Magnesium in PDB 9h5q: Crystal Structure of Thermoanaerobacterales Bacterium Monoamine Oxidase in Complex with Spermidine and Its Oxidation Products

The structure of Crystal Structure of Thermoanaerobacterales Bacterium Monoamine Oxidase in Complex with Spermidine and Its Oxidation Products, PDB code: 9h5q was solved by L.Basile, C.Poli, L.L.Santema, R.C.Lesenciuc, M.W.Fraaije, C.Binda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.95 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.335, 94.456, 127.74, 90, 90, 90
R / Rfree (%)	15.4 / 18.9

The binding sites of Magnesium atom in the Crystal Structure of Thermoanaerobacterales Bacterium Monoamine Oxidase in Complex with Spermidine and Its Oxidation Products (pdb code 9h5q). 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 Thermoanaerobacterales Bacterium Monoamine Oxidase in Complex with Spermidine and Its Oxidation Products, PDB code: 9h5q:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Thermoanaerobacterales Bacterium Monoamine Oxidase in Complex with Spermidine and Its Oxidation Products


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 Thermoanaerobacterales Bacterium Monoamine Oxidase in Complex with Spermidine and Its Oxidation Products within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg505 b:31.1 occ:1.00 O A:HOH758 2.0 31.9 1.0 O A:HOH662 2.0 29.9 1.0 O A:HOH737 2.0 25.5 1.0 O A:THR84 2.1 26.4 1.0 O A:HOH713 2.1 29.1 1.0 O A:HOH830 2.2 27.0 1.0 C A:THR84 3.2 26.6 1.0 CA A:THR84 3.8 27.4 1.0 OD1 A:ASP88 4.1 24.8 1.0 OD2 A:ASP88 4.1 27.0 1.0 CB A:THR84 4.2 27.4 1.0 O A:HOH708 4.3 34.6 1.0 O A:HOH709 4.4 30.1 1.0 N A:GLU85 4.4 24.3 1.0 O A:HOH828 4.4 26.0 1.0 O A:HOH848 4.4 40.9 1.0 O A:GLY86 4.5 25.6 1.0 O A:PRO101 4.5 44.6 1.0 CG A:ASP88 4.5 27.4 1.0 CA A:GLU85 4.8 26.9 1.0 OD1 A:ASP102 4.8 68.8 1.0 CB A:SER312 5.0 20.0 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Thermoanaerobacterales Bacterium Monoamine Oxidase in Complex with Spermidine and Its Oxidation Products


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 Thermoanaerobacterales Bacterium Monoamine Oxidase in Complex with Spermidine and Its Oxidation Products within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg505 b:28.5 occ:1.00 O B:HOH711 2.0 28.9 1.0 O B:THR84 2.0 27.2 1.0 O B:HOH692 2.1 28.6 1.0 O B:HOH653 2.1 29.8 1.0 O B:HOH798 2.2 24.5 1.0 O B:HOH699 2.2 26.7 1.0 C B:THR84 3.1 26.7 1.0 CA B:THR84 3.7 26.4 1.0 OD2 B:ASP88 4.1 31.4 1.0 OD1 B:ASP88 4.1 26.0 1.0 CB B:THR84 4.2 26.8 1.0 O B:HOH685 4.2 30.5 1.0 N B:GLU85 4.3 28.3 1.0 O B:PRO101 4.4 37.0 1.0 O B:HOH825 4.5 42.1 1.0 O B:GLY86 4.5 27.3 1.0 CG B:ASP88 4.5 26.4 1.0 O B:HOH766 4.6 28.6 1.0 O B:HOH605 4.7 31.7 1.0 OD2 B:ASP102 4.8 67.6 1.0 CA B:GLU85 4.8 29.0 1.0 C B:GLU85 5.0 27.2 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Thermoanaerobacterales Bacterium Monoamine Oxidase in Complex with Spermidine and Its Oxidation Products


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 Thermoanaerobacterales Bacterium Monoamine Oxidase in Complex with Spermidine and Its Oxidation Products within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg506 b:17.1 occ:1.00 O B:HOH764 1.9 21.5 1.0 OE1 B:GLU127 1.9 19.5 1.0 O B:HOH632 2.0 19.7 1.0 O B:HOH737 2.1 20.3 1.0 NE2 B:HIS190 2.2 15.8 1.0 CD B:GLU127 2.9 18.9 1.0 CD2 B:HIS190 3.2 17.0 1.0 CE1 B:HIS190 3.2 15.4 1.0 OE2 B:GLU127 3.4 22.0 1.0 O1 B:GOL504 4.1 28.2 1.0 CG B:GLU127 4.3 18.5 1.0 CG B:HIS190 4.3 15.3 1.0 ND1 B:HIS190 4.3 14.7 1.0

L.Basile, C.Poli, L.L.Santema, R.C.Lesenciuc, M.W.Fraaije, C.Binda. Altering Substrate Specificity of A Thermostable Bacterial Monoamine Oxidase By Structure-Based Mutagenesis. Arch.Biochem.Biophys. V. 764 10276 2024.
ISSN: ESSN 1096-0384
PubMed: 39706511
DOI: 10.1016/J.ABB.2024.110276