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Magnesium in PDB 5sit: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(4-Methylphenyl)Pyrimidin-4-Amine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(4-Methylphenyl)Pyrimidin-4-Amine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(4-Methylphenyl)Pyrimidin-4-Amine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(4-Methylphenyl)Pyrimidin-4-Amine, PDB code: 5sit was solved by C.Joseph, J.Benz, A.Flohr, M.Beresini, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.05 / 1.99
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.161, 135.161, 234.715, 90, 90, 120
R / Rfree (%) 19.6 / 22.6

Other elements in 5sit:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(4-Methylphenyl)Pyrimidin-4-Amine also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(4-Methylphenyl)Pyrimidin-4-Amine (pdb code 5sit). 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 6- Methyl-N-(4-Methylphenyl)Pyrimidin-4-Amine, PDB code: 5sit:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sit

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(4-Methylphenyl)Pyrimidin-4-Amine


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 6- Methyl-N-(4-Methylphenyl)Pyrimidin-4-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:23.7
occ:1.00
 O A:HOH1001 1.9 23.9 1.0
O A:HOH938 1.9 22.8 1.0
O A:HOH925 2.0 24.6 1.0
OD1 A:ASP564 2.1 23.6 1.0
O A:HOH936 2.1 22.1 1.0
O A:HOH951 2.2 19.9 1.0
CG A:ASP564 3.1 25.3 1.0
OD2 A:ASP564 3.4 26.6 1.0
ZN A:ZN801 3.8 29.5 1.0
NE2 A:HIS595 4.0 25.2 1.0
O A:HOH975 4.0 27.4 1.0
OE2 A:GLU592 4.1 29.1 1.0
O A:HOH965 4.2 33.8 1.0
CD2 A:HIS567 4.2 27.2 1.0
CD2 A:HIS563 4.3 24.0 1.0
OG1 A:THR633 4.3 29.2 1.0
CD2 A:HIS595 4.3 25.6 1.0
O A:HIS563 4.4 24.9 1.0
CB A:ASP564 4.4 24.5 1.0
OD2 A:ASP674 4.4 32.9 1.0
NE2 A:HIS567 4.4 28.2 1.0
O A:THR633 4.5 28.1 1.0
CD2 A:HIS525 4.6 26.9 1.0
NE2 A:HIS563 4.7 24.8 1.0
NE2 A:HIS525 4.7 29.2 1.0
CB A:THR633 4.7 28.3 1.0
CA A:ASP564 4.7 24.0 1.0
CG A:GLU592 4.8 27.1 1.0
CD A:GLU592 4.9 28.3 1.0

Magnesium binding site 2 out of 4 in 5sit

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Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(4-Methylphenyl)Pyrimidin-4-Amine


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 6- Methyl-N-(4-Methylphenyl)Pyrimidin-4-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:22.7
occ:1.00
 O B:HOH943 1.9 23.4 1.0
O B:HOH941 2.0 17.9 1.0
O B:HOH973 2.0 18.6 1.0
OD1 B:ASP564 2.0 24.9 1.0
O B:HOH1010 2.1 21.4 1.0
O B:HOH930 2.1 23.5 1.0
CG B:ASP564 3.1 24.8 1.0
OD2 B:ASP564 3.5 24.1 1.0
ZN B:ZN801 3.8 27.5 1.0
O B:HOH984 4.0 32.9 1.0
NE2 B:HIS595 4.0 25.3 1.0
OE2 B:GLU592 4.1 29.4 1.0
OG1 B:THR633 4.1 24.9 1.0
CD2 B:HIS595 4.2 27.6 1.0
O B:HIS563 4.3 23.7 1.0
CD2 B:HIS563 4.3 23.0 1.0
CD2 B:HIS567 4.3 25.2 1.0
OD2 B:ASP674 4.4 27.4 1.0
O B:HOH978 4.4 33.0 1.0
O B:HOH1021 4.4 56.2 1.0
CB B:ASP564 4.4 24.2 1.0
NE2 B:HIS567 4.4 26.0 1.0
O B:THR633 4.5 27.9 1.0
NE2 B:HIS563 4.6 21.8 1.0
CB B:THR633 4.7 24.7 1.0
CG B:GLU592 4.7 26.2 1.0
CA B:ASP564 4.7 24.3 1.0
CD2 B:HIS525 4.7 25.2 1.0
CD B:GLU592 4.8 26.5 1.0
NE2 B:HIS525 4.9 27.8 1.0

