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

Enzymatic activity of [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;

Protein crystallography data

The structure of [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors, PDB code: 6zqz 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) 87.07 / 1.88
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.960, 73.460, 92.230, 109.16, 91.37, 91.26
R / Rfree (%) 19.6 / 24.4

Other elements in 6zqz:

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

Fluorine (F) 8 atoms
Zinc (Zn) 4 atoms
Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors (pdb code 6zqz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors, PDB code: 6zqz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 6zqz

Go back to Magnesium Binding Sites List in 6zqz
Magnesium binding site 1 out of 5 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:11.2
occ:1.00
 O A:HOH1200 2.1 9.7 1.0
O A:HOH1183 2.1 9.2 1.0
OD1 A:ASP697 2.1 8.7 1.0
O A:HOH1141 2.1 8.4 1.0
O A:HOH1165 2.1 10.0 1.0
O A:HOH1214 2.2 9.3 1.0
CG A:ASP697 3.1 8.9 1.0
OD2 A:ASP697 3.4 8.9 1.0
ZN A:ZN1001 3.7 13.7 1.0
O A:HOH1326 3.8 19.6 1.0
O A:HOH1201 4.0 18.3 1.0
NE2 A:HIS730 4.1 10.0 1.0
OG1 A:THR768 4.2 10.1 1.0
CD2 A:HIS696 4.2 8.7 1.0
CD2 A:HIS730 4.3 9.7 1.0
O A:HOH1251 4.3 10.8 1.0
O A:HIS696 4.3 9.2 1.0
OE2 A:GLU727 4.4 11.6 1.0
NE2 A:HIS656 4.4 11.2 1.0
CD2 A:HIS700 4.5 11.2 1.0
CD2 A:HIS656 4.5 10.8 1.0
CB A:ASP697 4.5 9.0 1.0
OD2 A:ASP808 4.6 12.5 1.0
NE2 A:HIS696 4.6 8.9 1.0
CB A:THR768 4.6 10.6 1.0
O A:THR768 4.7 10.9 1.0
NE2 A:HIS700 4.8 11.3 1.0
CA A:ASP697 4.9 8.9 1.0
CG A:GLU727 4.9 10.8 1.0

Magnesium binding site 2 out of 5 in 6zqz

Go back to Magnesium Binding Sites List in 6zqz
Magnesium binding site 2 out of 5 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:12.3
occ:1.00
 O B:HOH1119 2.0 10.8 1.0
O B:HOH1124 2.1 10.4 1.0
O B:HOH1166 2.1 10.3 1.0
O B:HOH1160 2.2 9.5 1.0
OD1 B:ASP697 2.2 9.6 1.0
O B:HOH1178 2.2 11.8 1.0
CG B:ASP697 3.2 10.3 1.0
OD2 B:ASP697 3.5 9.9 1.0
ZN B:ZN1001 3.7 15.0 1.0
O B:HOH1312 4.0 18.0 1.0
O B:HOH1215 4.0 21.9 1.0
OG1 B:THR768 4.0 11.2 1.0
OE2 B:GLU727 4.1 16.3 1.0
NE2 B:HIS730 4.2 11.8 1.0
CD2 B:HIS696 4.2 10.2 1.0
O B:HOH1287 4.3 16.9 1.0
O B:HIS696 4.3 10.7 1.0
CD2 B:HIS730 4.4 11.9 1.0
OD2 B:ASP808 4.4 14.4 1.0
CB B:THR768 4.5 11.4 1.0
CB B:ASP697 4.6 10.5 1.0
O B:THR768 4.6 12.6 1.0
NE2 B:HIS656 4.6 13.2 1.0
CD2 B:HIS656 4.6 12.9 1.0
NE2 B:HIS696 4.6 10.6 1.0
CD2 B:HIS700 4.7 13.8 1.0
CA B:ASP697 4.9 11.2 1.0
CD B:GLU727 4.9 15.4 1.0
CG B:GLU727 4.9 15.1 1.0
NE2 B:HIS700 4.9 13.9 1.0

