Magnesium in PDB 6ijh: Crystal Structure of PDE10 in Complex with Inhibitor Af-399/14387019

All present enzymatic activity of Crystal Structure of PDE10 in Complex with Inhibitor Af-399/14387019:
3.1.4.17; 3.1.4.35;

The structure of Crystal Structure of PDE10 in Complex with Inhibitor Af-399/14387019, PDB code: 6ijh was solved by Y.Y.Huang, Y.F.Yu, C.Zhang, D.Wu, Y.Wu, H.B.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	79.91 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.342, 81.693, 159.816, 90.00, 90.00, 90.00
R / Rfree (%)	24 / 31.2

The structure of Crystal Structure of PDE10 in Complex with Inhibitor Af-399/14387019 also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of PDE10 in Complex with Inhibitor Af-399/14387019 (pdb code 6ijh). 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 PDE10 in Complex with Inhibitor Af-399/14387019, PDB code: 6ijh:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of PDE10 in Complex with Inhibitor Af-399/14387019


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 PDE10 in Complex with Inhibitor Af-399/14387019 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:21.4 occ:1.00 O A:HOH907 1.9 8.8 1.0 O A:HOH901 2.2 5.3 1.0 OD1 A:ASP564 2.2 23.8 1.0 O A:HOH902 2.4 18.9 1.0 OE2 A:GLU592 3.2 29.4 1.0 CG A:ASP564 3.3 24.0 1.0 OD2 A:ASP564 3.6 24.7 1.0 ZN A:ZN801 3.8 31.7 1.0 NE2 A:HIS567 4.0 29.6 1.0 CD2 A:HIS567 4.2 29.6 1.0 CD A:GLU592 4.3 29.8 1.0 NE2 A:HIS595 4.3 30.5 1.0 O A:HOH912 4.3 10.5 1.0 NE2 A:HIS525 4.3 23.6 1.0 CD2 A:HIS525 4.4 23.6 1.0 CD2 A:HIS595 4.4 31.9 1.0 OG1 A:THR633 4.4 29.0 1.0 O A:HIS563 4.6 23.4 1.0 CB A:ASP564 4.6 23.9 1.0 CG A:GLU592 4.6 30.4 1.0 OD2 A:ASP674 4.7 18.2 1.0 O A:THR633 4.7 28.0 1.0 O A:HOH910 4.8 15.6 1.0 CB A:THR633 4.8 28.5 1.0 CD2 A:HIS563 4.8 23.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of PDE10 in Complex with Inhibitor Af-399/14387019


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 PDE10 in Complex with Inhibitor Af-399/14387019 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg802 b:13.6 occ:1.00 O B:HOH922 1.8 8.1 1.0 O B:HOH909 2.0 10.9 1.0 O B:HOH924 2.0 22.8 1.0 O B:HOH913 2.2 15.2 1.0 O B:HOH919 2.2 16.9 1.0 OD1 B:ASP564 2.2 21.8 1.0 CG B:ASP564 3.2 22.4 1.0 OD2 B:ASP564 3.5 22.6 1.0 O B:HOH911 3.6 22.3 1.0 OE2 B:GLU592 3.7 36.4 1.0 ZN B:ZN801 3.9 51.7 1.0 OG1 B:THR633 4.2 24.8 1.0 O B:HIS563 4.2 21.7 1.0 NE2 B:HIS595 4.3 32.0 1.0 CD2 B:HIS563 4.3 20.1 1.0 CD2 B:HIS595 4.4 31.8 1.0 CD2 B:HIS525 4.4 31.9 1.0 CD2 B:HIS567 4.4 29.9 1.0 NE2 B:HIS567 4.5 29.4 1.0 NE2 B:HIS525 4.5 32.1 1.0 CB B:ASP564 4.6 22.4 1.0 CD B:GLU592 4.6 36.5 1.0 CB B:THR633 4.7 24.7 1.0 NE2 B:HIS563 4.8 19.9 1.0 CG B:GLU592 4.8 37.2 1.0 OD2 B:ASP674 4.9 22.3 1.0 CA B:ASP564 4.9 22.6 1.0 O B:THR633 5.0 25.3 1.0

Y.Y.Huang, Y.F.Yu, C.Zhang, Y.Chen, Q.Zhou, Z.Li, S.Zhou, Z.Li, L.Guo, D.Wu, Y.Wu, H.B.Luo. Validation of Phosphodiesterase-10 As A Novel Target For Pulmonary Arterial Hypertension Via Highly Selective and Subnanomolar Inhibitors. J. Med. Chem. V. 62 3707 2019.
ISSN: ISSN 1520-4804
PubMed: 30888810
DOI: 10.1021/ACS.JMEDCHEM.9B00224