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Magnesium in PDB 5sfy: Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[(E)-2-[2-Methyl-5-(1H-Pyrazol-4-Yl)-1,2,4-Triazol-3- Yl]Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyrazine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[(E)-2-[2-Methyl-5-(1H-Pyrazol-4-Yl)-1,2,4-Triazol-3- Yl]Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyrazine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[(E)-2-[2-Methyl-5-(1H-Pyrazol-4-Yl)-1,2,4-Triazol-3- Yl]Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyrazine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[(E)-2-[2-Methyl-5-(1H-Pyrazol-4-Yl)-1,2,4-Triazol-3- Yl]Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyrazine, PDB code: 5sfy was solved by C.Joseph, A.Flohr, J.Benz, D.Schlatter, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.47 / 2.08
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.137, 135.137, 234.83, 90, 90, 120
R / Rfree (%) 18.2 / 22.5

Other elements in 5sfy:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[(E)-2-[2-Methyl-5-(1H-Pyrazol-4-Yl)-1,2,4-Triazol-3- Yl]Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyrazine also contains other interesting chemical elements:

Zinc (Zn) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[(E)-2-[2-Methyl-5-(1H-Pyrazol-4-Yl)-1,2,4-Triazol-3- Yl]Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyrazine (pdb code 5sfy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[(E)-2-[2-Methyl-5-(1H-Pyrazol-4-Yl)-1,2,4-Triazol-3- Yl]Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyrazine, PDB code: 5sfy:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sfy

Go back to Magnesium Binding Sites List in 5sfy
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[(E)-2-[2-Methyl-5-(1H-Pyrazol-4-Yl)-1,2,4-Triazol-3- Yl]Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyrazine


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 Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[(E)-2-[2-Methyl-5-(1H-Pyrazol-4-Yl)-1,2,4-Triazol-3- Yl]Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:29.3
occ:1.00
 O A:HOH990 1.9 27.4 1.0
O A:HOH966 2.1 28.9 1.0
OD1 A:ASP564 2.1 26.2 1.0
O A:HOH911 2.1 24.0 1.0
O A:HOH923 2.2 23.6 1.0
O A:HOH929 2.2 24.8 1.0
CG A:ASP564 3.2 26.9 1.0
OD2 A:ASP564 3.5 28.5 1.0
ZN A:ZN801 3.8 31.5 1.0
ZN A:ZN804 3.9 49.9 0.5
OE2 A:GLU592 3.9 30.2 1.0
NE2 A:HIS595 4.0 24.5 1.0
O A:HOH974 4.0 33.1 1.0
O A:HOH958 4.1 31.9 1.0
OG1 A:THR633 4.2 28.2 1.0
CD2 A:HIS567 4.3 25.8 1.0
CD2 A:HIS595 4.3 23.2 1.0
CD2 A:HIS563 4.4 25.6 1.0
O A:HIS563 4.5 25.8 1.0
O A:THR633 4.5 29.8 1.0
CB A:ASP564 4.5 26.8 1.0
NE2 A:HIS567 4.6 29.7 1.0
OD2 A:ASP674 4.6 37.0 1.0
CD2 A:HIS525 4.6 29.1 1.0
NE2 A:HIS525 4.7 31.8 1.0
CB A:THR633 4.7 28.5 1.0
NE2 A:HIS563 4.8 27.4 1.0
CD A:GLU592 4.8 29.3 1.0
CA A:ASP564 4.8 28.5 1.0
CG A:GLU592 4.8 26.9 1.0

Magnesium binding site 2 out of 4 in 5sfy

Go back to Magnesium Binding Sites List in 5sfy
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[(E)-2-[2-Methyl-5-(1H-Pyrazol-4-Yl)-1,2,4-Triazol-3- Yl]Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyrazine


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 Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[(E)-2-[2-Methyl-5-(1H-Pyrazol-4-Yl)-1,2,4-Triazol-3- Yl]Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:27.4
occ:1.00
 O B:HOH939 2.0 19.7 1.0
O B:HOH929 2.0 26.8 1.0
O B:HOH993 2.0 27.6 1.0
O B:HOH903 2.0 22.3 1.0
O B:HOH950 2.1 21.9 1.0
OD1 B:ASP564 2.2 26.4 1.0
CG B:ASP564 3.2 26.2 1.0
OD2 B:ASP564 3.5 28.6 1.0
OE2 B:GLU592 3.8 27.1 1.0
O B:HOH995 3.8 39.3 1.0
ZN B:ZN801 3.9 30.6 1.0
ZN B:ZN804 4.0 50.2 0.5
NE2 B:HIS595 4.0 26.9 1.0
OG1 B:THR633 4.2 26.0 1.0
CD2 B:HIS563 4.2 23.6 1.0
O B:HOH949 4.3 25.9 1.0
O B:HIS563 4.3 26.2 1.0
CD2 B:HIS567 4.3 25.4 1.0
CD2 B:HIS595 4.4 24.9 1.0
OD2 B:ASP674 4.4 32.7 1.0
NE2 B:HIS567 4.5 26.6 1.0
CB B:ASP564 4.6 25.0 1.0
NE2 B:HIS563 4.6 24.4 1.0
O B:THR633 4.6 25.8 1.0
CD2 B:HIS525 4.7 23.2 1.0
CD B:GLU592 4.7 27.7 1.0
CG B:GLU592 4.7 26.3 1.0
CB B:THR633 4.7 26.5 1.0
CA B:ASP564 4.8 25.4 1.0
NE2 B:HIS525 4.8 24.4 1.0