Magnesium binding site 3 out of 5 in 6zqz

Go back to Magnesium Binding Sites List in 6zqz
Magnesium binding site 3 out of 5 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 3 of [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1004

b:27.5
occ:1.00
 O B:HOH1304 2.1 19.7 1.0
O B:HOH1308 2.1 28.0 1.0
O B:HOH1103 2.2 20.8 1.0
OD2 B:ASP789 4.1 22.7 1.0
ND2 B:ASN792 4.1 20.2 1.0
O B:HOH1320 4.2 25.8 1.0
O B:HOH1175 4.2 30.3 1.0

Magnesium binding site 4 out of 5 in 6zqz

Go back to Magnesium Binding Sites List in 6zqz
Magnesium binding site 4 out of 5 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 4 of [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1002

b:10.2
occ:1.00
 O C:HOH1171 2.1 10.9 1.0
O C:HOH1135 2.1 9.4 1.0
O C:HOH1172 2.1 9.5 1.0
OD1 C:ASP697 2.1 10.1 1.0
O C:HOH1154 2.1 9.8 1.0
O C:HOH1105 2.2 12.2 1.0
CG C:ASP697 3.2 11.1 1.0
OD2 C:ASP697 3.5 11.0 1.0
ZN C:ZN1001 3.7 15.4 1.0
O C:HOH1127 4.1 15.9 1.0
O C:HOH1264 4.1 17.0 1.0
OE2 C:GLU727 4.1 15.1 1.0
O C:HOH1119 4.1 13.1 1.0
NE2 C:HIS730 4.1 12.8 1.0
OG1 C:THR768 4.2 12.8 1.0
CD2 C:HIS696 4.2 11.1 1.0
O C:HIS696 4.3 11.5 1.0
CD2 C:HIS730 4.4 12.8 1.0
CD2 C:HIS700 4.4 14.6 1.0
NE2 C:HIS656 4.5 13.2 1.0
CB C:ASP697 4.5 11.3 1.0
OD2 C:ASP808 4.5 14.2 1.0
CD2 C:HIS656 4.6 12.7 1.0
CB C:THR768 4.6 13.6 1.0
O C:THR768 4.7 14.3 1.0
NE2 C:HIS700 4.7 13.8 1.0
NE2 C:HIS696 4.7 11.7 1.0
O C:HOH1140 4.8 27.2 1.0
CA C:ASP697 4.8 11.6 1.0
CD C:GLU727 4.9 15.0 1.0
CG C:GLU727 4.9 14.5 1.0

Magnesium binding site 5 out of 5 in 6zqz

Go back to Magnesium Binding Sites List in 6zqz
Magnesium binding site 5 out of 5 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 5 of [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1002

b:11.8
occ:1.00
 O D:HOH1252 2.1 9.8 1.0
O D:HOH1119 2.1 9.3 1.0
O D:HOH1138 2.1 9.1 1.0
O D:HOH1127 2.1 12.0 1.0
O D:HOH1226 2.1 9.9 1.0
OD1 D:ASP697 2.2 9.7 1.0
CG D:ASP697 3.1 10.3 1.0
OD2 D:ASP697 3.4 9.5 1.0
ZN D:ZN1001 3.7 14.5 1.0
O D:HOH1326 3.8 21.9 1.0
O D:HOH1238 4.0 18.6 1.0
OE2 D:GLU727 4.1 11.9 1.0
CD2 D:HIS696 4.1 10.7 1.0
O D:HOH1223 4.1 12.2 1.0
OG1 D:THR768 4.2 10.3 1.0
NE2 D:HIS730 4.2 10.2 1.0
O D:HIS696 4.3 11.0 1.0
OD2 D:ASP808 4.4 13.5 1.0
CD2 D:HIS730 4.4 9.9 1.0
CD2 D:HIS700 4.4 14.4 1.0
NE2 D:HIS656 4.4 14.8 1.0
NE2 D:HIS696 4.5 11.2 1.0
CB D:THR768 4.5 10.7 1.0
CD2 D:HIS656 4.5 14.9 1.0
CB D:ASP697 4.5 10.7 1.0
NE2 D:HIS700 4.7 13.9 1.0
O D:THR768 4.7 11.4 1.0
CA D:ASP697 4.8 11.0 1.0
CG D:GLU727 4.9 11.0 1.0
CD D:GLU727 5.0 11.6 1.0
O D:HOH1187 5.0 20.4 1.0

Reference:

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
Page generated: Wed Oct 2 02:36:15 2024

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