Zinc 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:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of PDE10A in Complex with A Benzimidazole Inhibitor, PDB code: 3ws8:
Jump to Zinc binding site number: 1; 2;

Zinc 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 Zinc with other atoms in the Zn 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:Zn801 b:41.6 occ:1.00 OD2 A:ASP564 2.1 34.9 1.0 OD1 A:ASP674 2.1 29.5 1.0 NE2 A:HIS563 2.2 36.6 1.0 NE2 A:HIS529 2.4 24.2 1.0 O A:HOH904 2.4 30.1 1.0 O A:HOH905 2.9 15.3 1.0 CG A:ASP674 3.0 34.2 1.0 CD2 A:HIS563 3.1 37.8 1.0 CG A:ASP564 3.2 37.9 1.0 CE1 A:HIS563 3.2 35.3 1.0 CE1 A:HIS529 3.2 24.4 1.0 OD2 A:ASP674 3.3 45.6 1.0 CD2 A:HIS529 3.4 24.7 1.0 O A:HOH906 3.6 10.6 1.0 MG A:MG802 3.6 26.4 1.0 OD1 A:ASP564 3.7 34.3 1.0 CD2 A:HIS525 4.0 46.0 1.0 CG A:HIS563 4.2 38.4 1.0 ND1 A:HIS563 4.2 39.5 1.0 CB A:ASP564 4.4 35.1 1.0 ND1 A:HIS529 4.4 26.7 1.0 CB A:ASP674 4.4 32.6 1.0 CG A:HIS529 4.5 25.9 1.0 NE2 A:HIS525 4.7 45.4 1.0 CG2 A:VAL533 4.8 22.7 1.0 O A:HOH907 4.8 33.4 1.0 O A:ASP674 4.9 29.1 1.0 O A:HOH903 4.9 32.9 1.0 CA A:ASP674 4.9 32.0 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn801 b:43.2 occ:1.00 O B:HOH903 1.6 63.0 1.0 NE2 B:HIS563 2.0 48.1 1.0 OD1 B:ASP674 2.2 37.0 1.0 OD2 B:ASP564 2.2 35.2 1.0 NE2 B:HIS529 2.4 33.1 1.0 CD2 B:HIS563 2.7 46.8 1.0 OD2 B:ASP674 2.8 36.5 1.0 CG B:ASP674 2.9 37.5 1.0 MG B:MG802 3.0 25.7 1.0 CG B:ASP564 3.0 34.3 1.0 CE1 B:HIS563 3.1 44.5 1.0 OD1 B:ASP564 3.3 34.8 1.0 CE1 B:HIS529 3.4 35.9 1.0 CD2 B:HIS529 3.4 32.5 1.0 O B:HOH906 3.8 23.3 1.0 O B:HOH904 3.8 36.7 1.0 CG B:HIS563 3.9 44.6 1.0 CD2 B:HIS525 4.0 42.0 1.0 ND1 B:HIS563 4.1 41.7 1.0 NE2 B:HIS525 4.2 41.6 1.0 CB B:ASP674 4.3 37.4 1.0 CB B:ASP564 4.4 38.4 1.0 O B:HOH901 4.4 21.1 1.0 ND1 B:HIS529 4.5 31.8 1.0 CG B:HIS529 4.5 32.4 1.0 O B:HOH902 4.9 26.8 1.0 CA B:ASP674 5.0 35.9 1.0 CB B:THR633 5.0 34.4 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