Magnesium in PDB 6kdx: 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: 6kdx 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)	26.66 / 2.44
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.417, 81.440, 159.976, 90.00, 90.00, 90.00
R / Rfree (%)	24.1 / 30.1

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 6kdx). 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: 6kdx:
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:43.8 occ:1.00 O A:HOH906 1.8 40.0 1.0 O A:HOH908 2.0 40.4 1.0 O A:HOH903 2.2 36.6 1.0 OD1 A:ASP564 2.2 45.4 1.0 O A:HOH910 2.6 36.3 1.0 CG A:ASP564 3.3 46.6 1.0 O A:HOH907 3.5 46.1 1.0 OG1 A:THR633 3.6 44.8 1.0 OE2 A:GLU592 3.6 70.8 1.0 NE2 A:HIS595 3.7 59.1 1.0 OD2 A:ASP564 3.8 39.0 1.0 CD2 A:HIS595 3.9 60.4 1.0 O A:HIS563 4.0 46.7 1.0 ZN A:ZN801 4.0 51.4 1.0 CD2 A:HIS563 4.1 44.3 1.0 CG A:GLU592 4.2 67.4 1.0 CB A:THR633 4.3 47.9 1.0 O A:HOH905 4.3 34.8 1.0 O A:THR633 4.3 48.9 1.0 CD A:GLU592 4.4 67.7 1.0 CB A:ASP564 4.6 45.5 1.0 NE2 A:HIS563 4.6 49.3 1.0 O A:HOH904 4.6 33.8 1.0 OD2 A:ASP674 4.6 45.8 1.0 CA A:ASP564 4.7 49.2 1.0 CD2 A:HIS567 4.7 60.5 1.0 C A:HIS563 4.8 47.8 1.0 C A:THR633 4.8 53.6 1.0 CE1 A:HIS595 4.9 59.8 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:34.8 occ:1.00 O B:HOH902 2.0 27.2 1.0 OD1 B:ASP564 2.0 30.4 1.0 O B:HOH907 2.1 34.7 1.0 O B:HOH903 2.1 28.8 1.0 O B:HOH901 2.5 36.3 1.0 O B:HOH906 2.5 32.8 1.0 CG B:ASP564 3.2 31.0 1.0 O B:HOH908 3.4 36.8 1.0 O B:HOH909 3.4 27.1 1.0 OD2 B:ASP564 3.5 28.7 1.0 ZN B:ZN801 3.7 39.2 1.0 OE2 B:GLU592 4.0 43.9 1.0 OG1 B:THR633 4.1 37.5 1.0 CD2 B:HIS563 4.1 42.2 1.0 O B:HOH905 4.2 30.9 1.0 NE2 B:HIS595 4.2 37.0 1.0 OD2 B:ASP674 4.3 40.3 1.0 NE2 B:HIS563 4.3 39.8 1.0 O B:HIS563 4.5 39.6 1.0 CB B:ASP564 4.5 29.0 1.0 CD2 B:HIS567 4.5 44.3 1.0 CD2 B:HIS595 4.6 37.7 1.0 O B:THR633 4.6 36.1 1.0 CB B:THR633 4.6 39.5 1.0 CD2 B:HIS525 4.6 45.2 1.0 NE2 B:HIS567 4.7 42.6 1.0 NE2 B:HIS525 4.8 44.8 1.0 CD B:GLU592 4.9 38.6 1.0 CG B:GLU592 4.9 43.9 1.0 CA B:ASP564 4.9 32.6 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