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Zinc in PDB 5shp: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- H]Quinoline

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- H]Quinoline

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- H]Quinoline:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- H]Quinoline, PDB code: 5shp was solved by C.Joseph, J.Benz, A.Flohr, A.Krasso, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.94 / 2.18
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 136.144, 136.144, 236.749, 90, 90, 120
R / Rfree (%) 18.7 / 23.1

Other elements in 5shp:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- H]Quinoline also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- H]Quinoline (pdb code 5shp). 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 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- H]Quinoline, PDB code: 5shp:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5shp

Go back to Zinc Binding Sites List in 5shp
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- H]Quinoline


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 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- H]Quinoline within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:31.1
occ:1.00
 NE2 A:HIS563 2.1 23.5 1.0
OD2 A:ASP564 2.1 28.9 1.0
O A:HOH954 2.1 24.8 1.0
NE2 A:HIS529 2.2 26.4 1.0
OD1 A:ASP674 2.2 27.8 1.0
O A:HOH1005 2.5 32.9 1.0
CD2 A:HIS563 3.0 24.0 1.0
CG A:ASP674 3.0 27.1 1.0
CE1 A:HIS529 3.1 27.1 1.0
CE1 A:HIS563 3.1 24.5 1.0
CG A:ASP564 3.1 26.2 1.0
CD2 A:HIS529 3.1 27.2 1.0
OD2 A:ASP674 3.2 32.9 1.0
OD1 A:ASP564 3.7 25.5 1.0
MG A:MG802 3.8 25.8 1.0
CG A:HIS563 4.1 25.0 1.0
O A:HOH1022 4.2 22.2 1.0
ND1 A:HIS563 4.2 23.4 1.0
CD2 A:HIS525 4.2 28.8 1.0
ND1 A:HIS529 4.2 26.3 1.0
CG A:HIS529 4.3 27.2 1.0
CB A:ASP564 4.3 26.7 1.0
O A:HOH943 4.4 40.0 1.0
CB A:ASP674 4.4 25.9 1.0
NE2 A:HIS525 4.6 27.7 1.0
O A:HOH938 4.6 20.1 1.0
CG2 A:VAL533 4.7 24.3 1.0
O A:ASP674 4.8 26.0 1.0
CA A:ASP674 4.8 25.4 1.0

Zinc binding site 2 out of 4 in 5shp

Go back to Zinc Binding Sites List in 5shp
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- H]Quinoline


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 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- H]Quinoline within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:29.2
occ:1.00
 NE2 B:HIS563 2.1 22.3 1.0
OD1 B:ASP674 2.1 28.9 1.0
NE2 B:HIS529 2.2 25.3 1.0
OD2 B:ASP564 2.2 26.0 1.0
O B:HOH910 2.2 18.8 1.0
O B:HOH992 2.3 34.7 1.0
CG B:ASP674 3.0 27.8 1.0
CD2 B:HIS563 3.0 23.7 1.0
CD2 B:HIS529 3.1 24.0 1.0
CE1 B:HIS563 3.1 24.3 1.0
CG B:ASP564 3.1 23.7 1.0
OD2 B:ASP674 3.2 28.1 1.0
CE1 B:HIS529 3.2 25.1 1.0
OD1 B:ASP564 3.6 24.9 1.0
MG B:MG802 3.8 18.1 1.0
O B:HOH1009 4.1 21.7 1.0
CD2 B:HIS525 4.1 28.2 1.0
CG B:HIS563 4.2 23.2 1.0
O B:HOH982 4.2 37.3 1.0
ND1 B:HIS563 4.2 22.4 1.0
CG B:HIS529 4.3 24.8 1.0
ND1 B:HIS529 4.3 24.6 1.0
CB B:ASP564 4.3 23.8 1.0
CB B:ASP674 4.4 26.5 1.0
O B:HOH925 4.5 20.1 1.0
NE2 B:HIS525 4.5 28.8 1.0
CG2 B:VAL533 4.8 25.5 1.0
CA B:ASP674 4.8 26.7 1.0
O B:ASP674 4.9 22.9 1.0

Zinc binding site 3 out of 4 in 5shp

Go back to Zinc Binding Sites List in 5shp
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- H]Quinoline


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 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- H]Quinoline within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:31.9
occ:1.00
 NE2 C:HIS563 2.1 25.7 1.0
O C:HOH976 2.1 24.2 1.0
OD1 C:ASP674 2.2 28.3 1.0
OD2 C:ASP564 2.2 24.0 1.0
NE2 C:HIS529 2.2 25.6 1.0
O C:HOH1010 2.4 36.1 1.0
CD2 C:HIS563 3.0 25.5 1.0
CG C:ASP674 3.1 27.9 1.0
CD2 C:HIS529 3.1 25.3 1.0
CG C:ASP564 3.1 24.5 1.0
CE1 C:HIS563 3.2 25.4 1.0
CE1 C:HIS529 3.2 26.8 1.0
OD2 C:ASP674 3.3 30.3 1.0
OD1 C:ASP564 3.6 23.9 1.0
MG C:MG802 3.9 27.0 1.0
CD2 C:HIS525 4.1 32.4 1.0
O C:HOH1023 4.2 26.6 1.0
CG C:HIS563 4.2 25.4 1.0
ND1 C:HIS563 4.2 24.1 1.0
CG C:HIS529 4.3 28.0 1.0
ND1 C:HIS529 4.3 26.4 1.0
CB C:ASP564 4.4 23.8 1.0
NE2 C:HIS525 4.5 31.7 1.0
CB C:ASP674 4.5 28.4 1.0
O C:HOH937 4.5 28.4 1.0
O C:HOH1045 4.6 53.1 1.0
O C:HOH1026 4.7 48.7 1.0
CG2 C:VAL533 4.8 25.3 1.0
CA C:ASP674 4.9 26.7 1.0

Zinc binding site 4 out of 4 in 5shp

Go back to Zinc Binding Sites List in 5shp
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- H]Quinoline


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 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- H]Quinoline within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:39.3
occ:1.00
 O D:HOH929 2.1 26.1 1.0
NE2 D:HIS563 2.1 29.4 1.0
NE2 D:HIS529 2.1 35.4 1.0
OD1 D:ASP674 2.2 37.8 1.0
OD2 D:ASP564 2.2 39.8 1.0
O D:HOH938 2.3 39.6 1.0
CD2 D:HIS563 3.0 30.3 1.0
CG D:ASP674 3.1 37.0 1.0
CD2 D:HIS529 3.1 36.6 1.0
CE1 D:HIS529 3.1 35.9 1.0
CG D:ASP564 3.2 33.9 1.0
CE1 D:HIS563 3.2 30.7 1.0
OD2 D:ASP674 3.3 37.1 1.0
OD1 D:ASP564 3.7 32.5 1.0
MG D:MG802 3.9 35.7 1.0
O D:HOH969 4.0 37.0 1.0
O D:HOH947 4.1 50.7 1.0
CD2 D:HIS525 4.2 35.5 1.0
CG D:HIS563 4.2 28.6 1.0
ND1 D:HIS529 4.2 33.9 1.0
ND1 D:HIS563 4.3 28.0 1.0
CG D:HIS529 4.3 35.2 1.0
CB D:ASP564 4.4 34.6 1.0
CB D:ASP674 4.5 37.9 1.0
O D:HOH925 4.5 32.7 1.0
NE2 D:HIS525 4.6 36.5 1.0
CG2 D:VAL533 4.7 38.4 1.0
O D:ASP674 4.7 45.2 1.0
CA D:ASP674 4.8 37.6 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: Fri Apr 7 22:27:48 2023

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