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Zinc in PDB 5sje: Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,2-Difluoro-1,3-Benzodioxol-4-Yl)Pyrazol-3-Yl]-1-(3- Methylsulfonylphenyl)Pyridazin-4-One

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,2-Difluoro-1,3-Benzodioxol-4-Yl)Pyrazol-3-Yl]-1-(3- Methylsulfonylphenyl)Pyridazin-4-One

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,2-Difluoro-1,3-Benzodioxol-4-Yl)Pyrazol-3-Yl]-1-(3- Methylsulfonylphenyl)Pyridazin-4-One:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,2-Difluoro-1,3-Benzodioxol-4-Yl)Pyrazol-3-Yl]-1-(3- Methylsulfonylphenyl)Pyridazin-4-One, PDB code: 5sje was solved by C.Joseph, J.Benz, A.Flohr, R.M.Rodriguez-Sarmiento, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.52 / 2.10
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.28, 135.28, 235.11, 90, 90, 120
R / Rfree (%) 18.9 / 23.2

Other elements in 5sje:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,2-Difluoro-1,3-Benzodioxol-4-Yl)Pyrazol-3-Yl]-1-(3- Methylsulfonylphenyl)Pyridazin-4-One also contains other interesting chemical elements:

Praseodymium (Pr) 8 atoms
Chlorine (Cl) 1 atom
Magnesium (Mg) 4 atoms
Fluorine (F) 16 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,2-Difluoro-1,3-Benzodioxol-4-Yl)Pyrazol-3-Yl]-1-(3- Methylsulfonylphenyl)Pyridazin-4-One (pdb code 5sje). 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 3-[2- (2,2-Difluoro-1,3-Benzodioxol-4-Yl)Pyrazol-3-Yl]-1-(3- Methylsulfonylphenyl)Pyridazin-4-One, PDB code: 5sje:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sje

Go back to Zinc Binding Sites List in 5sje
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,2-Difluoro-1,3-Benzodioxol-4-Yl)Pyrazol-3-Yl]-1-(3- Methylsulfonylphenyl)Pyridazin-4-One


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 3-[2- (2,2-Difluoro-1,3-Benzodioxol-4-Yl)Pyrazol-3-Yl]-1-(3- Methylsulfonylphenyl)Pyridazin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:28.1
occ:1.00
 NE2 A:HIS563 2.1 24.6 1.0
OD2 A:ASP564 2.1 22.2 1.0
NE2 A:HIS529 2.1 28.4 1.0
OD1 A:ASP674 2.2 27.1 1.0
O A:HOH1004 2.3 23.1 1.0
O A:HOH905 2.4 26.0 1.0
CE1 A:HIS563 3.0 25.2 1.0
CG A:ASP674 3.0 28.4 1.0
CD2 A:HIS529 3.0 24.9 1.0
CD2 A:HIS563 3.1 24.1 1.0
CG A:ASP564 3.1 22.7 1.0
CE1 A:HIS529 3.1 27.2 1.0
OD2 A:ASP674 3.2 34.2 1.0
OD1 A:ASP564 3.6 22.6 1.0
MG A:MG802 3.9 20.1 1.0
O A:HOH1017 4.1 23.5 1.0
ND1 A:HIS563 4.1 22.6 1.0
CG A:HIS563 4.2 23.6 1.0
O A:HOH949 4.2 26.2 1.0
CG A:HIS529 4.2 25.1 1.0
ND1 A:HIS529 4.2 25.8 1.0
CD2 A:HIS525 4.3 25.9 1.0
CB A:ASP564 4.3 21.9 1.0
F25 A:K1I804 4.4 39.3 0.5
CB A:ASP674 4.4 28.1 1.0
F25 A:K1I804 4.5 38.7 0.5
NE2 A:HIS525 4.5 24.9 1.0
O A:HOH915 4.6 17.3 1.0
CG2 A:VAL533 4.8 22.1 1.0
O A:ASP674 4.8 27.6 1.0
CA A:ASP674 4.8 25.4 1.0

Zinc binding site 2 out of 4 in 5sje

Go back to Zinc Binding Sites List in 5sje
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,2-Difluoro-1,3-Benzodioxol-4-Yl)Pyrazol-3-Yl]-1-(3- Methylsulfonylphenyl)Pyridazin-4-One


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 3-[2- (2,2-Difluoro-1,3-Benzodioxol-4-Yl)Pyrazol-3-Yl]-1-(3- Methylsulfonylphenyl)Pyridazin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:24.7
occ:1.00
 OD2 B:ASP564 2.1 19.3 1.0
NE2 B:HIS563 2.2 18.6 1.0
OD1 B:ASP674 2.2 19.8 1.0
O B:HOH923 2.2 17.6 1.0
NE2 B:HIS529 2.2 20.1 1.0
O B:HOH1002 2.2 23.4 1.0
CG B:ASP674 3.0 22.1 1.0
CG B:ASP564 3.1 20.9 1.0
CD2 B:HIS563 3.1 18.7 1.0
CD2 B:HIS529 3.2 22.1 1.0
CE1 B:HIS563 3.2 19.1 1.0
OD2 B:ASP674 3.2 22.7 1.0
CE1 B:HIS529 3.3 21.5 1.0
OD1 B:ASP564 3.5 20.3 1.0
MG B:MG802 3.9 17.4 1.0
O B:HOH990 3.9 18.9 1.0
O B:HOH986 4.1 22.6 1.0
CD2 B:HIS525 4.1 21.4 1.0
CG B:HIS563 4.2 19.5 1.0
ND1 B:HIS563 4.3 19.2 1.0
CB B:ASP564 4.3 20.5 1.0
CG B:HIS529 4.3 20.7 1.0
NE2 B:HIS525 4.4 23.4 1.0
ND1 B:HIS529 4.4 20.6 1.0
CB B:ASP674 4.4 22.6 1.0
F25 B:K1I809 4.5 42.7 0.5
F25 B:K1I809 4.5 43.8 0.5
O B:HOH951 4.6 20.5 1.0
CG2 B:VAL533 4.8 22.1 1.0
CA B:ASP674 4.9 22.7 1.0
O B:ASP674 4.9 21.4 1.0

