Magnesium in PDB 6pht: Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 5-[(3-Aminopropyl) Amino]Pentylboronic Acid

The structure of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 5-[(3-Aminopropyl) Amino]Pentylboronic Acid, PDB code: 6pht 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)	65.44 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.630, 163.480, 65.720, 90.00, 94.33, 90.00
R / Rfree (%)	19.4 / 22.6

The structure of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 5-[(3-Aminopropyl) Amino]Pentylboronic Acid also contains other interesting chemical elements:

Potassium	(K)	8 atoms
Zinc	(Zn)	4 atoms

The binding sites of Magnesium atom in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 5-[(3-Aminopropyl) Amino]Pentylboronic Acid (pdb code 6pht). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 5-[(3-Aminopropyl) Amino]Pentylboronic Acid, PDB code: 6pht:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

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


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]Pentylboronic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:10.6 occ:1.00 OD2 A:ASP106 2.0 11.7 1.0 O A:HOH580 2.1 9.4 1.0 OD2 A:ASP104 2.1 11.9 1.0 O A:HOH544 2.2 9.8 1.0 CG A:ASP104 3.1 10.5 1.0 CG A:ASP106 3.1 7.8 1.0 OD1 A:ASP104 3.4 10.2 1.0 CB A:ASP106 3.5 8.0 1.0 NZ A:LYS83 3.7 13.3 1.0 OD1 A:ASP106 4.2 9.5 1.0 CB A:ASP104 4.4 10.2 1.0 N A:ASP106 4.4 6.5 1.0 CA A:ASP106 4.6 4.3 1.0 CE A:LYS83 4.7 15.9 1.0

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


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]Pentylboronic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:26.5 occ:1.00 OE1 A:GLU288 2.0 24.2 1.0 O A:HOH635 2.1 22.6 1.0 O A:HOH605 2.1 14.8 1.0 O A:HOH629 2.2 29.6 1.0 O A:HOH503 2.2 22.2 1.0 CD A:GLU288 3.0 26.1 1.0 OE2 A:GLU288 3.5 30.4 1.0 OD1 A:ASP324 4.1 18.0 1.0 OD2 A:ASP326 4.2 19.8 1.0 CG A:GLU288 4.3 21.0 1.0 OD2 A:ASP324 4.5 16.2 1.0 CB A:GLU288 4.5 11.9 1.0 CG A:ASP324 4.7 16.9 1.0 CB A:ASP326 4.7 13.2 1.0 CG A:ASP326 5.0 23.4 1.0 OE1 B:GLU25 5.0 34.4 1.0

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


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 5-[(3-Aminopropyl) Amino]Pentylboronic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:8.9 occ:1.00 O D:HOH566 2.0 9.0 1.0 OD2 B:ASP104 2.0 8.4 1.0 O B:HOH553 2.0 7.9 1.0 OD2 B:ASP106 2.1 11.3 1.0 O D:HOH541 2.1 11.3 1.0 O B:HOH542 2.2 10.4 1.0 CG B:ASP104 3.0 9.8 1.0 CG B:ASP106 3.1 12.7 1.0 OD1 B:ASP104 3.4 9.7 1.0 CB B:ASP106 3.6 10.2 1.0 NZ B:LYS83 3.8 10.1 1.0 O D:HOH607 4.0 9.2 1.0 O D:HOH630 4.2 18.1 1.0 O D:LEU223 4.2 9.9 1.0 OD1 B:ASP106 4.3 9.7 1.0 NE2 D:HIS227 4.3 10.3 1.0 CB B:ASP104 4.3 9.2 1.0 N B:ASP106 4.4 7.6 1.0 CE1 D:HIS227 4.5 10.8 1.0 CA B:ASP106 4.6 7.6 1.0 CE B:LYS83 4.7 20.1 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 5-[(3-Aminopropyl) Amino]Pentylboronic Acid


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 5-[(3-Aminopropyl) Amino]Pentylboronic Acid within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg404 b:8.1 occ:1.00 OD2 C:ASP104 2.1 9.4 1.0 OD2 C:ASP106 2.1 11.5 1.0 O C:HOH616 2.2 11.3 1.0 O C:HOH535 2.2 10.0 1.0 CG C:ASP104 3.0 7.7 1.0 CG C:ASP106 3.1 8.1 1.0 OD1 C:ASP104 3.4 9.3 1.0 CB C:ASP106 3.5 8.1 1.0 O C:HOH647 3.8 26.4 1.0 NZ C:LYS83 3.9 10.6 1.0 OD1 C:ASP106 4.3 9.6 1.0 CB C:ASP104 4.3 11.4 1.0 N C:ASP106 4.5 7.7 1.0 CA C:ASP106 4.6 9.7 1.0 CE C:LYS83 4.8 16.7 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 5-[(3-Aminopropyl) Amino]Pentylboronic Acid within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg404 b:10.6 occ:1.00 OD2 D:ASP104 2.1 10.0 1.0 OD2 D:ASP106 2.1 10.6 1.0 O D:HOH580 2.1 9.6 1.0 O B:HOH567 2.2 9.3 1.0 O B:HOH522 2.2 9.9 1.0 O D:HOH531 2.2 10.4 1.0 CG D:ASP104 3.0 10.1 1.0 CG D:ASP106 3.1 14.0 1.0 OD1 D:ASP104 3.3 11.0 1.0 CB D:ASP106 3.6 6.3 1.0 NZ D:LYS83 3.7 12.5 1.0 O D:HOH633 3.9 22.6 1.0 O B:HOH607 4.1 7.5 1.0 O B:LEU223 4.2 8.2 1.0 O B:HOH632 4.2 17.3 1.0 OD1 D:ASP106 4.3 13.2 1.0 NE2 B:HIS227 4.3 9.6 1.0 CB D:ASP104 4.3 9.6 1.0 N D:ASP106 4.5 10.3 1.0 CE1 B:HIS227 4.5 11.7 1.0 CA D:ASP106 4.6 8.2 1.0 CE D:LYS83 4.7 15.4 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