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Magnesium in PDB 5sgi: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-(3- Methylphenoxy)-2-(4-Pyridin-2-Ylpiperazin-1-Yl)-9H-Purine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-(3- Methylphenoxy)-2-(4-Pyridin-2-Ylpiperazin-1-Yl)-9H-Purine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-(3- Methylphenoxy)-2-(4-Pyridin-2-Ylpiperazin-1-Yl)-9H-Purine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-(3- Methylphenoxy)-2-(4-Pyridin-2-Ylpiperazin-1-Yl)-9H-Purine, PDB code: 5sgi was solved by C.Joseph, J.Benz, A.Flohr, M.Brunner, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.63 / 1.97
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.86, 135.86, 235.3, 90, 90, 120
R / Rfree (%) 18.2 / 23.5

Other elements in 5sgi:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-(3- Methylphenoxy)-2-(4-Pyridin-2-Ylpiperazin-1-Yl)-9H-Purine 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-(3- Methylphenoxy)-2-(4-Pyridin-2-Ylpiperazin-1-Yl)-9H-Purine (pdb code 5sgi). 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-(3- Methylphenoxy)-2-(4-Pyridin-2-Ylpiperazin-1-Yl)-9H-Purine, PDB code: 5sgi:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sgi

Go back to Magnesium Binding Sites List in 5sgi
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-(3- Methylphenoxy)-2-(4-Pyridin-2-Ylpiperazin-1-Yl)-9H-Purine


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-(3- Methylphenoxy)-2-(4-Pyridin-2-Ylpiperazin-1-Yl)-9H-Purine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:32.8
occ:1.00
 OD1 A:ASP564 2.0 20.5 1.0
CG A:ASP564 2.9 23.9 1.0
OD2 A:ASP564 3.2 24.4 1.0
ZN A:ZN801 3.8 27.3 1.0
OE2 A:GLU592 4.0 24.8 1.0
O A:HOH1004 4.1 22.0 1.0
NE2 A:HIS595 4.1 22.3 1.0
O A:HOH1053 4.3 46.9 1.0
OG1 A:THR633 4.3 22.2 1.0
CD2 A:HIS567 4.3 20.5 1.0
CB A:ASP564 4.3 21.6 1.0
O A:HIS563 4.4 20.2 1.0
CD2 A:HIS563 4.4 21.3 1.0
CD2 A:HIS595 4.4 19.6 1.0
NE2 A:HIS567 4.6 20.9 1.0
CD2 A:HIS525 4.6 25.2 1.0
OD2 A:ASP674 4.6 28.7 1.0
NE2 A:HIS525 4.6 24.2 1.0
CB A:THR633 4.7 23.8 1.0
O A:THR633 4.7 30.5 1.0
NE2 A:HIS563 4.7 23.1 1.0
CA A:ASP564 4.8 23.2 1.0
CD A:GLU592 4.9 28.6 1.0
CG A:GLU592 5.0 24.6 1.0

Magnesium binding site 2 out of 4 in 5sgi

Go back to Magnesium Binding Sites List in 5sgi
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-(3- Methylphenoxy)-2-(4-Pyridin-2-Ylpiperazin-1-Yl)-9H-Purine


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-(3- Methylphenoxy)-2-(4-Pyridin-2-Ylpiperazin-1-Yl)-9H-Purine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:26.9
occ:1.00
 OD1 B:ASP564 2.2 19.8 1.0
CG B:ASP564 3.1 19.6 1.0
OD2 B:ASP564 3.3 18.7 1.0
ZN B:ZN801 3.6 26.8 1.0
OE2 B:GLU592 4.1 26.4 1.0
NE2 B:HIS595 4.2 17.8 1.0
CD2 B:HIS563 4.2 18.7 1.0
O B:HOH948 4.3 19.2 1.0
OG1 B:THR633 4.3 19.1 1.0
CD2 B:HIS567 4.3 20.0 1.0
O B:HIS563 4.4 20.8 1.0
CD2 B:HIS595 4.4 17.2 1.0
OD2 B:ASP674 4.4 19.6 1.0
NE2 B:HIS563 4.5 19.1 1.0
NE2 B:HIS567 4.5 18.2 1.0
CB B:ASP564 4.5 17.5 1.0
CD2 B:HIS525 4.6 20.3 1.0
O B:THR633 4.6 19.2 1.0
NE2 B:HIS525 4.6 23.8 1.0
CB B:THR633 4.7 20.1 1.0
CG B:GLU592 4.7 24.6 1.0
CA B:ASP564 4.8 18.6 1.0
CD B:GLU592 4.9 23.3 1.0

