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Magnesium in PDB 5sgb: Crystal Structure of Human Phosphodiesterase 10 in Complex with 5-(4- Chloronaphthalen-1-Yl)Oxythiadiazole

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5-(4- Chloronaphthalen-1-Yl)Oxythiadiazole

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5-(4- Chloronaphthalen-1-Yl)Oxythiadiazole:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5-(4- Chloronaphthalen-1-Yl)Oxythiadiazole, PDB code: 5sgb 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) 43.49 / 2.39
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.099, 135.099, 234.258, 90, 90, 120
R / Rfree (%) 17.9 / 24.2

Other elements in 5sgb:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5-(4- Chloronaphthalen-1-Yl)Oxythiadiazole also contains other interesting chemical elements:

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

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5-(4- Chloronaphthalen-1-Yl)Oxythiadiazole (pdb code 5sgb). 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 5-(4- Chloronaphthalen-1-Yl)Oxythiadiazole, PDB code: 5sgb:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sgb

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5-(4- Chloronaphthalen-1-Yl)Oxythiadiazole


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 5-(4- Chloronaphthalen-1-Yl)Oxythiadiazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:28.4
occ:1.00
 O A:HOH993 1.9 28.3 1.0
O A:HOH949 1.9 29.5 1.0
O A:HOH930 2.0 31.1 1.0
OD1 A:ASP564 2.0 28.5 1.0
O A:HOH925 2.1 28.2 1.0
O A:HOH946 2.1 26.2 1.0
CG A:ASP564 2.9 29.1 1.0
OD2 A:ASP564 3.2 30.6 1.0
ZN A:ZN801 3.8 33.6 1.0
NE2 A:HIS595 4.0 30.8 1.0
OE2 A:GLU592 4.0 38.4 1.0
O A:HOH977 4.1 34.0 1.0
CD2 A:HIS567 4.2 34.9 1.0
O A:HOH951 4.3 31.2 1.0
CD2 A:HIS595 4.3 30.7 1.0
OG1 A:THR633 4.3 32.4 1.0
CB A:ASP564 4.3 28.5 1.0
CD2 A:HIS563 4.3 26.0 1.0
O A:THR633 4.4 34.4 1.0
NE2 A:HIS567 4.5 37.5 1.0
O A:HOH1007 4.5 53.4 1.0
O A:HIS563 4.5 32.7 1.0
OD2 A:ASP674 4.5 45.7 1.0
CD2 A:HIS525 4.6 36.2 1.0
NE2 A:HIS563 4.7 25.0 1.0
CA A:ASP564 4.7 29.6 1.0
NE2 A:HIS525 4.7 33.2 1.0
CB A:THR633 4.8 31.7 1.0
CD A:GLU592 4.9 36.9 1.0
CG A:GLU592 4.9 32.7 1.0

Magnesium binding site 2 out of 4 in 5sgb

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Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5-(4- Chloronaphthalen-1-Yl)Oxythiadiazole


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 5-(4- Chloronaphthalen-1-Yl)Oxythiadiazole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:24.9
occ:1.00
 O B:HOH921 1.8 28.4 1.0
O B:HOH938 2.0 23.5 1.0
O B:HOH987 2.0 23.9 1.0
O B:HOH960 2.0 23.5 1.0
O B:HOH905 2.1 19.4 1.0
OD1 B:ASP564 2.2 29.9 1.0
CG B:ASP564 3.2 28.9 1.0
OD2 B:ASP564 3.6 34.0 1.0
ZN B:ZN801 3.9 35.1 1.0
OE2 B:GLU592 3.9 35.9 1.0
OG1 B:THR633 4.0 28.4 1.0
O B:HOH1005 4.1 60.0 1.0
NE2 B:HIS595 4.1 31.5 1.0
O B:HOH945 4.1 35.8 1.0
CD2 B:HIS563 4.3 28.2 1.0
OD2 B:ASP674 4.3 35.5 1.0
CD2 B:HIS595 4.4 34.8 1.0
CD2 B:HIS567 4.4 31.3 1.0
O B:HIS563 4.4 36.0 1.0
O B:HOH997 4.5 38.3 1.0
NE2 B:HIS567 4.5 32.5 1.0
O B:THR633 4.5 33.3 1.0
CB B:ASP564 4.5 28.7 1.0
NE2 B:HIS563 4.6 28.5 1.0
CD2 B:HIS525 4.7 33.9 1.0
CB B:THR633 4.7 30.2 1.0
CG B:GLU592 4.7 32.3 1.0
CD B:GLU592 4.8 31.4 1.0
NE2 B:HIS525 4.8 34.2 1.0
CA B:ASP564 4.8 30.4 1.0