Magnesium binding site 3 out of 4 in 5sfy

Go back to Magnesium Binding Sites List in 5sfy
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[(E)-2-[2-Methyl-5-(1H-Pyrazol-4-Yl)-1,2,4-Triazol-3- Yl]Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyrazine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[(E)-2-[2-Methyl-5-(1H-Pyrazol-4-Yl)-1,2,4-Triazol-3- Yl]Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:25.3
occ:1.00
 O C:HOH940 1.9 22.2 1.0
O C:HOH981 2.0 25.7 1.0
O C:HOH916 2.0 22.3 1.0
O C:HOH918 2.1 26.0 1.0
OD1 C:ASP564 2.2 27.0 1.0
O C:HOH982 2.2 23.6 1.0
CG C:ASP564 3.2 26.2 1.0
OD2 C:ASP564 3.6 28.4 1.0
ZN C:ZN801 3.7 31.1 1.0
ZN C:ZN804 3.8 46.4 0.5
O C:HOH967 4.0 37.5 1.0
OE2 C:GLU592 4.0 29.6 1.0
NE2 C:HIS595 4.1 28.2 1.0
OG1 C:THR633 4.1 28.5 1.0
O C:HOH950 4.2 32.7 1.0
CD2 C:HIS563 4.2 24.0 1.0
O C:HIS563 4.3 25.8 1.0
CD2 C:HIS567 4.3 31.1 1.0
OD2 C:ASP674 4.3 31.5 1.0
CD2 C:HIS595 4.4 26.8 1.0
O C:THR633 4.4 28.8 1.0
NE2 C:HIS567 4.5 32.3 1.0
CB C:THR633 4.5 26.0 1.0
CB C:ASP564 4.5 24.8 1.0
NE2 C:HIS563 4.7 24.7 1.0
CD2 C:HIS525 4.7 29.7 1.0
CG C:GLU592 4.7 25.3 1.0
CA C:ASP564 4.8 25.9 1.0
NE2 C:HIS525 4.8 30.4 1.0
CD C:GLU592 4.8 28.0 1.0

Magnesium binding site 4 out of 4 in 5sfy

Go back to Magnesium Binding Sites List in 5sfy
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[(E)-2-[2-Methyl-5-(1H-Pyrazol-4-Yl)-1,2,4-Triazol-3- Yl]Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyrazine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[(E)-2-[2-Methyl-5-(1H-Pyrazol-4-Yl)-1,2,4-Triazol-3- Yl]Ethenyl]-[1,2,4]Triazolo[1,5-A]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:37.8
occ:1.00
 O D:HOH936 2.0 31.8 1.0
OD1 D:ASP564 2.1 32.2 1.0
O D:HOH929 2.1 38.8 1.0
O D:HOH908 2.1 32.5 1.0
O D:HOH931 2.1 27.4 1.0
O D:HOH911 2.2 30.5 1.0
CG D:ASP564 3.1 33.0 1.0
OD2 D:ASP564 3.5 35.7 1.0
NE2 D:HIS595 3.8 31.2 1.0
ZN D:ZN801 3.8 36.7 1.0
O D:HOH952 3.8 42.8 1.0
O D:HOH924 3.9 42.3 1.0
ZN D:ZN804 4.0 55.6 0.5
OE2 D:GLU592 4.0 38.8 1.0
CD2 D:HIS567 4.1 39.7 1.0
CD2 D:HIS595 4.2 32.2 1.0
OG1 D:THR633 4.2 33.3 1.0
O D:HIS563 4.3 32.2 1.0
NE2 D:HIS567 4.4 36.6 1.0
CD2 D:HIS563 4.4 28.0 1.0
CB D:ASP564 4.5 31.5 1.0
CD2 D:HIS525 4.5 35.1 1.0
OD2 D:ASP674 4.6 37.0 1.0
O D:THR633 4.6 35.9 1.0
NE2 D:HIS525 4.6 43.5 1.0
CA D:ASP564 4.7 30.5 1.0
NE2 D:HIS563 4.8 24.9 1.0
CB D:THR633 4.8 35.2 1.0
CD D:GLU592 4.9 37.5 1.0
CE1 D:HIS595 4.9 33.5 1.0
O D:HOH961 4.9 39.7 1.0

Reference:

A.Tosstorff, M.G.Rudolph, J.C.Cole, M.Reutlinger, C.Kramer, H.Schaffhauser, A.Nilly, A.Flohr, B.Kuhn. A High Quality, Industrial Data Set For Binding Affinity Prediction: Performance Comparison in Different Early Drug Discovery Scenarios. J.Comput.Aided Mol.Des. V. 36 753 2022.
ISSN: ESSN 1573-4951
PubMed: 36153472
DOI: 10.1007/S10822-022-00478-X
Page generated: Mon Sep 30 03:40:50 2024

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