Magnesium binding site 3 out of 4 in 5sgi

Go back to Magnesium Binding Sites List in 5sgi
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-(3- Methylphenoxy)-2-(4-Pyridin-2-Ylpiperazin-1-Yl)-9H-Purine


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-(3- Methylphenoxy)-2-(4-Pyridin-2-Ylpiperazin-1-Yl)-9H-Purine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:34.8
occ:1.00
 OD1 C:ASP564 2.1 19.8 1.0
CG C:ASP564 3.1 20.2 1.0
OD2 C:ASP564 3.5 18.8 1.0
ZN C:ZN801 3.8 29.2 1.0
OE2 C:GLU592 4.0 21.3 1.0
NE2 C:HIS595 4.1 22.8 1.0
OG1 C:THR633 4.3 22.9 1.0
CD2 C:HIS563 4.3 19.5 1.0
CD2 C:HIS567 4.3 21.0 1.0
CD2 C:HIS595 4.3 21.2 1.0
O C:HIS563 4.3 20.8 1.0
O C:HOH1004 4.4 24.3 1.0
OD2 C:ASP674 4.4 29.6 1.0
O C:THR633 4.5 23.2 1.0
CB C:ASP564 4.5 18.4 1.0
O C:HOH1072 4.6 59.3 1.0
NE2 C:HIS567 4.6 20.6 1.0
CD2 C:HIS525 4.7 23.4 1.0
CB C:THR633 4.7 22.0 1.0
NE2 C:HIS563 4.7 25.0 1.0
NE2 C:HIS525 4.7 20.6 1.0
CG C:GLU592 4.8 24.2 1.0
CA C:ASP564 4.8 20.5 1.0
CD C:GLU592 4.8 22.0 1.0

Magnesium binding site 4 out of 4 in 5sgi

Go back to Magnesium Binding Sites List in 5sgi
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-(3- Methylphenoxy)-2-(4-Pyridin-2-Ylpiperazin-1-Yl)-9H-Purine


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-(3- Methylphenoxy)-2-(4-Pyridin-2-Ylpiperazin-1-Yl)-9H-Purine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:46.3
occ:1.00
 OD1 D:ASP564 2.1 27.9 1.0
CG D:ASP564 3.2 27.7 1.0
OD2 D:ASP564 3.7 26.1 1.0
ZN D:ZN801 3.9 33.7 1.0
NE2 D:HIS595 4.0 29.9 1.0
OE2 D:GLU592 4.0 25.2 1.0
O D:HOH998 4.0 30.4 1.0
OG1 D:THR633 4.1 31.4 1.0
CD2 D:HIS595 4.3 26.4 1.0
CD2 D:HIS567 4.3 30.3 1.0
O D:HIS563 4.4 23.9 1.0
CD2 D:HIS563 4.5 22.1 1.0
CB D:ASP564 4.5 27.1 1.0
NE2 D:HIS567 4.6 28.1 1.0
O D:THR633 4.6 29.0 1.0
NE2 D:HIS525 4.7 30.0 1.0
OD2 D:ASP674 4.7 26.9 1.0
CD2 D:HIS525 4.7 26.5 1.0
CB D:THR633 4.8 32.3 1.0
CD D:GLU592 4.8 31.4 1.0
CA D:ASP564 4.8 28.2 1.0
CG D:GLU592 4.8 32.8 1.0
NE2 D:HIS563 5.0 21.5 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 19:39:02 2025

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