Magnesium binding site 3 out of 4 in 5sit

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Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(4-Methylphenyl)Pyrimidin-4-Amine


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 6- Methyl-N-(4-Methylphenyl)Pyrimidin-4-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:24.8
occ:1.00
 O C:HOH991 2.0 25.4 1.0
O C:HOH1011 2.0 23.3 1.0
O C:HOH947 2.1 26.4 1.0
O C:HOH935 2.1 22.1 1.0
OD1 C:ASP564 2.1 21.6 1.0
O C:HOH946 2.1 20.6 1.0
CG C:ASP564 3.1 22.3 1.0
OD2 C:ASP564 3.5 23.1 1.0
ZN C:ZN801 3.8 28.5 1.0
OE2 C:GLU592 4.1 29.8 1.0
NE2 C:HIS595 4.1 25.4 1.0
O C:HOH995 4.1 31.3 1.0
O C:HOH970 4.1 31.3 1.0
OG1 C:THR633 4.2 25.3 1.0
CD2 C:HIS567 4.2 28.2 1.0
CD2 C:HIS563 4.2 24.3 1.0
OD2 C:ASP674 4.3 31.7 1.0
O C:HIS563 4.3 23.8 1.0
NE2 C:HIS567 4.4 28.0 1.0
CD2 C:HIS595 4.4 23.0 1.0
O C:THR633 4.5 26.5 1.0
CB C:ASP564 4.5 22.6 1.0
NE2 C:HIS563 4.6 28.1 1.0
CB C:THR633 4.7 25.4 1.0
CD2 C:HIS525 4.7 27.1 1.0
CA C:ASP564 4.8 23.5 1.0
CG C:GLU592 4.8 26.2 1.0
NE2 C:HIS525 4.8 27.4 1.0
CD C:GLU592 4.9 28.5 1.0

Magnesium binding site 4 out of 4 in 5sit

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Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(4-Methylphenyl)Pyrimidin-4-Amine


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 6- Methyl-N-(4-Methylphenyl)Pyrimidin-4-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:33.6
occ:1.00
 O D:HOH924 2.0 30.4 1.0
O D:HOH965 2.1 24.8 1.0
O D:HOH975 2.1 32.5 1.0
O D:HOH914 2.1 26.6 1.0
O D:HOH926 2.1 28.6 1.0
OD1 D:ASP564 2.2 32.0 1.0
CG D:ASP564 3.2 31.9 1.0
OD2 D:ASP564 3.5 32.1 1.0
ZN D:ZN801 3.8 36.1 1.0
O D:HOH972 3.9 34.3 1.0
OE2 D:GLU592 4.0 35.5 1.0
O D:HOH958 4.1 46.6 1.0
OG1 D:THR633 4.1 33.3 1.0
NE2 D:HIS595 4.2 33.0 1.0
CD2 D:HIS567 4.3 33.8 1.0
CD2 D:HIS563 4.3 28.4 1.0
CD2 D:HIS595 4.4 31.6 1.0
OD2 D:ASP674 4.4 33.5 1.0
O D:HIS563 4.4 30.0 1.0
O D:THR633 4.5 35.2 1.0
CB D:ASP564 4.5 31.2 1.0
NE2 D:HIS567 4.5 32.3 1.0
NE2 D:HIS563 4.7 26.9 1.0
CB D:THR633 4.7 33.3 1.0
CD2 D:HIS525 4.7 40.4 1.0
NE2 D:HIS525 4.9 42.5 1.0
CA D:ASP564 4.9 30.3 1.0
CD D:GLU592 4.9 36.9 1.0
CG D:GLU592 4.9 36.7 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 20:00:37 2025

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