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

The structure of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 6-Amino-N-Hydroxyhexanamide, PDB code: 6pic 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)	51.97 / 2.03
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	66.340, 67.040, 167.531, 90.00, 90.00, 92.60
R / Rfree (%)	22 / 24.7

The structure of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 6-Amino-N-Hydroxyhexanamide also contains other interesting chemical elements:

Magnesium	(Mg)	8 atoms
Potassium	(K)	16 atoms

The binding sites of Zinc atom in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 6-Amino-N-Hydroxyhexanamide (pdb code 6pic). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 6-Amino-N-Hydroxyhexanamide, PDB code: 6pic:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 6-Amino-N-Hydroxyhexanamide


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 6-Amino-N-Hydroxyhexanamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:6.4 occ:0.54 O9 A:6XA405 2.0 6.4 1.0 OD1 A:ASP284 2.0 7.3 1.0 OD2 A:ASP195 2.1 6.2 1.0 ND1 A:HIS197 2.3 5.8 1.0 O10 A:6XA405 2.3 7.6 1.0 OD1 A:ASP195 2.4 5.3 1.0 CG A:ASP195 2.6 6.3 1.0 N8 A:6XA405 2.7 5.3 1.0 C7 A:6XA405 2.8 7.0 1.0 CG A:ASP284 3.1 7.3 1.0 CE1 A:HIS197 3.1 5.3 1.0 CG A:HIS197 3.3 5.7 1.0 OD2 A:ASP284 3.6 7.4 1.0 CB A:HIS197 3.7 5.3 1.0 N A:HIS197 3.8 5.3 1.0 CA A:GLY321 4.1 7.0 1.0 CB A:ASP195 4.1 5.4 1.0 N A:PHE196 4.2 7.8 1.0 C6 A:6XA405 4.2 6.9 1.0 NE2 A:HIS158 4.2 5.4 1.0 NE2 A:HIS197 4.3 5.8 1.0 CB A:ASP284 4.3 7.2 1.0 CA A:HIS197 4.4 5.3 1.0 CD2 A:HIS197 4.4 5.3 1.0 N A:GLY321 4.4 5.3 1.0 CE1 A:HIS158 4.5 8.1 1.0 CE2 A:TYR323 4.6 8.4 1.0 OH A:TYR323 4.7 9.7 1.0 C A:PHE196 4.7 6.9 1.0 CB A:PHE196 4.7 5.3 1.0 CA A:PHE196 4.8 5.3 1.0 C A:ASP195 4.8 6.5 1.0 C A:GLY321 4.9 6.6 1.0 CA A:ASP195 4.9 5.4 1.0 NE2 A:HIS159 5.0 5.3 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 6-Amino-N-Hydroxyhexanamide


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 6-Amino-N-Hydroxyhexanamide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:10.7 occ:0.53 O9 B:6XA405 2.0 9.1 1.0 OD2 B:ASP284 2.0 8.6 1.0 OD1 B:ASP195 2.1 8.1 1.0 O10 B:6XA405 2.2 10.0 1.0 ND1 B:HIS197 2.3 8.5 1.0 OD2 B:ASP195 2.5 6.8 1.0 CG B:ASP195 2.6 7.1 1.0 N8 B:6XA405 2.7 9.0 1.0 C7 B:6XA405 2.7 9.7 1.0 CG B:ASP284 3.1 8.7 1.0 CE1 B:HIS197 3.2 8.8 1.0 CG B:HIS197 3.4 5.9 1.0 OD1 B:ASP284 3.6 9.4 1.0 CB B:HIS197 3.7 7.5 1.0 N B:HIS197 3.8 6.0 1.0 C6 B:6XA405 4.1 9.7 1.0 CB B:ASP195 4.2 7.3 1.0 N B:PHE196 4.2 9.6 1.0 NE2 B:HIS158 4.2 7.8 1.0 CA B:GLY321 4.2 5.3 1.0 NE2 B:HIS197 4.3 8.4 1.0 CB B:ASP284 4.4 7.0 1.0 CA B:HIS197 4.4 8.0 1.0 CD2 B:HIS197 4.4 5.9 1.0 CE1 B:HIS158 4.4 7.3 1.0 N B:GLY321 4.5 6.1 1.0 OH B:TYR323 4.6 10.9 1.0 CB B:PHE196 4.6 5.0 1.0 CE2 B:TYR323 4.7 10.9 1.0 C B:PHE196 4.7 9.9 1.0 CA B:PHE196 4.7 9.4 1.0 C B:ASP195 4.8 9.0 1.0 CA B:ASP195 4.9 7.4 1.0 C B:GLY321 5.0 10.1 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 6-Amino-N-Hydroxyhexanamide