Magnesium binding site 3 out of 4 in 5sgb

Go back to Magnesium Binding Sites List in 5sgb
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5-(4- Chloronaphthalen-1-Yl)Oxythiadiazole


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 5-(4- Chloronaphthalen-1-Yl)Oxythiadiazole within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:27.6
occ:1.00
 O C:HOH1004 1.9 25.9 1.0
O C:HOH909 1.9 28.3 1.0
O C:HOH950 2.0 24.4 1.0
O C:HOH976 2.0 29.3 1.0
OD1 C:ASP564 2.2 28.6 1.0
O C:HOH936 2.2 19.6 1.0
CG C:ASP564 3.1 30.2 1.0
OD2 C:ASP564 3.4 32.8 1.0
ZN C:ZN801 3.8 36.0 1.0
O C:HOH972 4.0 39.6 1.0
OE2 C:GLU592 4.0 31.1 1.0
NE2 C:HIS595 4.1 30.8 1.0
CD2 C:HIS567 4.2 36.6 1.0
CD2 C:HIS563 4.2 26.8 1.0
OG1 C:THR633 4.3 32.8 1.0
O C:HOH958 4.3 43.8 1.0
OD2 C:ASP674 4.3 30.3 1.0
CD2 C:HIS595 4.4 28.6 1.0
O C:HIS563 4.4 26.2 1.0
NE2 C:HIS567 4.4 36.4 1.0
CB C:ASP564 4.5 28.3 1.0
O C:THR633 4.5 35.5 1.0
NE2 C:HIS563 4.6 29.3 1.0
CB C:THR633 4.7 31.9 1.0
CD2 C:HIS525 4.7 39.8 1.0
NE2 C:HIS525 4.8 39.4 1.0
CG C:GLU592 4.8 30.8 1.0
CD C:GLU592 4.8 34.9 1.0
CA C:ASP564 4.9 28.6 1.0

Magnesium binding site 4 out of 4 in 5sgb

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Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5-(4- Chloronaphthalen-1-Yl)Oxythiadiazole


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 5-(4- Chloronaphthalen-1-Yl)Oxythiadiazole within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:47.3
occ:1.00
 O D:HOH925 1.9 34.0 1.0
O D:HOH916 1.9 45.5 1.0
O D:HOH909 2.0 38.5 1.0
O D:HOH929 2.0 37.2 1.0
O D:HOH946 2.1 41.0 1.0
OD1 D:ASP564 2.3 42.6 1.0
CG D:ASP564 3.2 43.0 1.0
OD2 D:ASP564 3.5 49.9 1.0
ZN D:ZN801 3.8 47.0 1.0
O D:HOH935 3.9 39.4 1.0
OE2 D:GLU592 3.9 47.5 1.0
O D:HOH941 3.9 39.2 1.0
OG1 D:THR633 4.1 38.1 1.0
OD2 D:ASP674 4.2 48.3 1.0
NE2 D:HIS595 4.2 45.4 1.0
O D:THR633 4.3 45.7 1.0
CD2 D:HIS563 4.3 38.2 1.0
CD2 D:HIS567 4.4 44.5 1.0
O D:HIS563 4.4 42.9 1.0
CD2 D:HIS595 4.4 46.2 1.0
NE2 D:HIS567 4.5 47.4 1.0
CB D:ASP564 4.6 42.0 1.0
CB D:THR633 4.7 38.8 1.0
NE2 D:HIS563 4.7 37.8 1.0
O D:HOH953 4.8 44.5 1.0
CA D:ASP564 4.9 40.5 1.0
CD D:GLU592 4.9 50.7 1.0
CD2 D:HIS525 4.9 55.7 1.0
NE2 D:HIS525 5.0 53.5 1.0
CG D:GLU592 5.0 49.3 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 19:37:32 2025

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