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Magnesium 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
Zinc (Zn) 4 atoms
Chlorine (Cl) 1 atom
Fluorine (F) 16 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 4 in 5sje

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

b:20.1
occ:1.00
 O A:HOH1017 1.9 23.5 1.0
O A:HOH915 2.0 17.3 1.0
OD1 A:ASP564 2.1 22.6 1.0
O A:HOH956 2.1 24.9 1.0
O A:HOH905 2.1 26.0 1.0
O A:HOH976 2.2 22.1 1.0
CG A:ASP564 3.1 22.7 1.0
OD2 A:ASP564 3.4 22.2 1.0
ZN A:ZN801 3.9 28.1 1.0
O A:HOH1004 4.0 23.1 1.0
OE2 A:GLU592 4.1 26.7 1.0
NE2 A:HIS595 4.1 24.6 1.0
O A:HOH990 4.2 35.1 1.0
CD2 A:HIS567 4.2 29.8 1.0
OG1 A:THR633 4.3 26.9 1.0
CD2 A:HIS595 4.3 24.5 1.0
CD2 A:HIS563 4.3 24.1 1.0
NE2 A:HIS567 4.4 30.1 1.0
OD2 A:ASP674 4.4 34.2 1.0
CB A:ASP564 4.4 21.9 1.0
O A:HIS563 4.5 23.1 1.0
O A:THR633 4.5 27.0 1.0
NE2 A:HIS563 4.6 24.6 1.0
NE2 A:HIS525 4.7 24.9 1.0
CD2 A:HIS525 4.7 25.9 1.0
CG A:GLU592 4.7 25.6 1.0
CB A:THR633 4.7 25.0 1.0
CD A:GLU592 4.8 26.1 1.0
CA A:ASP564 4.8 22.8 1.0
F25 A:K1I804 5.0 38.7 0.5
F25 A:K1I804 5.0 39.3 0.5

Magnesium binding site 2 out of 4 in 5sje

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

b:17.4
occ:1.00
 O B:HOH951 1.9 20.5 1.0
O B:HOH921 2.0 15.8 1.0
O B:HOH923 2.1 17.6 1.0
O B:HOH991 2.1 15.5 1.0
OD1 B:ASP564 2.1 20.3 1.0
O B:HOH990 2.1 18.9 1.0
CG B:ASP564 3.2 20.9 1.0
OD2 B:ASP564 3.6 19.3 1.0
ZN B:ZN801 3.9 24.7 1.0
NE2 B:HIS595 4.1 26.4 1.0
OE2 B:GLU592 4.1 23.9 1.0
O B:HOH1002 4.1 23.4 1.0
O B:HIS563 4.2 22.3 1.0
OG1 B:THR633 4.2 22.0 1.0
CD2 B:HIS563 4.2 18.7 1.0
CD2 B:HIS595 4.2 26.9 1.0
CD2 B:HIS567 4.3 21.9 1.0
O B:HOH1013 4.4 27.0 1.0
OD2 B:ASP674 4.4 22.7 1.0
NE2 B:HIS567 4.5 20.6 1.0
CB B:ASP564 4.5 20.5 1.0
O B:THR633 4.6 22.4 1.0
NE2 B:HIS563 4.6 18.6 1.0
CB B:THR633 4.7 22.0 1.0
NE2 B:HIS525 4.7 23.4 1.0
CG B:GLU592 4.7 23.9 1.0
CD2 B:HIS525 4.7 21.4 1.0
CA B:ASP564 4.8 21.2 1.0
CD B:GLU592 4.8 24.3 1.0
F25 B:K1I809 5.0 42.7 0.5

Magnesium binding site 3 out of 4 in 5sje

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

b:20.2
occ:1.00
 OD1 C:ASP564 2.0 21.8 1.0
O C:HOH1008 2.0 20.6 1.0
O C:HOH952 2.1 20.1 1.0
O C:HOH1023 2.1 23.1 1.0
O C:HOH914 2.2 20.4 1.0
O C:HOH939 2.2 19.2 1.0
CG C:ASP564 3.0 21.9 1.0
OD2 C:ASP564 3.4 20.9 1.0
ZN C:ZN801 3.8 27.4 1.0
NE2 C:HIS595 4.1 27.0 1.0
OE2 C:GLU592 4.1 27.8 1.0
CD2 C:HIS567 4.1 25.0 1.0
O C:HOH1005 4.1 22.6 1.0
O C:HOH994 4.2 27.1 1.0
O C:HIS563 4.3 24.1 1.0
OG1 C:THR633 4.3 22.9 1.0
NE2 C:HIS567 4.3 26.4 1.0
OD2 C:ASP674 4.3 29.0 1.0
CD2 C:HIS595 4.3 25.6 1.0
CB C:ASP564 4.3 20.9 1.0
CD2 C:HIS563 4.3 22.4 1.0
O C:THR633 4.5 26.8 1.0
CA C:ASP564 4.7 22.8 1.0
CB C:THR633 4.7 23.5 1.0
NE2 C:HIS525 4.7 25.2 1.0
CD2 C:HIS525 4.8 23.9 1.0
CG C:GLU592 4.8 25.6 1.0
NE2 C:HIS563 4.8 24.1 1.0
CD C:GLU592 4.9 27.8 1.0
F25 C:K1I806 5.0 42.8 0.5
F25 C:K1I806 5.0 41.8 0.5

Magnesium binding site 4 out of 4 in 5sje

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

b:29.2
occ:1.00
 O D:HOH971 2.0 24.1 1.0
O D:HOH947 2.0 24.4 1.0
O D:HOH991 2.0 31.0 1.0
O D:HOH935 2.1 28.0 1.0
OD1 D:ASP564 2.1 28.0 1.0
O D:HOH921 2.2 23.2 1.0
CG D:ASP564 3.2 27.4 1.0
OD2 D:ASP564 3.6 29.0 1.0
NE2 D:HIS595 3.9 31.4 1.0
ZN D:ZN801 4.0 31.9 1.0
OE2 D:GLU592 4.0 33.5 1.0
O D:HOH973 4.0 36.9 1.0
O D:HOH985 4.1 23.2 1.0
CD2 D:HIS567 4.2 32.3 1.0
CD2 D:HIS595 4.3 29.3 1.0
OG1 D:THR633 4.3 25.4 1.0
O D:HIS563 4.3 25.2 1.0
O D:THR633 4.4 31.4 1.0
CD2 D:HIS563 4.4 25.1 1.0
NE2 D:HIS567 4.5 32.0 1.0
OD2 D:ASP674 4.5 31.7 1.0
CB D:ASP564 4.5 26.8 1.0
NE2 D:HIS525 4.7 34.6 1.0
CB D:THR633 4.7 27.0 1.0
CG D:GLU592 4.7 32.3 1.0
CD2 D:HIS525 4.7 32.5 1.0
CA D:ASP564 4.8 26.8 1.0
CD D:GLU592 4.8 32.4 1.0
NE2 D:HIS563 4.9 23.9 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 Sep 30 04:21:22 2024

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