Magnesium in PDB 6phz: Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 7-[(3-Aminopropyl)Amino]-1,1, 1-Trifluoroheptan-2-One

The structure of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 7-[(3-Aminopropyl)Amino]-1,1, 1-Trifluoroheptan-2-One, PDB code: 6phz 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)	60.69 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.370, 82.360, 90.720, 90.00, 98.22, 90.00
R / Rfree (%)	16.1 / 21.2

The structure of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 7-[(3-Aminopropyl)Amino]-1,1, 1-Trifluoroheptan-2-One also contains other interesting chemical elements:

Fluorine	(F)	6 atoms
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 7-[(3-Aminopropyl)Amino]-1,1, 1-Trifluoroheptan-2-One (pdb code 6phz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 7-[(3-Aminopropyl)Amino]-1,1, 1-Trifluoroheptan-2-One, PDB code: 6phz:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 7-[(3-Aminopropyl)Amino]-1,1, 1-Trifluoroheptan-2-One


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 7-[(3-Aminopropyl)Amino]-1,1, 1-Trifluoroheptan-2-One within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:10.5 occ:1.00 OD1 A:ASP104 2.0 7.5 1.0 OD2 A:ASP106 2.1 13.1 1.0 O B:HOH591 2.1 8.4 1.0 O B:HOH554 2.1 14.6 1.0 O A:HOH649 2.2 13.0 1.0 O A:HOH564 2.2 10.8 1.0 CG A:ASP104 2.9 10.8 1.0 CG A:ASP106 3.1 12.4 1.0 OD2 A:ASP104 3.3 8.5 1.0 CB A:ASP106 3.4 8.4 1.0 NZ A:LYS83 3.8 10.3 1.0 OD1 A:ASP106 4.2 9.9 1.0 O B:LEU223 4.2 7.6 1.0 CB A:ASP104 4.3 5.6 1.0 N A:ASP106 4.3 6.5 1.0 NE2 B:HIS227 4.3 9.3 1.0 O B:HOH640 4.4 25.0 1.0 CA A:ASP106 4.5 8.3 1.0 CE1 B:HIS227 4.6 6.0 1.0 CE A:LYS83 4.7 9.4 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 7-[(3-Aminopropyl)Amino]-1,1, 1-Trifluoroheptan-2-One


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 7-[(3-Aminopropyl)Amino]-1,1, 1-Trifluoroheptan-2-One within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:21.4 occ:1.00 O A:HOH600 2.1 17.1 1.0 O A:HOH523 2.1 14.9 1.0 O A:HOH528 2.3 20.3 1.0 O A:HOH692 2.3 19.4 1.0 O A:ALA273 4.2 5.5 1.0 OD1 A:ASP275 4.2 13.8 1.0 OD2 A:ASP275 4.5 13.4 1.0 O A:HOH558 4.7 18.1 1.0 CG A:ASP275 4.7 10.1 1.0 CE A:LYS188 4.9 18.1 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 7-[(3-Aminopropyl)Amino]-1,1, 1-Trifluoroheptan-2-One


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 7-[(3-Aminopropyl)Amino]-1,1, 1-Trifluoroheptan-2-One within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:11.6 occ:1.00 OD2 B:ASP106 2.0 12.1 1.0 O B:HOH520 2.1 12.7 1.0 O B:HOH614 2.2 14.6 1.0 OD2 B:ASP104 2.2 8.6 1.0 O A:HOH517 2.2 8.4 1.0 O A:HOH595 2.2 8.8 1.0 CG B:ASP106 3.1 9.8 1.0 CG B:ASP104 3.1 13.4 1.0 OD1 B:ASP104 3.4 9.6 1.0 CB B:ASP106 3.4 7.2 1.0 NZ B:LYS83 3.9 10.9 1.0 OD1 B:ASP106 4.2 7.7 1.0 NE2 A:HIS227 4.3 10.0 1.0 N B:ASP106 4.3 6.0 1.0 O A:LEU223 4.4 9.1 1.0 CB B:ASP104 4.4 10.2 1.0 CA B:ASP106 4.5 8.9 1.0 O A:HOH668 4.6 4.2 1.0 O A:HOH684 4.6 26.3 1.0 CE1 A:HIS227 4.6 7.4 1.0 CE B:LYS83 4.7 10.5 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 7-[(3-Aminopropyl)Amino]-1,1, 1-Trifluoroheptan-2-One


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 7-[(3-Aminopropyl)Amino]-1,1, 1-Trifluoroheptan-2-One within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg405 b:29.8 occ:1.00 O B:HOH515 1.9 30.5 1.0 OE2 B:GLU288 2.4 35.4 1.0 O B:HOH503 2.6 21.8 1.0 CD B:GLU288 3.6 36.5 1.0 OE1 B:GLU288 4.1 42.2 1.0 OD1 B:ASP324 4.2 29.0 1.0 OD1 B:ASP326 4.3 21.3 1.0 OD2 B:ASP324 4.3 24.6 1.0 CG B:ASP324 4.7 25.1 1.0 CB B:ASP326 4.7 23.7 1.0 CG B:GLU288 4.8 21.6 1.0 O B:HOH501 4.8 18.9 1.0 CG B:ASP326 5.0 35.8 1.0 CB B:GLU288 5.0 32.7 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