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Zinc 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:

Magnesium (Mg) 4 atoms
Chlorine (Cl) 4 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 4 in 5sgb

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Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:33.6
occ:1.00
 NE2 A:HIS529 2.0 31.5 1.0
OD2 A:ASP564 2.1 30.6 1.0
NE2 A:HIS563 2.1 25.0 1.0
OD1 A:ASP674 2.2 40.4 1.0
O A:HOH949 2.2 29.5 1.0
O A:HOH977 2.6 34.0 1.0
CE1 A:HIS529 2.9 28.3 1.0
CD2 A:HIS563 3.0 26.0 1.0
CD2 A:HIS529 3.0 29.4 1.0
CG A:ASP674 3.0 35.6 1.0
CG A:ASP564 3.1 29.1 1.0
CE1 A:HIS563 3.2 26.4 1.0
OD2 A:ASP674 3.2 45.7 1.0
OD1 A:ASP564 3.8 28.5 1.0
MG A:MG802 3.8 28.4 1.0
ND1 A:HIS529 4.1 30.6 1.0
CG A:HIS529 4.1 27.9 1.0
CG A:HIS563 4.2 26.2 1.0
CB A:ASP564 4.2 28.5 1.0
CD2 A:HIS525 4.2 36.2 1.0
ND1 A:HIS563 4.2 24.4 1.0
O A:HOH993 4.2 28.3 1.0
O A:HOH990 4.4 47.5 1.0
CB A:ASP674 4.4 32.9 1.0
NE2 A:HIS525 4.6 33.2 1.0
O A:HOH930 4.7 31.1 1.0
CG2 A:VAL533 4.7 29.1 1.0
O A:ASP674 4.7 34.0 1.0
CA A:ASP674 4.9 31.9 1.0
O A:HOH1007 5.0 53.4 1.0

Zinc binding site 2 out of 4 in 5sgb

Go back to Zinc Binding Sites List in 5sgb
Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:35.1
occ:1.00
 O B:HOH938 2.0 23.5 1.0
NE2 B:HIS563 2.1 28.5 1.0
NE2 B:HIS529 2.1 28.5 1.0
OD2 B:ASP564 2.1 34.0 1.0
OD1 B:ASP674 2.3 31.2 1.0
O B:HOH945 2.6 35.8 1.0
CD2 B:HIS563 3.0 28.2 1.0
CE1 B:HIS529 3.1 30.3 1.0
CG B:ASP564 3.1 28.9 1.0
CG B:ASP674 3.1 30.9 1.0
CD2 B:HIS529 3.1 29.3 1.0
CE1 B:HIS563 3.1 28.8 1.0
OD2 B:ASP674 3.3 35.5 1.0
OD1 B:ASP564 3.5 29.9 1.0
MG B:MG802 3.9 24.9 1.0
O B:HOH987 4.0 23.9 1.0
O B:HOH1018 4.1 36.3 1.0
CG B:HIS563 4.2 27.8 1.0
ND1 B:HIS529 4.2 30.4 1.0
ND1 B:HIS563 4.2 25.9 1.0
CD2 B:HIS525 4.2 33.9 1.0
CG B:HIS529 4.3 28.6 1.0
CB B:ASP564 4.3 28.7 1.0
O B:HOH1005 4.3 60.0 1.0
CB B:ASP674 4.5 29.5 1.0
O B:HOH921 4.6 28.4 1.0
NE2 B:HIS525 4.6 34.2 1.0
CG2 B:VAL533 4.7 26.1 1.0
O B:ASP674 4.8 31.1 1.0
CA B:ASP674 4.9 29.7 1.0

Zinc binding site 3 out of 4 in 5sgb

Go back to Zinc Binding Sites List in 5sgb
Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:36.0
occ:1.00
 O C:HOH950 2.1 24.4 1.0
NE2 C:HIS563 2.1 29.3 1.0
OD1 C:ASP674 2.1 33.2 1.0
OD2 C:ASP564 2.2 32.8 1.0
NE2 C:HIS529 2.2 34.3 1.0
O C:HOH972 2.4 39.6 1.0
CG C:ASP674 3.0 31.5 1.0
CD2 C:HIS563 3.0 26.8 1.0
CD2 C:HIS529 3.1 32.5 1.0
CE1 C:HIS529 3.2 33.8 1.0
CE1 C:HIS563 3.2 29.1 1.0
OD2 C:ASP674 3.2 30.3 1.0
CG C:ASP564 3.2 30.2 1.0
OD1 C:ASP564 3.7 28.6 1.0
MG C:MG802 3.8 27.6 1.0
CD2 C:HIS525 4.1 39.8 1.0
O C:HOH1004 4.1 25.9 1.0
CG C:HIS563 4.2 26.3 1.0
ND1 C:HIS563 4.2 25.5 1.0
CG C:HIS529 4.2 32.6 1.0
ND1 C:HIS529 4.3 33.5 1.0
O C:HOH992 4.3 39.6 1.0
CB C:ASP674 4.4 32.1 1.0
CB C:ASP564 4.4 28.3 1.0
NE2 C:HIS525 4.4 39.4 1.0
O C:HOH909 4.5 28.3 1.0
O C:HOH1016 4.7 50.9 1.0
CA C:ASP674 4.8 31.0 1.0
O C:ASP674 4.8 34.2 1.0
CG2 C:VAL533 4.9 30.3 1.0

Zinc binding site 4 out of 4 in 5sgb

Go back to Zinc Binding Sites List in 5sgb
Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:47.0
occ:1.00
 NE2 D:HIS563 2.0 37.8 1.0
O D:HOH925 2.1 34.0 1.0
OD1 D:ASP674 2.2 49.3 1.0
OD2 D:ASP564 2.2 49.9 1.0
NE2 D:HIS529 2.3 44.8 1.0
O D:HOH935 2.7 39.4 1.0
CD2 D:HIS563 2.9 38.2 1.0
CG D:ASP674 3.0 46.1 1.0
CG D:ASP564 3.1 43.0 1.0
CE1 D:HIS563 3.2 38.8 1.0
CD2 D:HIS529 3.2 47.3 1.0
OD2 D:ASP674 3.2 48.3 1.0
CE1 D:HIS529 3.4 45.3 1.0
OD1 D:ASP564 3.7 42.6 1.0
MG D:MG802 3.8 47.3 1.0
O D:HOH946 4.0 41.0 1.0
CG D:HIS563 4.1 39.3 1.0
CB D:ASP564 4.1 42.0 1.0
ND1 D:HIS563 4.2 41.2 1.0
O D:HOH936 4.2 47.5 1.0
CD2 D:HIS525 4.3 55.7 1.0
O D:HOH909 4.4 38.5 1.0
CG D:HIS529 4.4 42.7 1.0
CB D:ASP674 4.4 48.4 1.0
ND1 D:HIS529 4.5 42.9 1.0
CG2 D:VAL533 4.7 43.3 1.0
O D:ASP674 4.8 49.7 1.0
NE2 D:HIS525 4.8 53.5 1.0
CA D:ASP674 4.9 45.2 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: Thu Aug 21 07:51:20 2025

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