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 6-Amino-N-Hydroxyhexanamide within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:8.4 occ:0.48 OD2 C:ASP284 2.1 7.6 1.0 O9 C:6XA405 2.1 8.8 1.0 OD1 C:ASP195 2.2 5.9 1.0 ND1 C:HIS197 2.2 5.5 1.0 N8 C:6XA405 2.3 8.3 1.0 O10 C:6XA405 2.4 7.2 1.0 C7 C:6XA405 2.4 8.4 1.0 OD2 C:ASP195 2.5 5.8 1.0 CG C:ASP195 2.7 5.5 1.0 CE1 C:HIS197 3.1 8.0 1.0 CG C:ASP284 3.2 7.9 1.0 CG C:HIS197 3.3 7.0 1.0 C6 C:6XA405 3.6 9.4 1.0 CB C:HIS197 3.6 5.5 1.0 N C:HIS197 3.8 5.5 1.0 OD1 C:ASP284 3.8 7.8 1.0 CA C:GLY321 4.1 6.7 1.0 NE2 C:HIS158 4.2 9.0 1.0 CB C:ASP195 4.2 7.0 1.0 NE2 C:HIS197 4.2 7.1 1.0 N C:PHE196 4.3 9.3 1.0 OH C:TYR323 4.3 5.4 1.0 CD2 C:HIS197 4.3 5.5 1.0 CA C:HIS197 4.4 9.1 1.0 CB C:ASP284 4.4 7.7 1.0 CE1 C:HIS158 4.5 5.5 1.0 N C:GLY321 4.5 6.1 1.0 O C:HOH519 4.5 13.8 1.0 CE1 C:TYR323 4.6 8.4 1.0 CB C:PHE196 4.7 5.4 1.0 C C:PHE196 4.7 5.5 1.0 CA C:PHE196 4.8 5.4 1.0 NE2 C:HIS159 4.8 6.8 1.0 C C:ASP195 4.8 8.5 1.0 C5 C:6XA405 4.9 9.2 1.0 CZ C:TYR323 4.9 7.9 1.0 C C:GLY321 5.0 7.9 1.0 CA C:ASP195 5.0 8.5 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 6-Amino-N-Hydroxyhexanamide


