Magnesium in PDB 6phr: Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 5-[(3-Aminopropyl) Amino]Pentane-1-Thiol

The structure of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 5-[(3-Aminopropyl) Amino]Pentane-1-Thiol, PDB code: 6phr 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)	61.77 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.874, 120.680, 65.360, 90.00, 109.09, 90.00
R / Rfree (%)	17.9 / 20.8

The structure of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 5-[(3-Aminopropyl) Amino]Pentane-1-Thiol 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 5-[(3-Aminopropyl) Amino]Pentane-1-Thiol (pdb code 6phr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 5-[(3-Aminopropyl) Amino]Pentane-1-Thiol, PDB code: 6phr:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 5-[(3-Aminopropyl) Amino]Pentane-1-Thiol


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 5-[(3-Aminopropyl) Amino]Pentane-1-Thiol within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:14.3 occ:1.00 OD2 A:ASP104 2.2 19.5 1.0 OD2 A:ASP106 2.3 10.5 1.0 O B:HOH622 2.3 9.4 1.0 O B:HOH607 2.3 16.7 1.0 O A:HOH655 2.4 13.2 1.0 CG A:ASP104 2.9 17.0 1.0 OD1 A:ASP104 3.1 21.0 1.0 CG A:ASP106 3.2 17.4 1.0 CB A:ASP106 3.6 14.9 1.0 NZ A:LYS83 3.9 15.9 1.0 O3S B:MES501 4.2 17.6 1.0 O B:LEU223 4.2 10.4 1.0 O B:HOH713 4.3 21.7 1.0 CB A:ASP104 4.3 14.2 1.0 N A:ASP106 4.3 12.2 1.0 OD1 A:ASP106 4.4 15.4 1.0 NE2 B:HIS227 4.5 10.6 1.0 O B:HOH606 4.5 23.3 1.0 CA A:ASP106 4.6 14.3 1.0 CE1 B:HIS227 4.7 12.3 1.0 CE A:LYS83 4.9 16.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 5-[(3-Aminopropyl) Amino]Pentane-1-Thiol


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 5-[(3-Aminopropyl) Amino]Pentane-1-Thiol within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg504 b:14.3 occ:1.00 OD2 B:ASP106 2.3 10.8 1.0 OD2 B:ASP104 2.3 17.2 1.0 O A:HOH606 2.3 15.9 1.0 O B:HOH724 2.3 21.8 1.0 O A:HOH637 2.3 11.9 1.0 O B:HOH633 2.4 16.8 1.0 CG B:ASP104 2.9 16.3 1.0 OD1 B:ASP104 2.9 19.0 1.0 CG B:ASP106 3.3 17.3 1.0 CB B:ASP106 3.6 12.4 1.0 NZ B:LYS83 3.8 17.8 1.0 O2S A:MES501 4.1 19.7 1.0 O B:HOH740 4.1 28.6 1.0 O A:HOH686 4.2 26.7 1.0 O A:LEU223 4.2 11.1 1.0 CB B:ASP104 4.3 14.9 1.0 N B:ASP106 4.3 12.0 1.0 O A:HOH622 4.4 23.9 1.0 OD1 B:ASP106 4.4 13.5 1.0 NE2 A:HIS227 4.5 13.4 1.0 CA B:ASP106 4.6 14.4 1.0 O B:HOH704 4.6 24.6 1.0 CE1 A:HIS227 4.8 11.9 1.0 CE B:LYS83 4.8 17.6 1.0 C8 A:MES501 5.0 23.6 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