Magnesium in PDB 3ws9: Crystal Structure of PDE10A in Complex with A Benzimdazole Inhibitor

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

The structure of Crystal Structure of PDE10A in Complex with A Benzimdazole Inhibitor, PDB code: 3ws9 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)	29.50 / 2.99
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.421, 81.542, 161.255, 90.00, 90.00, 90.00
R / Rfree (%)	22.3 / 34.6

The structure of Crystal Structure of PDE10A in Complex with A Benzimdazole 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 Benzimdazole Inhibitor (pdb code 3ws9). 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 Benzimdazole Inhibitor, PDB code: 3ws9:
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 Benzimdazole 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 Benzimdazole Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:19.7 occ:1.00 O A:HOH901 1.9 44.5 1.0 OD1 A:ASP564 2.3 36.6 1.0 O A:HOH902 2.5 7.7 1.0 CG A:ASP564 3.3 35.5 1.0 ZN A:ZN801 3.5 37.0 1.0 OD2 A:ASP564 3.5 39.0 1.0 OE2 A:GLU592 3.6 54.0 1.0 OG1 A:THR633 3.8 28.9 1.0 OD2 A:ASP674 4.0 37.2 1.0 O A:THR633 4.0 29.3 1.0 NE2 A:HIS525 4.4 42.1 1.0 NE2 A:HIS595 4.4 47.0 1.0 CD2 A:HIS563 4.4 40.2 1.0 CD2 A:HIS525 4.5 41.1 1.0 CB A:THR633 4.6 27.4 1.0 CD2 A:HIS595 4.6 45.7 1.0 CD A:GLU592 4.7 52.2 1.0 O A:HIS563 4.7 36.9 1.0 CB A:ASP564 4.7 33.2 1.0 C A:THR633 4.8 27.8 1.0 CD2 A:HIS567 4.8 40.8 1.0 NE2 A:HIS563 4.8 41.0 1.0 NE2 A:HIS567 4.9 38.1 1.0 CG A:ASP674 5.0 32.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of PDE10A in Complex with A Benzimdazole 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 Benzimdazole Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg802 b:14.2 occ:1.00 O B:HOH901 1.9 19.4 1.0 OD1 B:ASP564 2.1 35.5 1.0 O B:HOH902 2.5 17.6 1.0 OD2 B:ASP564 2.6 34.0 1.0 CG B:ASP564 2.7 33.2 1.0 O B:HOH903 2.7 22.9 1.0 ZN B:ZN801 3.1 34.6 1.0 OD2 B:ASP674 3.5 22.7 1.0 CD2 B:HIS563 3.6 32.2 1.0 NE2 B:HIS563 3.9 32.9 1.0 OE2 B:GLU592 4.0 42.1 1.0 CB B:THR633 4.0 22.3 1.0 OG1 B:THR633 4.1 22.6 1.0 CB B:ASP564 4.1 31.8 1.0 CG B:ASP674 4.4 23.2 1.0 CD2 B:HIS525 4.5 42.0 1.0 OD1 B:ASP674 4.7 24.0 1.0 NE2 B:HIS525 4.7 41.8 1.0 CG2 B:THR633 4.7 21.0 1.0 CA B:ASP564 4.7 33.8 1.0 CD2 B:HIS567 4.8 36.0 1.0 CG B:HIS563 4.9 31.3 1.0 CG B:GLU592 4.9 45.7 1.0 CD B:GLU592 4.9 43.3 1.0 NE2 B:HIS595 5.0 37.7 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