Magnesium in PDB 6pi8: Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with Acetate

The structure of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with Acetate, PDB code: 6pi8 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)	28.08 / 1.64
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.371, 121.060, 66.556, 90.00, 109.53, 90.00
R / Rfree (%)	16.8 / 19.4

The structure of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with Acetate 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 Acetate (pdb code 6pi8). 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 Acetate, PDB code: 6pi8:
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 Acetate


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 Acetate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:9.2 occ:1.00 OE1 A:GLU288 2.3 20.0 1.0 OD1 A:ASP324 2.4 18.7 1.0 OD2 A:ASP326 2.4 15.9 1.0 O A:HOH575 2.5 18.9 1.0 OD2 A:ASP324 2.6 18.6 1.0 CG A:ASP324 2.9 19.6 1.0 CG A:ASP326 3.4 20.8 1.0 CD A:GLU288 3.5 25.4 1.0 OD1 A:ASP326 3.6 16.3 1.0 CB A:GLU288 4.1 18.7 1.0 OE2 A:GLU288 4.4 24.6 1.0 CB A:ASP324 4.4 13.8 1.0 CG A:GLU288 4.4 21.7 1.0 CB A:ALA327 4.6 15.9 1.0 CE2 A:PHE286 4.7 16.2 1.0 CB A:ASP326 4.8 16.1 1.0 N A:ALA327 4.8 15.1 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with Acetate


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 Acetate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:11.2 occ:1.00 O A:HOH661 2.3 25.8 1.0 OD2 A:ASP106 2.3 21.9 1.0 O B:HOH548 2.4 20.3 1.0 O B:HOH550 2.4 21.2 1.0 OD2 A:ASP104 2.5 22.3 1.0 O A:HOH682 2.5 21.8 1.0 OD1 A:ASP104 2.5 22.9 1.0 CG A:ASP104 2.8 22.6 1.0 CG A:ASP106 3.4 26.6 1.0 CB A:ASP106 3.7 17.9 1.0 NZ A:LYS83 3.9 24.7 1.0 O B:LEU223 4.2 21.2 1.0 CB A:ASP104 4.3 17.6 1.0 N A:ASP106 4.4 17.7 1.0 O B:HOH709 4.4 21.7 1.0 O A:HOH687 4.5 26.2 1.0 OD1 A:ASP106 4.5 22.3 1.0 NE2 B:HIS227 4.6 14.6 1.0 CE1 B:HIS227 4.7 18.2 1.0 O A:HOH537 4.7 24.4 1.0 CA A:ASP106 4.7 19.7 1.0 O A:HOH577 4.8 28.3 1.0 CE A:LYS83 4.8 25.8 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with Acetate


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 Acetate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:12.6 occ:1.00 OD2 B:ASP106 2.3 24.2 1.0 O A:HOH608 2.3 22.6 1.0 O A:HOH522 2.4 24.0 1.0 O B:HOH708 2.4 22.4 1.0 O B:HOH667 2.4 23.5 1.0 OD1 B:ASP104 2.5 25.7 1.0 OD2 B:ASP104 2.6 23.4 1.0 CG B:ASP104 2.8 21.6 1.0 CG B:ASP106 3.4 26.4 1.0 CB B:ASP106 3.8 18.5 1.0 NZ B:LYS83 3.8 27.2 1.0 O A:LEU223 4.3 21.9 1.0 CB B:ASP104 4.3 16.6 1.0 N B:ASP106 4.4 16.7 1.0 O B:HOH719 4.5 32.7 1.0 OD1 B:ASP106 4.5 23.8 1.0 O B:HOH521 4.5 27.7 1.0 O A:HOH673 4.5 21.6 1.0 O B:HOH677 4.6 30.3 1.0 NE2 A:HIS227 4.6 16.3 1.0 CE1 A:HIS227 4.6 17.4 1.0 CA B:ASP106 4.7 18.6 1.0 CE B:LYS83 4.8 24.2 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