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 6-Amino-N-Hydroxyhexanamide within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:7.8 occ:0.53 O9 D:6XA405 1.9 8.9 1.0 OD2 D:ASP284 2.0 6.6 1.0 OD2 D:ASP195 2.1 6.9 1.0 ND1 D:HIS197 2.2 5.4 1.0 O10 D:6XA405 2.5 6.4 1.0 OD1 D:ASP195 2.5 5.5 1.0 N8 D:6XA405 2.5 6.7 1.0 CG D:ASP195 2.7 5.5 1.0 C7 D:6XA405 2.7 6.9 1.0 CE1 D:HIS197 3.1 5.5 1.0 CG D:ASP284 3.1 6.8 1.0 CG D:HIS197 3.3 5.4 1.0 OD1 D:ASP284 3.6 6.4 1.0 CB D:HIS197 3.7 5.4 1.0 N D:HIS197 3.8 5.4 1.0 CA D:GLY321 4.1 7.2 1.0 C6 D:6XA405 4.1 6.5 1.0 N D:PHE196 4.2 11.9 1.0 CB D:ASP195 4.2 5.5 1.0 NE2 D:HIS197 4.2 5.6 1.0 NE2 D:HIS158 4.3 7.5 1.0 CB D:ASP284 4.3 7.1 1.0 CD2 D:HIS197 4.4 5.4 1.0 CA D:HIS197 4.4 10.3 1.0 OH D:TYR323 4.4 7.0 1.0 N D:GLY321 4.5 7.1 1.0 CE1 D:TYR323 4.5 6.6 1.0 CE1 D:HIS158 4.5 7.0 1.0 CB D:PHE196 4.7 5.4 1.0 C D:PHE196 4.7 5.4 1.0 CA D:PHE196 4.7 5.4 1.0 C D:ASP195 4.8 5.4 1.0 C D:GLY321 4.9 7.4 1.0 C5 D:6XA405 4.9 7.5 1.0 CA D:ASP195 4.9 8.4 1.0 NE2 D:HIS159 5.0 5.8 1.0 CZ D:TYR323 5.0 6.7 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 6-Amino-N-Hydroxyhexanamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 6-Amino-N-Hydroxyhexanamide within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn401 b:9.4 occ:0.46 OD2 E:ASP284 2.0 9.2 1.0 O9 E:6XA405 2.0 11.0 1.0 OD1 E:ASP195 2.1 7.5 1.0 ND1 E:HIS197 2.2 5.4 1.0 O10 E:6XA405 2.3 8.8 1.0 OD2 E:ASP195 2.4 7.2 1.0 CG E:ASP195 2.6 6.6 1.0 N8 E:6XA405 2.7 9.3 1.0 C7 E:6XA405 2.8 8.0 1.0 CE1 E:HIS197 3.0 8.6 1.0 CG E:ASP284 3.1 9.4 1.0 CG E:HIS197 3.3 7.3 1.0 OD1 E:ASP284 3.6 8.0 1.0 CB E:HIS197 3.7 8.3 1.0 N E:HIS197 3.8 8.0 1.0 CB E:ASP195 4.1 7.0 1.0 N E:PHE196 4.1 7.3 1.0 CA E:GLY321 4.2 5.7 1.0 NE2 E:HIS197 4.2 5.4 1.0 C6 E:6XA405 4.2 7.1 1.0 NE2 E:HIS158 4.3 6.7 1.0 CB E:ASP284 4.3 5.5 1.0 CD2 E:HIS197 4.3 7.5 1.0 CA E:HIS197 4.4 8.6 1.0 CE1 E:HIS158 4.5 7.5 1.0 OH E:TYR323 4.5 7.2 1.0 N E:GLY321 4.6 9.1 1.0 CE2 E:TYR323 4.6 7.2 1.0 C E:PHE196 4.7 7.5 1.0 CB E:PHE196 4.7 6.9 1.0 CA E:PHE196 4.7 5.5 1.0 C E:ASP195 4.7 7.5 1.0 CA E:ASP195 4.9 8.0 1.0 NE2 E:HIS159 5.0 7.0 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 6-Amino-N-Hydroxyhexanamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 6-Amino-N-Hydroxyhexanamide within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn401 b:6.8 occ:0.54 OD2 F:ASP284 2.0 7.9 1.0 O9 F:6XA405 2.1 6.5 1.0 ND1 F:HIS197 2.2 5.6 1.0 OD1 F:ASP195 2.2 5.2 1.0 OD2 F:ASP195 2.4 5.2 1.0 N8 F:6XA405 2.5 6.2 1.0 O10 F:6XA405 2.5 7.2 1.0 CG F:ASP195 2.6 5.2 1.0 C7 F:6XA405 2.7 7.8 1.0 CE1 F:HIS197 3.0 5.2 1.0 CG F:ASP284 3.1 8.3 1.0 CG F:HIS197 3.2 5.3 1.0 CB F:HIS197 3.7 6.2 1.0 OD1 F:ASP284 