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Magnesium in PDB 5sk1: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N,2- Dimethyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole-3,4- Dicarboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N,2- Dimethyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole-3,4- Dicarboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N,2- Dimethyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole-3,4- Dicarboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N,2- Dimethyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole-3,4- Dicarboxamide, PDB code: 5sk1 was solved by C.Joseph, J.Benz, A.Flohr, J.Peters, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.37 / 2.30
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 134.851, 134.851, 234.435, 90, 90, 120
R / Rfree (%) 18.5 / 23.8

Other elements in 5sk1:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N,2- Dimethyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole-3,4- Dicarboxamide also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N,2- Dimethyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole-3,4- Dicarboxamide (pdb code 5sk1). 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 4-N,2- Dimethyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole-3,4- Dicarboxamide, PDB code: 5sk1:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sk1

Go back to Magnesium Binding Sites List in 5sk1
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N,2- Dimethyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole-3,4- Dicarboxamide


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 4-N,2- Dimethyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole-3,4- Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:35.7
occ:1.00
 O A:HOH985 1.9 27.9 1.0
O A:HOH957 2.0 28.9 1.0
O A:HOH944 2.0 36.5 1.0
OD1 A:ASP564 2.0 30.1 1.0
O A:HOH906 2.0 30.0 1.0
O A:HOH933 2.1 30.9 1.0
CG A:ASP564 3.0 32.0 1.0
OD2 A:ASP564 3.4 37.4 1.0
ZN A:ZN801 3.9 37.9 1.0
O A:HOH978 3.9 34.7 1.0
O A:HOH952 4.0 40.2 1.0
OE2 A:GLU592 4.0 39.0 1.0
NE2 A:HIS595 4.0 35.9 1.0
CD2 A:HIS567 4.1 35.8 1.0
CD2 A:HIS563 4.3 29.7 1.0
NE2 A:HIS567 4.3 37.7 1.0
CD2 A:HIS595 4.3 33.8 1.0
O A:HIS563 4.4 29.7 1.0
CB A:ASP564 4.4 30.3 1.0
OG1 A:THR633 4.4 32.3 1.0
O A:THR633 4.6 34.5 1.0
CD2 A:HIS525 4.6 36.8 1.0
OD2 A:ASP674 4.7 43.3 1.0
NE2 A:HIS563 4.7 28.1 1.0
NE2 A:HIS525 4.8 34.6 1.0
CA A:ASP564 4.8 32.1 1.0
CD A:GLU592 4.8 39.5 1.0
CB A:THR633 4.9 31.8 1.0
CG A:GLU592 4.9 37.2 1.0

Magnesium binding site 2 out of 4 in 5sk1

Go back to Magnesium Binding Sites List in 5sk1
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N,2- Dimethyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole-3,4- Dicarboxamide


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 4-N,2- Dimethyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole-3,4- Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:32.6
occ:1.00
 O B:HOH936 1.9 22.8 1.0
O B:HOH922 2.0 31.4 1.0
O B:HOH965 2.0 29.4 1.0
O B:HOH945 2.0 23.6 1.0
OD1 B:ASP564 2.1 29.1 1.0
O B:HOH906 2.2 25.6 1.0
CG B:ASP564 3.2 29.7 1.0
OD2 B:ASP564 3.6 32.2 1.0
ZN B:ZN801 3.9 37.8 1.0
O B:HOH950 3.9 34.5 1.0
OE2 B:GLU592 4.0 33.5 1.0
NE2 B:HIS595 4.0 36.2 1.0
O B:HOH957 4.1 32.3 1.0
CD2 B:HIS567 4.2 31.9 1.0
CD2 B:HIS595 4.3 38.4 1.0
CD2 B:HIS563 4.3 30.7 1.0
OG1 B:THR633 4.4 32.1 1.0
NE2 B:HIS567 4.4 35.0 1.0
OD2 B:ASP674 4.4 36.9 1.0
O B:HIS563 4.5 37.9 1.0
CB B:ASP564 4.5 29.2 1.0
O B:THR633 4.6 29.5 1.0
CD2 B:HIS525 4.6 36.3 1.0
NE2 B:HIS525 4.6 36.6 1.0
NE2 B:HIS563 4.6 29.9 1.0
CD B:GLU592 4.8 33.7 1.0
CG B:GLU592 4.8 35.4 1.0
CA B:ASP564 4.8 31.0 1.0
CB B:THR633 4.9 32.7 1.0

