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

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-(3- Methylphenyl)Sulfanyl-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- Methylphenyl)Sulfanyl-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- Methylphenyl)Sulfanyl-2-(4-Pyridin-2-Ylpiperazin-1-Yl)-9H-Purine, PDB code: 5sih 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) 43.69 / 1.90
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.7, 135.7, 235.82, 90, 90, 120
R / Rfree (%) 19.4 / 24.3

Other elements in 5sih:

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

Magnesium binding site 1 out of 4 in 5sih

Go back to Magnesium Binding Sites List in 5sih
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-(3- Methylphenyl)Sulfanyl-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- Methylphenyl)Sulfanyl-2-(4-Pyridin-2-Ylpiperazin-1-Yl)-9H-Purine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:18.0
occ:1.00
 OD1 A:ASP564 1.9 22.1 1.0
O A:HOH1036 2.0 18.6 1.0
O A:HOH924 2.1 17.2 1.0
O A:HOH931 2.1 13.7 1.0
O A:HOH960 2.1 15.2 1.0
O A:HOH968 2.1 17.6 1.0
CG A:ASP564 2.9 21.9 1.0
OD2 A:ASP564 3.3 18.4 1.0
ZN A:ZN801 3.7 22.9 1.0
O A:HOH998 3.8 26.4 1.0
O A:HOH1006 4.1 21.0 1.0
OE2 A:GLU592 4.1 21.8 1.0
NE2 A:HIS595 4.2 19.5 1.0
O A:HOH1075 4.3 42.0 1.0
O A:HIS563 4.3 20.4 1.0
CD2 A:HIS563 4.3 17.2 1.0
CB A:ASP564 4.3 20.3 1.0
OG1 A:THR633 4.4 18.3 1.0
CD2 A:HIS567 4.4 21.7 1.0
OD2 A:ASP674 4.5 24.2 1.0
CD2 A:HIS595 4.5 16.8 1.0
CD2 A:HIS525 4.5 21.1 1.0
NE2 A:HIS525 4.5 21.2 1.0
O A:THR633 4.6 21.0 1.0
NE2 A:HIS563 4.6 16.9 1.0
CB A:THR633 4.7 18.1 1.0
NE2 A:HIS567 4.7 23.7 1.0
CA A:ASP564 4.8 20.2 1.0
CG A:GLU592 4.8 20.0 1.0
CD A:GLU592 4.9 21.3 1.0

Magnesium binding site 2 out of 4 in 5sih

Go back to Magnesium Binding Sites List in 5sih
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-(3- Methylphenyl)Sulfanyl-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- Methylphenyl)Sulfanyl-2-(4-Pyridin-2-Ylpiperazin-1-Yl)-9H-Purine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:9.6
occ:1.00
 O B:HOH961 2.0 9.3 1.0
O B:HOH954 2.0 11.5 1.0
OD1 B:ASP564 2.1 20.9 1.0
O B:HOH917 2.1 9.3 1.0
O B:HOH1021 2.1 12.9 1.0
O B:HOH1003 2.2 11.9 1.0
CG B:ASP564 3.0 16.0 1.0
OD2 B:ASP564 3.3 14.0 1.0
ZN B:ZN801 3.6 18.8 1.0
O B:HOH1005 3.7 31.4 1.0
NE2 B:HIS595 4.0 15.6 1.0
O B:HOH1098 4.0 45.7 1.0
OE2 B:GLU592 4.1 20.5 1.0
OG1 B:THR633 4.2 17.1 1.0
CD2 B:HIS563 4.2 15.3 1.0
O B:HIS563 4.2 17.0 1.0
CD2 B:HIS595 4.3 17.8 1.0
O B:HOH1008 4.3 18.4 1.0
CB B:ASP564 4.4 13.6 1.0
OD2 B:ASP674 4.4 14.8 1.0
CD2 B:HIS567 4.5 18.2 1.0
O B:THR633 4.5 15.6 1.0
NE2 B:HIS563 4.6 17.8 1.0
CB B:THR633 4.6 16.8 1.0
NE2 B:HIS567 4.6 18.9 1.0
CD2 B:HIS525 4.7 18.9 1.0
NE2 B:HIS525 4.7 23.4 1.0
CA B:ASP564 4.7 13.3 1.0
CG B:GLU592 4.8 19.1 1.0
CD B:GLU592 4.9 19.7 1.0

