.0 C B:GLY321 4.9 11.1 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide


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 Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:10.7 occ:0.45 OD2 C:ASP284 1.9 9.3 1.0 O4 C:B3N405 2.0 12.7 1.0 OD1 C:ASP195 2.0 9.5 1.0 O2 C:B3N405 2.1 15.1 1.0 ND1 C:HIS197 2.2 11.2 1.0 OD2 C:ASP195 2.5 7.8 1.0 CG C:ASP195 2.6 8.0 1.0 C1 C:B3N405 2.7 15.9 1.0 N3 C:B3N405 2.7 13.7 1.0 CG C:ASP284 3.0 9.2 1.0 CE1 C:HIS197 3.1 6.8 1.0 CG C:HIS197 3.3 9.9 1.0 OD1 C:ASP284 3.5 9.3 1.0 CB C:HIS197 3.7 8.6 1.0 N C:HIS197 3.9 6.8 1.0 CA C:GLY321 4.1 11.2 1.0 CB C:ASP195 4.1 8.0 1.0 C5 C:B3N405 4.2 15.5 1.0 NE2 C:HIS158 4.2 13.3 1.0 NE2 C:HIS197 4.2 6.7 1.0 N C:PHE196 4.3 5.7 1.0 CB C:ASP284 4.3 8.5 1.0 CD2 C:HIS197 4.4 8.1 1.0 N C:GLY321 4.4 9.6 1.0 CA C:HIS197 4.4 8.2 1.0 CE1 C:HIS158 4.5 13.9 1.0 OH C:TYR323 4.6 11.6 1.0 CE2 C:TYR323 4.6 13.4 1.0 C6 C:B3N405 4.7 16.3 1.0 CB C:PHE196 4.8 7.7 1.0 C C:ASP195 4.8 7.3 1.0 C7 C:B3N405 4.8 17.7 1.0 C C:PHE196 4.8 7.6 1.0 CA C:ASP195 4.9 9.0 1.0 CA C:PHE196 4.9 6.6 1.0 C C:GLY321 4.9 13.1 1.0 NE2 C:HIS159 4.9 7.0 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide


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 Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 4-(Dimethylamino)-N-[7- Hydroxyamino)-7-Oxoheptyl]Benzamide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:13.0 occ:0.46 O4 D:B3N405 1.9 22.1 1.0 OD2 D:ASP284 2.0 11.2 1.0 O2 D:B3N405 2.1 15.3 1.0 OD1 D:ASP195 2.1 10.9 1.0 ND1 D:HIS197 2.3 9.8 1.0 OD2 D:ASP195 2.5 12.5 1.0 N3 D:B3N405 2.6 14.6 1.0 CG D:ASP195 2.6 12.1 1.0 C1 D:B3N405 2.6 14.8 1.0 CE1 D:HIS197 3.0 11.3 1.0 CG D:ASP284 3.1 11.1 1.0 CG D:HIS197 3.4 9.3 1.0 OD1 D:ASP284 3.5 9.7 1.0 CB D:HIS197 3.8 8.2 1.0 N D:HIS197 3.9 9.4 1.0 C5 D:B3N405 4.1 20.6 1.0 CA D:GLY321 4.1 9.8 1.0 CB D:ASP195 4.1 10.9 1.0 NE2 D:HIS158 4.2 10.7 1.0 N D:PHE196 4.2 8.6 1.0 NE2 D:HIS197 4.2 14.6 1.0 CB D:ASP284 4.3 11.7 1.0 N D:GLY321 4.4 11.9 1.0 CD2 D:HIS197 4.4 9.5 1.0 CA D:HIS197 4.5 8.5 1.0 OH D:TYR323 4.5 13.7 1.0 CE1 D:HIS158 4.5 13.1 1.0 CE1 D:TYR323 4.5 14.2 1.0 CB D:PHE196 4.6 8.7 1.0 C6 D:B3N405 4.6 17.0 1.0 CA D:PHE196 4.7 10.7 1.0 C D:PHE196 4.8 12.3 1.0 C D:ASP195 4.8 6.9 1.0 NE2 D:HIS159 4.8 9.2 1.0 C D:GLY321 4.9 12.6 1.0 CA D:ASP195 4.9 9.7 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