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

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,5-Difluorophenyl)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- (2,5-Difluorophenyl)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- (2,5-Difluorophenyl)Pyrazol-3-Yl]-1-(3-Methylsulfonylphenyl) Pyridazin-4-One, PDB code: 5sif was solved by C.Joseph, J.Benz, A.Flohr, M.Rogers-Evans, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.45 / 2.20
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.135, 135.135, 235.085, 90, 90, 120
R / Rfree (%) 18.2 / 23.1

Other elements in 5sif:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,5-Difluorophenyl)Pyrazol-3-Yl]-1-(3-Methylsulfonylphenyl) Pyridazin-4-One also contains other interesting chemical elements:

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

Zinc Binding Sites:

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

Zinc binding site 1 out of 4 in 5sif

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,5-Difluorophenyl)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- (2,5-Difluorophenyl)Pyrazol-3-Yl]-1-(3-Methylsulfonylphenyl) Pyridazin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:29.8
occ:1.00
 OD2 A:ASP564 2.1 24.6 1.0
OD1 A:ASP674 2.1 25.7 1.0
O A:HOH968 2.1 21.1 1.0
NE2 A:HIS563 2.2 24.7 1.0
NE2 A:HIS529 2.2 31.6 1.0
O A:HOH957 2.3 24.1 1.0
CG A:ASP674 3.0 27.5 1.0
CD2 A:HIS563 3.0 25.0 1.0
CG A:ASP564 3.1 24.8 1.0
CD2 A:HIS529 3.1 27.8 1.0
CE1 A:HIS529 3.2 29.5 1.0
CE1 A:HIS563 3.3 26.7 1.0
OD2 A:ASP674 3.3 32.2 1.0
OD1 A:ASP564 3.6 25.0 1.0
MG A:MG802 4.0 22.9 1.0
O A:HOH992 4.0 17.2 1.0
CD2 A:HIS525 4.2 27.3 1.0
CG A:HIS563 4.2 25.0 1.0
CB A:ASP564 4.2 24.9 1.0
O A:HOH963 4.3 25.8 1.0
CG A:HIS529 4.3 28.3 1.0
ND1 A:HIS529 4.3 28.5 1.0
ND1 A:HIS563 4.3 24.9 1.0
NE2 A:HIS525 4.4 26.5 1.0
CB A:ASP674 4.4 26.8 1.0
CG2 A:VAL533 4.7 22.1 1.0
O A:HOH915 4.7 23.6 1.0
CA A:ASP674 4.8 25.6 1.0
O A:ASP674 4.9 25.6 1.0

Zinc binding site 2 out of 4 in 5sif

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Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,5-Difluorophenyl)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- (2,5-Difluorophenyl)Pyrazol-3-Yl]-1-(3-Methylsulfonylphenyl) Pyridazin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:30.0
occ:1.00
 NE2 B:HIS563 2.0 22.1 1.0
O B:HOH937 2.1 17.3 1.0
O B:HOH986 2.1 31.8 1.0
OD2 B:ASP564 2.2 23.5 1.0
OD1 B:ASP674 2.2 26.0 1.0
NE2 B:HIS529 2.2 27.8 1.0
CD2 B:HIS563 3.0 22.2 1.0
CG B:ASP674 3.0 26.3 1.0
CE1 B:HIS563 3.1 23.0 1.0
CG B:ASP564 3.1 23.5 1.0
CD2 B:HIS529 3.2 27.4 1.0
CE1 B:HIS529 3.2 29.6 1.0
OD2 B:ASP674 3.3 26.2 1.0
OD1 B:ASP564 3.5 22.9 1.0
MG B:MG802 3.9 23.6 1.0
O B:HOH990 4.1 24.4 1.0
CG B:HIS563 4.1 22.9 1.0
ND1 B:HIS563 4.1 21.8 1.0
CD2 B:HIS525 4.2 26.4 1.0
O B:HOH955 4.2 28.2 1.0
CB B:ASP564 4.3 24.0 1.0
CG B:HIS529 4.3 28.4 1.0
ND1 B:HIS529 4.3 29.3 1.0
NE2 B:HIS525 4.4 25.4 1.0
CB B:ASP674 4.4 25.7 1.0
O B:HOH926 4.5 21.7 1.0
O B:HOH1028 4.7 40.2 1.0
CG2 B:VAL533 4.7 27.6 1.0
CA B:ASP674 4.8 25.1 1.0
O B:ASP674 4.8 24.2 1.0