Magnesium binding site 3 out of 4 in 5sk1

Go back to Magnesium Binding Sites List in 5sk1
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N,2- Dimethyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole-3,4- Dicarboxamide


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 4-N,2- Dimethyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole-3,4- Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:32.0
occ:1.00
 O C:HOH969 2.0 32.8 1.0
O C:HOH987 2.1 32.7 1.0
O C:HOH930 2.1 33.5 1.0
OD1 C:ASP564 2.1 27.5 1.0
O C:HOH917 2.1 25.6 1.0
O C:HOH941 2.2 27.1 1.0
CG C:ASP564 3.1 29.7 1.0
OD2 C:ASP564 3.4 31.6 1.0
O C:HOH933 3.7 39.5 1.0
ZN C:ZN801 3.8 39.4 1.0
NE2 C:HIS595 4.1 36.3 1.0
CD2 C:HIS567 4.1 37.9 1.0
OE2 C:GLU592 4.1 34.9 1.0
CD2 C:HIS563 4.2 27.4 1.0
O C:HIS563 4.3 32.0 1.0
NE2 C:HIS567 4.3 37.0 1.0
O C:HOH956 4.3 37.3 1.0
OG1 C:THR633 4.3 33.0 1.0
OD2 C:ASP674 4.3 33.2 1.0
CD2 C:HIS595 4.4 33.8 1.0
CB C:ASP564 4.4 29.2 1.0
NE2 C:HIS563 4.6 29.0 1.0
O C:THR633 4.6 31.5 1.0
CB C:THR633 4.8 32.2 1.0
CD2 C:HIS525 4.8 43.8 1.0
CA C:ASP564 4.8 30.5 1.0
NE2 C:HIS525 4.8 42.9 1.0
CG C:GLU592 4.9 37.9 1.0
CD C:GLU592 5.0 36.5 1.0

Magnesium binding site 4 out of 4 in 5sk1

Go back to Magnesium Binding Sites List in 5sk1
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N,2- Dimethyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole-3,4- Dicarboxamide


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 4-N,2- Dimethyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole-3,4- Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:49.4
occ:1.00
 O D:HOH915 2.0 37.0 1.0
O D:HOH925 2.1 40.4 1.0
O D:HOH924 2.1 49.9 1.0
O D:HOH904 2.2 53.3 1.0
OD1 D:ASP564 2.2 51.2 1.0
O D:HOH905 2.2 48.7 1.0
CG D:ASP564 3.2 51.6 1.0
OD2 D:ASP564 3.5 62.4 1.0
O D:HOH932 3.8 42.9 1.0
OE2 D:GLU592 3.9 55.9 1.0
ZN D:ZN801 4.0 57.8 1.0
O D:HOH916 4.1 42.1 1.0
NE2 D:HIS595 4.1 58.9 1.0
CD2 D:HIS567 4.2 54.9 1.0
NE2 D:HIS567 4.3 54.5 1.0
OG1 D:THR633 4.3 47.4 1.0
CD2 D:HIS595 4.4 62.3 1.0
O D:HIS563 4.4 47.2 1.0
CD2 D:HIS563 4.4 49.5 1.0
OD2 D:ASP674 4.5 60.1 1.0
CB D:ASP564 4.5 50.7 1.0
O D:THR633 4.6 53.8 1.0
CD2 D:HIS525 4.7 58.7 1.0
NE2 D:HIS525 4.7 62.2 1.0
CA D:ASP564 4.8 48.4 1.0
CD D:GLU592 4.8 54.2 1.0
CB D:THR633 4.8 48.8 1.0
NE2 D:HIS563 4.9 48.6 1.0

Reference:

A.Flohr, D.Schlatter, B.Kuhn, M.G.Rudolph. Crystal Structure of A Human Phosphodiesterase 10 Complex To Be Published.
Page generated: Tue Aug 12 20:13:07 2025

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