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Magnesium 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:

Zinc (Zn) 4 atoms
Chlorine (Cl) 1 atom
Praseodymium (Pr) 8 atoms
Fluorine (F) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sif

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg802

b:22.9
occ:1.00
 O A:HOH977 2.0 18.4 1.0
O A:HOH992 2.0 17.2 1.0
OD1 A:ASP564 2.0 25.0 1.0
O A:HOH915 2.1 23.6 1.0
O A:HOH968 2.1 21.1 1.0
O A:HOH917 2.2 27.0 1.0
CG A:ASP564 3.1 24.8 1.0
OD2 A:ASP564 3.5 24.6 1.0
OE2 A:GLU592 3.8 31.9 1.0
ZN A:ZN801 4.0 29.8 1.0
NE2 A:HIS595 4.0 25.1 1.0
O A:HOH988 4.0 37.0 1.0
O A:HIS563 4.2 23.2 1.0
CD2 A:HIS595 4.2 26.8 1.0
OG1 A:THR633 4.2 29.8 1.0
O A:HOH957 4.2 24.1 1.0
CD2 A:HIS567 4.3 32.2 1.0
CD2 A:HIS563 4.3 25.0 1.0
CB A:ASP564 4.4 24.9 1.0
O A:THR633 4.4 26.3 1.0
OD2 A:ASP674 4.5 32.2 1.0
NE2 A:HIS567 4.6 31.8 1.0
CG A:GLU592 4.6 27.3 1.0
CD A:GLU592 4.6 30.3 1.0
CB A:THR633 4.7 27.3 1.0
CA A:ASP564 4.7 25.0 1.0
NE2 A:HIS525 4.8 26.5 1.0
NE2 A:HIS563 4.8 24.7 1.0
CD2 A:HIS525 4.8 27.3 1.0
O A:HOH996 5.0 30.2 1.0
C A:HIS563 5.0 23.7 1.0

Magnesium binding site 2 out of 4 in 5sif

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Magnesium 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 Magnesium with other atoms in the Mg 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:Mg802

b:23.6
occ:1.00
 O B:HOH926 2.0 21.7 1.0
O B:HOH964 2.0 13.8 1.0
O B:HOH937 2.0 17.3 1.0
OD1 B:ASP564 2.1 22.9 1.0
O B:HOH990 2.1 24.4 1.0
O B:HOH911 2.1 19.8 1.0
CG B:ASP564 3.1 23.5 1.0
OD2 B:ASP564 3.5 23.5 1.0
ZN B:ZN801 3.9 30.0 1.0
NE2 B:HIS595 3.9 25.7 1.0
OE2 B:GLU592 4.0 26.4 1.0
O B:HOH986 4.0 31.8 1.0
OG1 B:THR633 4.1 28.3 1.0
CD2 B:HIS563 4.2 22.2 1.0
O B:HOH1028 4.2 40.2 1.0
O B:HIS563 4.2 27.9 1.0
CD2 B:HIS595 4.2 25.9 1.0
CD2 B:HIS567 4.2 25.1 1.0
O B:HOH984 4.3 28.6 1.0
NE2 B:HIS567 4.4 27.0 1.0
OD2 B:ASP674 4.4 26.2 1.0
CB B:ASP564 4.4 24.0 1.0
O B:THR633 4.4 27.0 1.0
NE2 B:HIS563 4.5 22.1 1.0
CD2 B:HIS525 4.6 26.4 1.0
NE2 B:HIS525 4.6 25.4 1.0
CB B:THR633 4.7 30.2 1.0
CA B:ASP564 4.8 25.9 1.0
CD B:GLU592 4.8 26.7 1.0
CG B:GLU592 4.8 26.3 1.0
O B:HOH1006 5.0 36.0 1.0

Magnesium binding site 3 out of 4 in 5sif

Go back to Magnesium Binding Sites List in 5sif
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg802

b:24.5
occ:1.00
 O C:HOH965 2.0 28.5 1.0
O C:HOH932 2.0 26.1 1.0
O C:HOH977 2.1 25.5 1.0
O C:HOH979 2.1 24.2 1.0
OD1 C:ASP564 2.1 28.9 1.0
O C:HOH924 2.2 23.7 1.0
CG C:ASP564 3.1 27.8 1.0
OD2 C:ASP564 3.5 26.0 1.0
O C:HOH963 3.8 22.4 1.0
ZN C:ZN801 3.9 31.9 1.0
NE2 C:HIS595 4.0 26.6 1.0
CD2 C:HIS567 4.0 30.1 1.0
NE2 C:HIS567 4.2 28.8 1.0
OE2 C:GLU592 4.2 31.8 1.0
O C:HOH998 4.3 37.5 1.0
CD2 C:HIS563 4.4 25.4 1.0
O C:HIS563 4.4 26.1 1.0
CD2 C:HIS595 4.4 25.9 1.0
OD2 C:ASP674 4.4 33.6 1.0
CB C:ASP564 4.5 26.3 1.0
CD2 C:HIS525 4.5 34.2 1.0
OG1 C:THR633 4.5 27.3 1.0
NE2 C:HIS525 4.6 35.6 1.0
F30 C:JOO806 4.6 56.8 1.0
O C:THR633 4.7 26.1 1.0
NE2 C:HIS563 4.7 25.3 1.0
CA C:ASP564 4.8 26.2 1.0
CB C:THR633 4.9 28.9 1.0

Magnesium binding site 4 out of 4 in 5sif

Go back to Magnesium Binding Sites List in 5sif
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg802

b:33.0
occ:1.00
 O D:HOH989 2.0 26.9 1.0
O D:HOH943 2.0 25.0 1.0
O D:HOH935 2.1 28.6 1.0
O D:HOH973 2.1 31.5 1.0
OD1 D:ASP564 2.2 31.2 1.0
O D:HOH929 2.2 27.0 1.0
CG D:ASP564 3.2 30.3 1.0
OD2 D:ASP564 3.5 35.1 1.0
OE2 D:GLU592 3.8 33.7 1.0
O D:HOH952 3.8 34.9 1.0
ZN D:ZN801 4.0 35.4 1.0
NE2 D:HIS595 4.1 39.1 1.0
O D:HOH975 4.1 33.8 1.0
CD2 D:HIS567 4.2 35.5 1.0
NE2 D:HIS567 4.2 34.9 1.0
CD2 D:HIS595 4.3 37.2 1.0
OG1 D:THR633 4.4 30.4 1.0
O D:HIS563 4.4 28.7 1.0
CB D:ASP564 4.5 29.8 1.0
O D:THR633 4.5 36.0 1.0
CD2 D:HIS563 4.5 29.5 1.0
OD2 D:ASP674 4.5 31.6 1.0
NE2 D:HIS525 4.6 36.6 1.0
CD2 D:HIS525 4.7 36.9 1.0
CD D:GLU592 4.8 33.8 1.0
CB D:THR633 4.8 31.5 1.0
CA D:ASP564 4.8 30.9 1.0
O D:HOH993 4.8 30.4 1.0
CG D:GLU592 4.9 33.7 1.0
NE2 D:HIS563 5.0 26.8 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 19:56:56 2025

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