Magnesium binding site 3 out of 4 in 5sih

Go back to Magnesium Binding Sites List in 5sih
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-(3- Methylphenyl)Sulfanyl-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- Methylphenyl)Sulfanyl-2-(4-Pyridin-2-Ylpiperazin-1-Yl)-9H-Purine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:14.0
occ:1.00
 OD1 C:ASP564 2.0 16.8 1.0
O C:HOH969 2.1 13.7 1.0
O C:HOH957 2.1 16.0 1.0
O C:HOH1011 2.1 15.1 1.0
O C:HOH916 2.2 16.3 1.0
O C:HOH929 2.3 12.6 1.0
CG C:ASP564 3.0 15.6 1.0
OD2 C:ASP564 3.4 15.7 1.0
ZN C:ZN801 3.8 21.2 1.0
O C:HOH977 3.9 27.8 1.0
NE2 C:HIS595 4.0 19.1 1.0
OE2 C:GLU592 4.0 19.9 1.0
O C:HIS563 4.2 20.6 1.0
CD2 C:HIS567 4.2 18.1 1.0
CD2 C:HIS595 4.3 17.5 1.0
CD2 C:HIS563 4.3 14.7 1.0
CB C:ASP564 4.3 13.7 1.0
OG1 C:THR633 4.3 15.7 1.0
O C:HOH1087 4.4 50.2 1.0
O C:HOH996 4.4 18.9 1.0
OD2 C:ASP674 4.5 23.2 1.0
NE2 C:HIS567 4.5 19.6 1.0
O C:THR633 4.5 18.6 1.0
NE2 C:HIS563 4.7 16.1 1.0
NE2 C:HIS525 4.7 22.0 1.0
CA C:ASP564 4.7 16.9 1.0
CB C:THR633 4.7 17.6 1.0
CD2 C:HIS525 4.7 21.4 1.0
CG C:GLU592 4.8 22.0 1.0
CD C:GLU592 4.8 20.9 1.0
C C:HIS563 5.0 14.3 1.0

Magnesium binding site 4 out of 4 in 5sih

Go back to Magnesium Binding Sites List in 5sih
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-(3- Methylphenyl)Sulfanyl-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- Methylphenyl)Sulfanyl-2-(4-Pyridin-2-Ylpiperazin-1-Yl)-9H-Purine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:22.2
occ:1.00
 OD1 D:ASP564 1.9 21.5 1.0
O D:HOH969 2.0 18.7 1.0
O D:HOH927 2.1 18.3 1.0
O D:HOH968 2.1 18.2 1.0
O D:HOH948 2.2 19.3 1.0
O D:HOH922 2.2 29.6 1.0
CG D:ASP564 3.0 25.9 1.0
OD2 D:ASP564 3.4 21.3 1.0
O D:HOH959 3.7 34.4 1.0
ZN D:ZN801 3.8 26.7 1.0
NE2 D:HIS595 3.9 24.7 1.0
O D:HOH978 4.0 26.7 1.0
OE2 D:GLU592 4.1 26.7 1.0
CD2 D:HIS595 4.2 26.5 1.0
OG1 D:THR633 4.3 24.6 1.0
O D:HIS563 4.3 20.5 1.0
CD2 D:HIS567 4.3 28.2 1.0
CB D:ASP564 4.4 22.4 1.0
O D:THR633 4.4 28.2 1.0
CD2 D:HIS563 4.4 21.1 1.0
NE2 D:HIS525 4.5 28.1 1.0
CD2 D:HIS525 4.6 28.1 1.0
NE2 D:HIS567 4.6 27.2 1.0
OD2 D:ASP674 4.6 25.2 1.0
CA D:ASP564 4.7 23.1 1.0
CB D:THR633 4.8 24.0 1.0
CG D:GLU592 4.8 27.1 1.0
NE2 D:HIS563 4.9 21.1 1.0
CD D:GLU592 4.9 26.9 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: Mon Sep 30 04:11:01 2024

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