Zinc binding site 3 out of 4 in 5sje

Go back to Zinc Binding Sites List in 5sje
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,2-Difluoro-1,3-Benzodioxol-4-Yl)Pyrazol-3-Yl]-1-(3- Methylsulfonylphenyl)Pyridazin-4-One


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 3-[2- (2,2-Difluoro-1,3-Benzodioxol-4-Yl)Pyrazol-3-Yl]-1-(3- Methylsulfonylphenyl)Pyridazin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:27.4
occ:1.00
 OD2 C:ASP564 2.1 20.9 1.0
O C:HOH1005 2.1 22.6 1.0
NE2 C:HIS529 2.1 23.0 1.0
O C:HOH914 2.1 20.4 1.0
OD1 C:ASP674 2.1 22.6 1.0
NE2 C:HIS563 2.3 24.1 1.0
CG C:ASP674 3.0 25.6 1.0
CD2 C:HIS563 3.1 22.4 1.0
CG C:ASP564 3.1 21.9 1.0
CE1 C:HIS529 3.1 23.7 1.0
OD2 C:ASP674 3.1 29.0 1.0
CD2 C:HIS529 3.2 23.9 1.0
CE1 C:HIS563 3.4 24.2 1.0
OD1 C:ASP564 3.6 21.8 1.0
MG C:MG802 3.8 20.2 1.0
O C:HOH1023 4.1 23.1 1.0
O C:HOH988 4.1 25.8 1.0
CD2 C:HIS525 4.2 23.9 1.0
ND1 C:HIS529 4.2 22.1 1.0
CG C:HIS563 4.3 22.7 1.0
CB C:ASP564 4.3 20.9 1.0
CG C:HIS529 4.3 22.2 1.0
CB C:ASP674 4.4 25.6 1.0
ND1 C:HIS563 4.4 24.1 1.0
F25 C:K1I806 4.4 42.8 0.5
F25 C:K1I806 4.4 41.8 0.5
NE2 C:HIS525 4.4 25.2 1.0
O C:HOH952 4.7 20.1 1.0
CA C:ASP674 4.8 26.1 1.0
CG2 C:VAL533 4.8 25.0 1.0
O C:ASP674 4.9 25.6 1.0

Zinc binding site 4 out of 4 in 5sje

Go back to Zinc Binding Sites List in 5sje
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,2-Difluoro-1,3-Benzodioxol-4-Yl)Pyrazol-3-Yl]-1-(3- Methylsulfonylphenyl)Pyridazin-4-One


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 3-[2- (2,2-Difluoro-1,3-Benzodioxol-4-Yl)Pyrazol-3-Yl]-1-(3- Methylsulfonylphenyl)Pyridazin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:31.9
occ:1.00
 NE2 D:HIS529 2.2 34.4 1.0
O D:HOH921 2.2 23.2 1.0
OD2 D:ASP564 2.2 29.0 1.0
NE2 D:HIS563 2.2 23.9 1.0
O D:HOH985 2.2 23.2 1.0
OD1 D:ASP674 2.2 27.8 1.0
CD2 D:HIS563 3.0 25.1 1.0
CG D:ASP564 3.1 27.4 1.0
CD2 D:HIS529 3.1 33.6 1.0
CG D:ASP674 3.1 30.5 1.0
CE1 D:HIS529 3.2 34.2 1.0
OD2 D:ASP674 3.3 31.7 1.0
CE1 D:HIS563 3.3 25.6 1.0
OD1 D:ASP564 3.5 28.0 1.0
MG D:MG802 4.0 29.2 1.0
O D:HOH991 4.1 31.0 1.0
O D:HOH933 4.1 31.2 1.0
CD2 D:HIS525 4.2 32.5 1.0
CB D:ASP564 4.2 26.8 1.0
CG D:HIS563 4.2 25.3 1.0
CG D:HIS529 4.3 31.7 1.0
ND1 D:HIS529 4.3 32.7 1.0
ND1 D:HIS563 4.3 25.1 1.0
F25 D:K1I803 4.4 51.4 0.5
NE2 D:HIS525 4.5 34.6 1.0
CB D:ASP674 4.5 30.6 1.0
F25 D:K1I803 4.5 49.5 0.5
O D:HOH935 4.7 28.0 1.0
CG2 D:VAL533 4.7 29.9 1.0
O D:ASP674 4.8 28.2 1.0
CA D:ASP674 4.9 30.1 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 Oct 28 05:58:45 2024

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