Magnesium 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:

Potassium	(K)	4 atoms
Zinc	(Zn)	2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 8-Amino-N-Hydroxyoctanamide, PDB code: 6pid:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 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 Magnesium with other atoms in the Mg 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:Mg402 b:2.0 occ:1.00 O A:HOH574 2.3 12.0 1.0 OD2 A:ASP324 2.3 9.1 1.0 OE1 A:GLU288 2.4 13.4 1.0 OD1 A:ASP326 2.5 10.9 1.0 OD1 A:ASP324 2.7 10.2 1.0 CG A:ASP324 2.9 10.2 1.0 CG A:ASP326 3.4 11.5 1.0 CD A:GLU288 3.6 12.6 1.0 OD2 A:ASP326 3.7 10.9 1.0 CB A:GLU288 4.2 13.6 1.0 CB A:ASP324 4.4 7.4 1.0 OE2 A:GLU288 4.5 20.4 1.0 CG A:GLU288 4.5 10.7 1.0 CB A:ALA327 4.5 7.1 1.0 O A:HOH623 4.5 14.5 1.0 CE2 A:PHE286 4.7 9.6 1.0 N A:ALA327 4.8 8.6 1.0 CB A:ASP326 4.8 6.1 1.0

Magnesium binding site 2 out of 3 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 Magnesium with other atoms in the Mg 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 A:Mg403 b:5.2 occ:1.00 OD2 A:ASP106 2.3 15.8 1.0 O B:HOH549 2.3 14.0 1.0 OD1 A:ASP104 2.3 17.9 1.0 O B:HOH524 2.4 10.9 1.0 OD2 A:ASP104 2.5 19.8 1.0 O A:HOH591 2.5 16.9 1.0 O A:HOH606 2.6 16.0 1.0 CG A:ASP104 2.7 19.6 1.0 CG A:ASP106 3.3 13.1 1.0 CB A:ASP106 3.8 9.7 1.0 O B:LEU223 4.0 11.3 1.0 NZ A:LYS83 4.2 11.3 1.0 CB A:ASP104 4.2 11.1 1.0 O A:HOH625 4.3 24.0 1.0 N A:ASP106 4.3 8.0 1.0 O A:HOH609 4.4 13.1 1.0 OD1 A:ASP106 4.4 11.4 1.0 O A:HOH541 4.5 16.5 1.0 NE2 B:HIS227 4.6 10.4 1.0 O B:HOH606 4.7 4.2 1.0 CA A:ASP106 4.7 13.1 1.0 CE1 B:HIS227 4.7 13.0 1.0 CE A:LYS83 4.8 12.5 1.0 O A:HOH575 4.8 15.6 1.0 N A:ILE105 4.9 10.6 1.0

Magnesium binding site 3 out of 3 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 Magnesium with other atoms in the Mg binding site number 3 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:Mg402 b:4.1 occ:1.00 O A:HOH595 2.1 11.7 1.0 O A:HOH532 2.2 15.7 1.0 O B:HOH588 2.3 14.6 1.0 OD2 B:ASP106 2.3 14.6 1.0 O B:HOH597 2.4 19.4 1.0 OD1 B:ASP104 2.4 12.3 1.0 OD2 B:ASP104 2.7 11.2 1.0 CG B:ASP104 2.8 12.1 1.0 CG B:ASP106 3.4 13.6 1.0 CB B:ASP106 3.7 11.1 1.0 O A:LEU223 4.0 12.6 1.0 NZ B:LYS83 4.1 13.4 1.0 CB B:ASP104 4.3 6.5 1.0 N B:ASP106 4.4 12.2 1.0 O B:HOH580 4.4 16.9 1.0 OD1 B:ASP106 4.5 12.3 1.0 O A:HOH628 4.5 22.9 1.0 O A:HOH615 4.6 1.3 1.0 NE2 A:HIS227 4.6 9.5 1.0 CE1 A:HIS227 4.7 11.6 1.0 CA B:ASP106 4.7 12.4 1.0 CE B:LYS83 4.9 9.1 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