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Magnesium in PDB 5sio: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-(2-Methylpyrrolidine-1-Carbonyl)-N-(2-Phenylimidazo[1,2- A]Pyridin-7-Yl)Pyrazole-3-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-(2-Methylpyrrolidine-1-Carbonyl)-N-(2-Phenylimidazo[1,2- A]Pyridin-7-Yl)Pyrazole-3-Carboxamide

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

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-(2-Methylpyrrolidine-1-Carbonyl)-N-(2-Phenylimidazo[1,2- A]Pyridin-7-Yl)Pyrazole-3-Carboxamide, PDB code: 5sio 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) 41.46 / 2.20
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.306, 135.306, 235.568, 90, 90, 120
R / Rfree (%) 18.4 / 23.3

Other elements in 5sio:

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

Zinc (Zn) 4 atoms
Chlorine (Cl) 1 atom
Praseodymium (Pr) 5 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 4 in 5sio

Go back to Magnesium Binding Sites List in 5sio
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-(2-Methylpyrrolidine-1-Carbonyl)-N-(2-Phenylimidazo[1,2- A]Pyridin-7-Yl)Pyrazole-3-Carboxamide


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 2- Methyl-4-(2-Methylpyrrolidine-1-Carbonyl)-N-(2-Phenylimidazo[1,2- A]Pyridin-7-Yl)Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:28.6
occ:1.00
 OD1 A:ASP564 1.9 29.5 1.0
O A:HOH961 2.0 29.2 1.0
O A:HOH990 2.0 25.4 1.0
O A:HOH910 2.0 23.4 1.0
O A:HOH957 2.1 23.8 1.0
O A:HOH930 2.2 29.9 1.0
CG A:ASP564 2.9 30.0 1.0
OD2 A:ASP564 3.2 31.4 1.0
ZN A:ZN801 3.7 33.6 1.0
O A:HOH991 3.9 33.4 1.0
NE2 A:HIS595 4.1 32.1 1.0
OE2 A:GLU592 4.2 35.9 1.0
CD2 A:HIS563 4.2 27.2 1.0
O A:HIS563 4.3 27.7 1.0
CB A:ASP564 4.3 29.6 1.0
O A:HOH1003 4.3 42.6 1.0
OG1 A:THR633 4.3 31.0 1.0
CD2 A:HIS567 4.3 31.6 1.0
CD2 A:HIS595 4.4 28.8 1.0
CD2 A:HIS525 4.5 33.6 1.0
O A:THR633 4.5 35.0 1.0
NE2 A:HIS563 4.6 26.1 1.0
NE2 A:HIS525 4.6 34.1 1.0
NE2 A:HIS567 4.6 33.3 1.0
OD2 A:ASP674 4.6 39.2 1.0
CA A:ASP564 4.7 29.0 1.0
CB A:THR633 4.8 28.8 1.0
CG A:GLU592 5.0 32.3 1.0

Magnesium binding site 2 out of 4 in 5sio

Go back to Magnesium Binding Sites List in 5sio
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-(2-Methylpyrrolidine-1-Carbonyl)-N-(2-Phenylimidazo[1,2- A]Pyridin-7-Yl)Pyrazole-3-Carboxamide


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 2- Methyl-4-(2-Methylpyrrolidine-1-Carbonyl)-N-(2-Phenylimidazo[1,2- A]Pyridin-7-Yl)Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:22.9
occ:1.00
 O B:HOH920 2.0 22.1 1.0
O B:HOH929 2.0 27.9 1.0
O B:HOH969 2.0 25.4 1.0
OD1 B:ASP564 2.1 25.7 1.0
O B:HOH904 2.1 23.0 1.0
O B:HOH958 2.1 18.3 1.0
CG B:ASP564 3.1 26.8 1.0
OD2 B:ASP564 3.4 28.8 1.0
ZN B:ZN801 3.7 32.9 1.0
O B:HOH954 3.8 32.8 1.0
OE2 B:GLU592 4.0 33.2 1.0
NE2 B:HIS595 4.1 30.4 1.0
O B:HOH997 4.2 42.1 1.0
CD2 B:HIS567 4.2 27.8 1.0
CD2 B:HIS563 4.3 25.3 1.0
OD2 B:ASP674 4.3 33.8 1.0
O B:HOH956 4.3 35.3 1.0
NE2 B:HIS567 4.3 28.0 1.0
OG1 B:THR633 4.3 26.9 1.0
O B:HIS563 4.3 30.7 1.0
CD2 B:HIS595 4.4 31.7 1.0
CB B:ASP564 4.4 27.5 1.0
CD2 B:HIS525 4.5 30.6 1.0
NE2 B:HIS525 4.5 30.9 1.0
NE2 B:HIS563 4.5 25.0 1.0
O B:THR633 4.6 28.9 1.0
CB B:THR633 4.7 29.2 1.0
CA B:ASP564 4.8 28.3 1.0
CD B:GLU592 4.9 32.4 1.0
CG B:GLU592 4.9 30.8 1.0

