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Magnesium in PDB 5skf: Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile, PDB code: 5skf 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) 39.07 / 2.10
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.05, 135.05, 234.4, 90, 90, 120
R / Rfree (%) 17.1 / 18.7

Other elements in 5skf:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Zinc (Zn) 4 atoms
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-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile (pdb code 5skf). 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-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile, PDB code: 5skf:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5skf

Go back to Magnesium Binding Sites List in 5skf
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile


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-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:22.3
occ:1.00
 O A:HOH921 1.9 21.8 1.0
O A:HOH992 2.0 24.7 1.0
O A:HOH1001 2.0 25.9 1.0
OD1 A:ASP564 2.0 26.1 1.0
O A:HOH938 2.1 30.5 1.0
O A:HOH962 2.2 30.5 1.0
CG A:ASP564 3.0 25.5 1.0
OD2 A:ASP564 3.4 25.7 1.0
ZN A:ZN801 3.8 28.9 1.0
OE2 A:GLU592 4.1 30.5 1.0
NE2 A:HIS595 4.1 26.2 1.0
O A:HIS563 4.2 27.4 1.0
O A:HOH1002 4.2 23.4 1.0
CD2 A:HIS567 4.3 32.7 1.0
CD2 A:HIS563 4.3 27.2 1.0
CD2 A:HIS595 4.3 26.9 1.0
OG1 A:THR633 4.3 28.3 1.0
CB A:ASP564 4.4 24.8 1.0
N18 A:KF9805 4.5 30.9 1.0
NE2 A:HIS567 4.5 31.5 1.0
O A:HOH982 4.5 36.9 1.0
OD2 A:ASP674 4.5 29.4 1.0
CD2 A:HIS525 4.6 27.2 1.0
O A:THR633 4.6 30.6 1.0
NE2 A:HIS563 4.7 26.2 1.0
NE2 A:HIS525 4.7 26.4 1.0
CA A:ASP564 4.7 25.5 1.0
CB A:THR633 4.8 26.2 1.0
CG A:GLU592 4.9 26.7 1.0
CD A:GLU592 4.9 28.0 1.0

Magnesium binding site 2 out of 4 in 5skf

Go back to Magnesium Binding Sites List in 5skf
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile


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-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:22.0
occ:1.00
 O B:HOH947 1.9 30.4 1.0
O B:HOH926 2.0 19.9 1.0
O B:HOH980 2.0 17.5 1.0
OD1 B:ASP564 2.1 26.2 1.0
O B:HOH927 2.1 18.3 1.0
O B:HOH996 2.2 17.2 1.0
CG B:ASP564 3.2 24.3 1.0
OD2 B:ASP564 3.7 22.8 1.0
OE2 B:GLU592 3.8 27.8 1.0
ZN B:ZN801 4.0 27.2 1.0
NE2 B:HIS595 4.0 28.1 1.0
O B:HOH1002 4.1 28.1 1.0
O B:HIS563 4.2 25.7 1.0
CD2 B:HIS595 4.2 27.2 1.0
OG1 B:THR633 4.2 24.3 1.0
O B:HOH1015 4.3 33.9 1.0
CD2 B:HIS563 4.3 22.7 1.0
CD2 B:HIS567 4.3 23.3 1.0
NE2 B:HIS567 4.4 22.9 1.0
CB B:ASP564 4.5 23.2 1.0
OD2 B:ASP674 4.5 23.8 1.0
O B:THR633 4.5 27.7 1.0
N18 B:KF9808 4.5 30.4 1.0
CB B:THR633 4.7 25.7 1.0
CD B:GLU592 4.7 29.2 1.0
CG B:GLU592 4.7 28.3 1.0
NE2 B:HIS563 4.7 23.1 1.0
CA B:ASP564 4.7 24.6 1.0
NE2 B:HIS525 4.8 24.1 1.0
CD2 B:HIS525 4.8 24.0 1.0

Magnesium binding site 3 out of 4 in 5skf

Go back to Magnesium Binding Sites List in 5skf
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile


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-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:24.1
occ:1.00
 O C:HOH941 2.0 27.3 1.0
O C:HOH933 2.0 25.3 1.0
O C:HOH1014 2.0 26.9 1.0
O C:HOH960 2.0 23.0 1.0
OD1 C:ASP564 2.0 25.9 1.0
O C:HOH982 2.1 23.2 1.0
CG C:ASP564 3.2 24.8 1.0
OD2 C:ASP564 3.6 24.6 1.0
ZN C:ZN801 3.9 29.7 1.0
NE2 C:HIS595 4.0 28.6 1.0
CD2 C:HIS567 4.0 28.0 1.0
O C:HOH994 4.1 28.1 1.0
OE2 C:GLU592 4.1 31.1 1.0
O C:HIS563 4.2 25.4 1.0
O C:HOH999 4.2 37.5 1.0
CD2 C:HIS563 4.2 22.7 1.0
CD2 C:HIS595 4.3 27.1 1.0
NE2 C:HIS567 4.3 30.1 1.0
OG1 C:THR633 4.3 26.5 1.0
OD2 C:ASP674 4.4 31.2 1.0
N18 C:KF9806 4.4 32.8 1.0
CB C:ASP564 4.4 23.5 1.0
O C:THR633 4.5 31.3 1.0
NE2 C:HIS563 4.6 22.6 1.0
CD2 C:HIS525 4.7 28.0 1.0
CA C:ASP564 4.7 24.0 1.0
NE2 C:HIS525 4.8 28.6 1.0
CB C:THR633 4.8 28.1 1.0
CD C:GLU592 5.0 30.7 1.0
C C:HIS563 5.0 23.9 1.0

Magnesium binding site 4 out of 4 in 5skf

Go back to Magnesium Binding Sites List in 5skf
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile


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-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:29.9
occ:1.00
 O D:HOH937 2.1 29.7 1.0
O D:HOH911 2.2 31.4 1.0
O D:HOH971 2.2 27.8 1.0
OD1 D:ASP564 2.2 28.6 1.0
O D:HOH904 2.3 31.2 1.0
O D:HOH924 2.3 26.3 1.0
CG D:ASP564 3.2 27.7 1.0
OD2 D:ASP564 3.5 30.0 1.0
O D:HOH985 3.9 35.8 1.0
OE2 D:GLU592 3.9 37.4 1.0
ZN D:ZN801 3.9 33.8 1.0
NE2 D:HIS595 4.1 31.8 1.0
O D:HOH982 4.1 30.8 1.0
CD2 D:HIS567 4.2 35.0 1.0
N18 D:KF9803 4.3 37.9 1.0
NE2 D:HIS567 4.4 33.9 1.0
CD2 D:HIS595 4.4 31.8 1.0
O D:HIS563 4.5 29.4 1.0
OD2 D:ASP674 4.5 25.8 1.0
OG1 D:THR633 4.5 34.0 1.0
CD2 D:HIS525 4.5 37.0 1.0
O D:THR633 4.5 36.1 1.0
CD2 D:HIS563 4.5 27.1 1.0
CB D:ASP564 4.6 28.0 1.0
NE2 D:HIS525 4.6 33.9 1.0
CD D:GLU592 4.8 36.0 1.0
NE2 D:HIS563 4.9 27.1 1.0
C19 D:KF9803 4.9 36.8 1.0
CB D:THR633 4.9 35.8 1.0
CG D:GLU592 4.9 34.6 1.0
CA D:ASP564 4.9 29.2 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 20:16:34 2025

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