Atomistry » Magnesium » PDB 6zii-6zt3 » 6zqz
Atomistry »
  Magnesium »
    PDB 6zii-6zt3 »
      6zqz »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy