Magnesium in PDB 6znd: [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors

All present enzymatic activity of [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors:
3.1.4.17;

The structure of [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors, PDB code: 6znd was solved by G.Tresadern, P.M.Leonard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	85.51 / 2.35
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	171.060, 69.520, 55.090, 90.00, 91.16, 90.00
R / Rfree (%)	21.5 / 29.1

The structure of [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors (pdb code 6znd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors, PDB code: 6znd:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:2.0 occ:1.00 OD1 A:ASP697 1.9 9.3 1.0 O A:HOH1114 2.0 3.9 1.0 O A:HOH1126 2.0 6.4 1.0 O A:HOH1142 2.0 4.6 1.0 O A:HOH1173 2.0 11.3 1.0 O A:HOH1150 2.1 2.5 1.0 CG A:ASP697 2.9 12.8 1.0 OD2 A:ASP697 3.3 7.3 1.0 ZN A:ZN1001 3.5 12.4 1.0 O A:HOH1187 3.9 17.3 1.0 CD2 A:HIS696 4.0 18.5 1.0 OG1 A:THR768 4.1 12.6 1.0 NE2 A:HIS730 4.1 14.9 1.0 O A:HIS696 4.2 14.8 1.0 OE2 A:GLU727 4.2 14.5 1.0 OD2 A:ASP808 4.3 15.1 1.0 CB A:ASP697 4.3 13.9 1.0 O A:HOH1143 4.3 8.6 1.0 NE2 A:HIS696 4.4 17.2 1.0 CD2 A:HIS730 4.4 15.3 1.0 CB A:THR768 4.5 13.5 1.0 CD2 A:HIS700 4.6 14.5 1.0 NE2 A:HIS656 4.6 17.5 1.0 CD2 A:HIS656 4.6 17.0 1.0 CA A:ASP697 4.7 14.3 1.0 NE2 A:HIS700 4.7 13.8 1.0 O A:THR768 4.7 14.8 1.0 OD1 A:ASP808 4.8 13.1 1.0 C A:HIS696 4.9 15.1 1.0

Magnesium binding site 2 out of 2 in the [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:2.0 occ:1.00 O B:HOH1146 1.8 8.2 1.0 O B:HOH1133 2.0 13.3 1.0 O B:HOH1135 2.0 9.4 1.0 OD1 B:ASP697 2.1 11.4 1.0 O B:HOH1113 2.1 8.6 1.0 O B:HOH1112 2.1 9.7 1.0 CG B:ASP697 3.1 15.5 1.0 OD2 B:ASP697 3.5 11.5 1.0 O B:HOH1151 3.6 27.5 1.0 OE2 B:GLU727 3.7 25.2 1.0 ZN B:ZN1001 3.8 9.6 1.0 O B:HOH1164 4.0 18.5 1.0 CD2 B:HIS696 4.2 16.4 1.0 NE2 B:HIS730 4.2 25.3 1.0 O B:HIS696 4.2 17.2 1.0 OG1 B:THR768 4.2 15.6 1.0 NE2 B:HIS656 4.4 25.3 1.0 CD2 B:HIS730 4.4 25.3 1.0 CD2 B:HIS656 4.5 24.6 1.0 CB B:ASP697 4.5 16.9 1.0 OD2 B:ASP808 4.5 14.1 1.0 CB B:THR768 4.5 16.6 1.0 CD2 B:HIS700 4.6 21.3 1.0 NE2 B:HIS696 4.7 14.9 1.0 O B:THR768 4.7 17.2 1.0 CD B:GLU727 4.7 26.5 1.0 CA B:ASP697 4.8 17.1 1.0 NE2 B:HIS700 4.9 21.7 1.0 CG B:GLU727 4.9 26.3 1.0

G.Tresadern, I.Velter, A.A.Trabanco, F.Van Den Keybus, G.J.Macdonald, M.V.F.Somers, G.Vanhoof, P.M.Leonard, M.B.A.C.Lamers, Y.E.M.Van Roosbroeck, P.J.J.A.Buijnsters. [1,2,4]Triazolo[1,5- A ]Pyrimidine Phosphodiesterase 2A Inhibitors: Structure and Free-Energy Perturbation-Guided Exploration. J.Med.Chem. V. 63 12887 2020.
ISSN: ISSN 0022-2623
PubMed: 33105987
DOI: 10.1021/ACS.JMEDCHEM.0C01272