Zinc binding site 3 out of 4 in 5sif

Go back to Zinc Binding Sites List in 5sif
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,5-Difluorophenyl)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- (2,5-Difluorophenyl)Pyrazol-3-Yl]-1-(3-Methylsulfonylphenyl) Pyridazin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:31.9
occ:1.00
 O C:HOH963 2.0 22.4 1.0
NE2 C:HIS529 2.1 26.0 1.0
OD2 C:ASP564 2.1 26.0 1.0
OD1 C:ASP674 2.1 28.7 1.0
NE2 C:HIS563 2.1 25.3 1.0
O C:HOH924 2.1 23.7 1.0
CE1 C:HIS529 3.0 28.3 1.0
CD2 C:HIS563 3.0 25.4 1.0
CG C:ASP674 3.1 31.2 1.0
CG C:ASP564 3.1 27.8 1.0
CD2 C:HIS529 3.1 28.3 1.0
CE1 C:HIS563 3.2 24.0 1.0
OD2 C:ASP674 3.4 33.6 1.0
OD1 C:ASP564 3.6 28.9 1.0
MG C:MG802 3.9 24.5 1.0
O C:HOH979 4.1 24.2 1.0
ND1 C:HIS529 4.2 27.5 1.0
CD2 C:HIS525 4.2 34.2 1.0
CG C:HIS563 4.2 24.5 1.0
O C:HOH974 4.2 30.4 1.0
CG C:HIS529 4.2 29.5 1.0
ND1 C:HIS563 4.2 23.3 1.0
CB C:ASP564 4.3 26.3 1.0
CB C:ASP674 4.4 31.3 1.0
O C:HOH932 4.4 26.1 1.0
NE2 C:HIS525 4.5 35.6 1.0
CG2 C:VAL533 4.8 24.0 1.0
O C:ASP674 4.8 30.6 1.0
CA C:ASP674 4.8 30.3 1.0

Zinc binding site 4 out of 4 in 5sif

Go back to Zinc Binding Sites List in 5sif
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,5-Difluorophenyl)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- (2,5-Difluorophenyl)Pyrazol-3-Yl]-1-(3-Methylsulfonylphenyl) Pyridazin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:35.4
occ:1.00
 NE2 D:HIS529 2.1 32.2 1.0
O D:HOH975 2.1 33.8 1.0
OD2 D:ASP564 2.1 35.1 1.0
OD1 D:ASP674 2.2 33.5 1.0
NE2 D:HIS563 2.3 26.8 1.0
O D:HOH943 2.4 25.0 1.0
CE1 D:HIS529 3.1 32.3 1.0
CD2 D:HIS563 3.1 29.5 1.0
CG D:ASP564 3.1 30.3 1.0
CD2 D:HIS529 3.1 32.0 1.0
CG D:ASP674 3.1 31.7 1.0
CE1 D:HIS563 3.4 28.5 1.0
OD2 D:ASP674 3.4 31.6 1.0
OD1 D:ASP564 3.6 31.2 1.0
MG D:MG802 4.0 33.0 1.0
CB D:ASP564 4.2 29.8 1.0
ND1 D:HIS529 4.2 30.5 1.0
O D:HOH973 4.2 31.5 1.0
CG D:HIS529 4.2 31.7 1.0
CD2 D:HIS525 4.2 36.9 1.0
CG D:HIS563 4.3 29.3 1.0
O D:HOH926 4.3 34.6 1.0
ND1 D:HIS563 4.4 29.3 1.0
NE2 D:HIS525 4.5 36.6 1.0
CB D:ASP674 4.5 32.1 1.0
O D:HOH929 4.6 27.0 1.0
CG2 D:VAL533 4.7 35.9 1.0
O D:ASP674 4.8 31.9 1.0
CA D:ASP674 4.9 32.5 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 05:45:12 2024

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