3.7 8.1 1.0 N F:HIS197 3.8 5.2 1.0 C6 F:6XA405 3.9 9.2 1.0 CA F:GLY321 4.1 7.5 1.0 CB F:ASP195 4.1 5.2 1.0 NE2 F:HIS197 4.2 5.3 1.0 NE2 F:HIS158 4.2 7.6 1.0 N F:PHE196 4.2 5.2 1.0 CD2 F:HIS197 4.3 5.3 1.0 CB F:ASP284 4.3 5.2 1.0 CA F:HIS197 4.4 6.3 1.0 N F:GLY321 4.5 7.2 1.0 CE1 F:HIS158 4.5 7.6 1.0 OH F:TYR323 4.5 5.5 1.0 CE1 F:TYR323 4.6 7.6 1.0 C F:PHE196 4.8 7.7 1.0 CB F:PHE196 4.8 7.3 1.0 CA F:PHE196 4.8 5.2 1.0 C F:ASP195 4.8 5.2 1.0 CA F:ASP195 4.9 5.2 1.0 NE2 F:HIS159 4.9 5.2 1.0 C F:GLY321 4.9 6.7 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 6-Amino-N-Hydroxyhexanamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 6-Amino-N-Hydroxyhexanamide within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn401 b:8.9 occ:0.51 OD2 G:ASP284 2.0 8.3 1.0 O9 G:6XA405 2.0 8.8 1.0 OD1 G:ASP195 2.1 7.6 1.0 O10 G:6XA405 2.2 9.1 1.0 ND1 G:HIS197 2.3 9.0 1.0 OD2 G:ASP195 2.5 6.0 1.0 CG G:ASP195 2.6 7.5 1.0 N8 G:6XA405 2.7 7.7 1.0 C7 G:6XA405 2.8 8.2 1.0 CE1 G:HIS197 3.1 9.6 1.0 CG G:ASP284 3.1 9.2 1.0 CG G:HIS197 3.3 6.0 1.0 CB G:HIS197 3.7 6.7 1.0 OD1 G:ASP284 3.7 9.2 1.0 N G:HIS197 3.8 6.3 1.0 CB G:ASP195 4.1 8.1 1.0 CA G:GLY321 4.2 5.9 1.0 NE2 G:HIS158 4.2 6.0 1.0 C6 G:6XA405 4.2 8.6 1.0 N G:PHE196 4.2 8.1 1.0 NE2 G:HIS197 4.3 6.0 1.0 CB G:ASP284 4.3 5.9 1.0 CE1 G:HIS158 4.4 6.3 1.0 CA G:HIS197 4.4 7.0 1.0 CD2 G:HIS197 4.4 6.0 1.0 N G:GLY321 4.5 5.9 1.0 OH G:TYR323 4.6 8.7 1.0 CE1 G:TYR323 4.7 10.3 1.0 CB G:PHE196 4.7 7.4 1.0 C G:PHE196 4.7 7.6 1.0 CA G:PHE196 4.8 7.7 1.0 C G:ASP195 4.8 7.5 1.0 CA G:ASP195 4.9 7.8 1.0 C G:GLY321 5.0 9.7 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 6-Amino-N-Hydroxyhexanamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 6-Amino-N-Hydroxyhexanamide within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn401 b:9.1 occ:0.46 OD2 H:ASP284 2.0 9.6 1.0 O9 H:6XA405 2.0 9.0 1.0 ND1 H:HIS197 2.1 9.2 1.0 OD1 H:ASP195 2.2 7.1 1.0 O10 H:6XA405 2.4 7.3 1.0 OD2 H:ASP195 2.5 7.4 1.0 CG H:ASP195 2.6 5.5 1.0 N8 H:6XA405 2.7 8.2 1.0 C7 H:6XA405 2.8 7.4 1.0 CE1 H:HIS197 3.0 8.5 1.0 CG H:ASP284 3.1 9.2 1.0 CG H:HIS197 3.2 8.6 1.0 CB H:HIS197 3.6 8.4 1.0 OD1 H:ASP284 3.7 9.1 1.0 N H:HIS197 3.7 6.4 1.0 NE2 H:HIS197 4.1 8.5 1.0 N H:PHE196 4.1 8.1 1.0 CB H:ASP195 4.2 5.5 1.0 C6 H:6XA405 4.2 7.1 1.0 CA H:GLY321 4.2 8.1 1.0 NE2 H:HIS158 4.2 8.7 1.0 CD2 H:HIS197 4.2 8.4 1.0 CA H:HIS197 4.3 7.6 1.0 CB H:ASP284 4.3 8.1 1.0 OH H:TYR323 4.5 12.8 1.0 CE1 H:HIS158 4.5 8.7 1.0 N H:GLY321 4.6 8.0 1.0 CE2 H:TYR323 4.6 12.3 1.0 C H:PHE196 4.6 7.6 1.0 CB H:PHE196 4.6 7.9 1.0 CA H:PHE196 4.7 7.4 1.0 C H:ASP195 4.7 7.6 1.0 CA H:ASP195 4.9 8.7 1.0 NE2 H:HIS159 5.0 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