Magnesium in PDB 6kdz: Crystal Structure of PDE10A in Complex with A Triazolopyrimidine Inhibitor

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

The structure of Crystal Structure of PDE10A in Complex with A Triazolopyrimidine Inhibitor, PDB code: 6kdz 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)	47.97 / 3.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.218, 81.044, 162.136, 90.00, 90.00, 90.00
R / Rfree (%)	25.3 / 32.5

The structure of Crystal Structure of PDE10A in Complex with A Triazolopyrimidine 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 Triazolopyrimidine Inhibitor (pdb code 6kdz). 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 Triazolopyrimidine Inhibitor, PDB code: 6kdz:
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 Triazolopyrimidine 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 Triazolopyrimidine Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:41.3 occ:1.00 OD1 A:ASP564 2.3 58.7 1.0 CG A:ASP564 3.2 60.2 1.0 ZN A:ZN801 3.2 59.2 1.0 OD2 A:ASP564 3.3 60.2 1.0 OE2 A:GLU592 3.7 75.7 1.0 OG1 A:THR633 4.1 64.7 1.0 CD2 A:HIS563 4.2 53.6 1.0 O A:THR633 4.2 65.7 1.0 OD2 A:ASP674 4.2 59.8 1.0 CB A:THR633 4.3 65.2 1.0 NE2 A:HIS595 4.5 90.0 1.0 NE2 A:HIS563 4.5 55.7 1.0 CB A:ASP564 4.7 59.5 1.0 O A:HIS563 4.7 64.3 1.0 CD2 A:HIS595 4.7 84.0 1.0 CD A:GLU592 4.7 83.8 1.0 C A:THR633 4.8 62.2 1.0 CD2 A:HIS567 4.8 69.2 1.0 CD2 A:HIS525 4.8 66.5 1.0 CG A:GLU592 4.9 86.8 1.0 NE2 A:HIS567 5.0 68.4 1.0 OD1 A:ASP674 5.0 64.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of PDE10A in Complex with A Triazolopyrimidine 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 Triazolopyrimidine Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg802 b:34.9 occ:1.00 OD1 B:ASP564 2.4 43.8 1.0 CG B:ASP564 3.2 43.5 1.0 OD2 B:ASP564 3.3 41.4 1.0 ZN B:ZN801 3.5 63.5 1.0 OE2 B:GLU592 3.9 69.8 1.0 OD2 B:ASP674 4.1 46.1 1.0 O B:THR633 4.2 66.9 1.0 CD2 B:HIS563 4.3 55.0 1.0 OG1 B:THR633 4.3 54.9 1.0 CB B:THR633 4.5 57.8 1.0 NE2 B:HIS595 4.5 61.1 1.0 NE2 B:HIS563 4.6 56.1 1.0 CD2 B:HIS525 4.6 70.7 1.0 CB B:ASP564 4.7 43.6 1.0 CD2 B:HIS595 4.7 63.6 1.0 CD2 B:HIS567 4.8 70.6 1.0 O B:HIS563 4.8 59.5 1.0 NE2 B:HIS525 4.8 77.6 1.0 CD B:GLU592 4.9 65.9 1.0 C B:THR633 4.9 63.7 1.0 NE2 B:HIS567 4.9 71.7 1.0 CG B:ASP674 5.0 47.1 1.0

A.Chino, S.Honda, M.Morita, K.Yonezawa, W.Hamaguchi, Y.Amano, H.Moriguchi, M.Yamazaki, M.Aota, M.Tomishima, N.Masuda. Synthesis, Sar Study, and Biological Evaluation of Novel 2,3-Dihydro-1H-Imidazo[1,2-A]Benzimidazole Derivatives As Phosphodiesterase 10A Inhibitors. Bioorg.Med.Chem. V. 27 3692 2019.
ISSN: ESSN 1464-3391
PubMed: 31301949
DOI: 10.1016/J.BMC.2019.07.010