Magnesium binding site 3 out of 4 in 5sio

Go back to Magnesium Binding Sites List in 5sio
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-(2-Methylpyrrolidine-1-Carbonyl)-N-(2-Phenylimidazo[1,2- A]Pyridin-7-Yl)Pyrazole-3-Carboxamide


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 2- Methyl-4-(2-Methylpyrrolidine-1-Carbonyl)-N-(2-Phenylimidazo[1,2- A]Pyridin-7-Yl)Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:25.6
occ:1.00
 O C:HOH931 2.1 26.7 1.0
OD1 C:ASP564 2.1 27.9 1.0
O C:HOH925 2.1 20.3 1.0
O C:HOH971 2.1 26.6 1.0
O C:HOH974 2.2 27.8 1.0
O C:HOH959 2.2 29.1 1.0
CG C:ASP564 3.1 27.6 1.0
OD2 C:ASP564 3.4 28.9 1.0
ZN C:ZN801 3.8 34.3 1.0
O C:HOH977 4.0 47.9 1.0
NE2 C:HIS595 4.1 31.2 1.0
OE2 C:GLU592 4.1 38.0 1.0
O C:HIS563 4.2 28.5 1.0
CD2 C:HIS567 4.2 31.2 1.0
O C:HOH996 4.3 46.4 1.0
CD2 C:HIS563 4.3 26.2 1.0
O C:HOH985 4.3 39.5 1.0
OG1 C:THR633 4.3 27.2 1.0
NE2 C:HIS567 4.4 32.3 1.0
OD2 C:ASP674 4.4 31.1 1.0
CD2 C:HIS595 4.4 29.2 1.0
CB C:ASP564 4.4 26.1 1.0
O C:THR633 4.6 32.7 1.0
CD2 C:HIS525 4.6 35.5 1.0
NE2 C:HIS525 4.7 32.4 1.0
NE2 C:HIS563 4.7 26.8 1.0
CA C:ASP564 4.8 26.8 1.0
CB C:THR633 4.8 30.6 1.0
CG C:GLU592 4.9 35.3 1.0
CD C:GLU592 5.0 35.9 1.0

Magnesium binding site 4 out of 4 in 5sio

Go back to Magnesium Binding Sites List in 5sio
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-(2-Methylpyrrolidine-1-Carbonyl)-N-(2-Phenylimidazo[1,2- A]Pyridin-7-Yl)Pyrazole-3-Carboxamide


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 2- Methyl-4-(2-Methylpyrrolidine-1-Carbonyl)-N-(2-Phenylimidazo[1,2- A]Pyridin-7-Yl)Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:43.4
occ:1.00
 O D:HOH936 2.0 48.1 1.0
O D:HOH929 2.1 31.2 1.0
O D:HOH951 2.1 36.1 1.0
OD1 D:ASP564 2.1 42.1 1.0
O D:HOH933 2.1 38.2 1.0
O D:HOH909 2.1 37.5 1.0
CG D:ASP564 3.1 42.9 1.0
OD2 D:ASP564 3.5 47.1 1.0
O D:HOH940 3.7 40.4 1.0
ZN D:ZN801 3.8 47.7 1.0
O D:HOH952 4.0 42.0 1.0
NE2 D:HIS595 4.0 48.7 1.0
OE2 D:GLU592 4.1 46.6 1.0
OG1 D:THR633 4.1 42.3 1.0
CD2 D:HIS567 4.1 53.8 1.0
NE2 D:HIS567 4.3 50.1 1.0
CD2 D:HIS595 4.3 49.4 1.0
O D:HIS563 4.4 39.1 1.0
CD2 D:HIS563 4.4 36.1 1.0
CB D:ASP564 4.5 43.7 1.0
OD2 D:ASP674 4.5 48.5 1.0
NE2 D:HIS525 4.6 52.0 1.0
CD2 D:HIS525 4.6 47.6 1.0
CA D:ASP564 4.7 42.5 1.0
CB D:THR633 4.7 44.9 1.0
O D:THR633 4.7 48.0 1.0
NE2 D:HIS563 4.8 35.8 1.0
CD D:GLU592 5.0 51.6 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 19:59:27 2025

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