Magnesium in PDB 3ws8: Crystal Structure of PDE10A in Complex with A Benzimidazole Inhibitor

All present enzymatic activity of Crystal Structure of PDE10A in Complex with A Benzimidazole Inhibitor:
3.1.4.17; 3.1.4.35;

The structure of Crystal Structure of PDE10A in Complex with A Benzimidazole Inhibitor, PDB code: 3ws8 was solved by Y.Amano, K.Honbou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.96 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.310, 81.107, 160.470, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 31.4

The structure of Crystal Structure of PDE10A in Complex with A Benzimidazole Inhibitor also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of PDE10A in Complex with A Benzimidazole Inhibitor (pdb code 3ws8). 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 PDE10A in Complex with A Benzimidazole Inhibitor, PDB code: 3ws8:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of PDE10A in Complex with A Benzimidazole Inhibitor


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 PDE10A in Complex with A Benzimidazole Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:26.4 occ:1.00 OD1 A:ASP564 2.0 34.3 1.0 O A:HOH902 2.0 32.7 1.0 O A:HOH903 2.1 32.9 1.0 O A:HOH905 2.1 15.3 1.0 O A:HOH904 2.2 30.1 1.0 O A:HOH901 2.8 29.4 1.0 CG A:ASP564 2.9 37.9 1.0 OD2 A:ASP564 3.2 34.9 1.0 ZN A:ZN801 3.6 41.6 1.0 NE2 A:HIS595 3.9 39.7 1.0 O A:HOH906 3.9 10.6 1.0 CD2 A:HIS567 4.1 42.3 1.0 CD2 A:HIS595 4.2 39.4 1.0 CB A:ASP564 4.3 35.1 1.0 O A:THR633 4.3 34.6 1.0 OE2 A:GLU592 4.3 45.6 1.0 NE2 A:HIS567 4.3 43.2 1.0 OG1 A:THR633 4.4 37.9 1.0 CD2 A:HIS563 4.4 37.8 1.0 NE2 A:HIS563 4.6 36.6 1.0 CD2 A:HIS525 4.6 46.0 1.0 O A:HIS563 4.6 33.6 1.0 CA A:ASP564 4.8 37.1 1.0 CB A:THR633 4.8 35.1 1.0 OD2 A:ASP674 4.8 45.6 1.0 CG A:GLU592 4.9 46.0 1.0 NE2 A:HIS525 5.0 45.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of PDE10A in Complex with A Benzimidazole Inhibitor


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 PDE10A in Complex with A Benzimidazole Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg802 b:25.7 occ:1.00 OD1 B:ASP564 2.1 34.8 1.0 O B:HOH901 2.1 21.1 1.0 O B:HOH902 2.1 26.8 1.0 O B:HOH906 2.4 23.3 1.0 O B:HOH903 2.7 63.0 1.0 ZN B:ZN801 3.0 43.2 1.0 CG B:ASP564 3.1 34.3 1.0 OD2 B:ASP564 3.4 35.2 1.0 CD2 B:HIS563 3.6 46.8 1.0 OG1 B:THR633 3.7 28.7 1.0 OD2 B:ASP674 3.9 36.5 1.0 O B:HOH904 3.9 36.7 1.0 NE2 B:HIS563 4.0 48.1 1.0 O B:HIS563 4.0 47.2 1.0 CB B:THR633 4.2 34.4 1.0 CD2 B:HIS525 4.2 42.0 1.0 NE2 B:HIS525 4.2 41.6 1.0 NE2 B:HIS595 4.3 38.7 1.0 CB B:ASP564 4.4 38.4 1.0 OE2 B:GLU592 4.4 64.8 1.0 CD2 B:HIS595 4.5 38.6 1.0 O B:THR633 4.5 39.0 1.0 O B:HOH905 4.6 25.2 1.0 CD2 B:HIS567 4.7 39.7 1.0 CG B:ASP674 4.8 37.5 1.0 CA B:ASP564 4.8 39.3 1.0 OD1 B:ASP674 4.8 37.0 1.0 CG B:HIS563 4.8 44.6 1.0 C B:HIS563 4.8 43.0 1.0 C B:THR633 4.9 38.3 1.0

A.Chino, N.Masuda, Y.Amano, K.Honbou, T.Mihara, M.Yamazaki, M.Tomishima. Novel Benzimidazole Derivatives As Phosphodiesterase 10A (PDE10A) Inhibitors with Improved Metabolic Stability. Bioorg.Med.Chem. 2014.
ISSN: ESSN 1464-3391
PubMed: 24837154
DOI: 10.1016/J.BMC.2014.04.023