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Magnesium in PDB 5skd: Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,5-Difluorophenyl)Pyrazol-3-Yl]-1-[3-(Trifluoromethoxy) Phenyl]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-(Trifluoromethoxy) Phenyl]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-(Trifluoromethoxy) Phenyl]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-(Trifluoromethoxy) Phenyl]Pyridazin-4-One, PDB code: 5skd 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) 43.61 / 2.30
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.64, 135.64, 234.83, 90, 90, 120
R / Rfree (%) 16.3 / 17.8

Other elements in 5skd:

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

Praseodymium (Pr) 8 atoms
Zinc (Zn) 4 atoms
Fluorine (F) 25 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-(Trifluoromethoxy) Phenyl]Pyridazin-4-One (pdb code 5skd). 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-(Trifluoromethoxy) Phenyl]Pyridazin-4-One, PDB code: 5skd:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5skd

Go back to Magnesium Binding Sites List in 5skd
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-(Trifluoromethoxy) Phenyl]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-(Trifluoromethoxy) Phenyl]Pyridazin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:26.1
occ:1.00
 O A:HOH995 1.9 22.2 1.0
O A:HOH923 2.0 25.5 1.0
O A:HOH935 2.0 23.7 1.0
OD1 A:ASP564 2.0 30.6 1.0
O A:HOH926 2.1 29.8 1.0
O A:HOH950 2.2 27.9 1.0
CG A:ASP564 3.1 31.7 1.0
OD2 A:ASP564 3.5 33.6 1.0
OE2 A:GLU592 3.9 32.5 1.0
O A:HOH981 3.9 49.7 1.0
ZN A:ZN801 3.9 32.8 1.0
NE2 A:HIS595 4.1 24.5 1.0
O A:HOH978 4.1 35.4 1.0
CD2 A:HIS567 4.2 35.6 1.0
CD2 A:HIS595 4.4 25.6 1.0
CB A:ASP564 4.4 30.1 1.0
O A:HIS563 4.4 28.1 1.0
CD2 A:HIS563 4.5 28.1 1.0
NE2 A:HIS567 4.5 35.1 1.0
OG1 A:THR633 4.5 33.1 1.0
O A:THR633 4.5 32.0 1.0
OD2 A:ASP674 4.7 28.6 1.0
CD2 A:HIS525 4.7 30.7 1.0
NE2 A:HIS525 4.7 31.0 1.0
CA A:ASP564 4.8 28.9 1.0
CD A:GLU592 4.8 32.2 1.0
NE2 A:HIS563 4.8 27.5 1.0
CG A:GLU592 4.9 27.5 1.0
CB A:THR633 4.9 30.6 1.0
O A:HOH944 4.9 30.7 1.0

Magnesium binding site 2 out of 4 in 5skd

Go back to Magnesium Binding Sites List in 5skd
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-(Trifluoromethoxy) Phenyl]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-(Trifluoromethoxy) Phenyl]Pyridazin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:27.8
occ:1.00
 O B:HOH952 1.9 31.7 1.0
O B:HOH951 1.9 23.2 1.0
O B:HOH917 1.9 24.4 1.0
O B:HOH980 2.1 21.4 1.0
O B:HOH955 2.1 18.9 1.0
OD1 B:ASP564 2.2 27.8 1.0
CG B:ASP564 3.2 28.5 1.0
OD2 B:ASP564 3.6 29.6 1.0
ZN B:ZN801 3.9 30.9 1.0
O B:HOH971 3.9 35.9 1.0
OE2 B:GLU592 3.9 30.2 1.0
NE2 B:HIS595 4.1 31.8 1.0
CD2 B:HIS563 4.2 25.5 1.0
OG1 B:THR633 4.2 27.1 1.0
O B:HOH1000 4.2 36.3 1.0
CD2 B:HIS595 4.4 29.9 1.0
O B:HIS563 4.4 30.4 1.0
CD2 B:HIS567 4.4 30.6 1.0
OD2 B:ASP674 4.4 30.6 1.0
NE2 B:HIS567 4.5 32.0 1.0
CB B:ASP564 4.5 27.5 1.0
O B:THR633 4.6 28.0 1.0
NE2 B:HIS563 4.6 28.0 1.0
CD2 B:HIS525 4.7 24.4 1.0
CD B:GLU592 4.7 31.0 1.0
CB B:THR633 4.8 29.3 1.0
NE2 B:HIS525 4.8 28.1 1.0
CG B:GLU592 4.8 29.2 1.0
CA B:ASP564 4.8 28.3 1.0

Magnesium binding site 3 out of 4 in 5skd

Go back to Magnesium Binding Sites List in 5skd
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-(Trifluoromethoxy) Phenyl]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-(Trifluoromethoxy) Phenyl]Pyridazin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:24.1
occ:1.00
 O C:HOH1009 2.0 24.9 1.0
O C:HOH932 2.0 27.4 1.0
OD1 C:ASP564 2.0 30.3 1.0
O C:HOH955 2.1 27.7 1.0
O C:HOH975 2.2 20.8 1.0
O C:HOH942 2.3 25.9 1.0
CG C:ASP564 3.1 29.9 1.0
OD2 C:ASP564 3.6 28.2 1.0
ZN C:ZN801 4.0 34.4 1.0
OE2 C:GLU592 4.0 33.5 1.0
O C:HOH983 4.1 36.9 1.0
NE2 C:HIS595 4.1 30.5 1.0
CD2 C:HIS567 4.1 31.9 1.0
O C:HIS563 4.2 29.6 1.0
NE2 C:HIS567 4.3 32.5 1.0
CD2 C:HIS595 4.4 28.7 1.0
OG1 C:THR633 4.4 30.8 1.0
CD2 C:HIS563 4.4 28.2 1.0
CB C:ASP564 4.4 27.4 1.0
O C:THR633 4.5 29.9 1.0
O C:HOH1000 4.5 48.4 1.0
OD2 C:ASP674 4.6 29.1 1.0
CB C:THR633 4.7 29.9 1.0
CA C:ASP564 4.7 30.9 1.0
CD2 C:HIS525 4.8 34.2 1.0
NE2 C:HIS525 4.8 34.8 1.0
CD C:GLU592 4.8 32.9 1.0
NE2 C:HIS563 4.8 30.3 1.0
CG C:GLU592 4.8 32.3 1.0
O C:HOH1020 5.0 37.0 1.0

Magnesium binding site 4 out of 4 in 5skd

Go back to Magnesium Binding Sites List in 5skd
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-(Trifluoromethoxy) Phenyl]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-(Trifluoromethoxy) Phenyl]Pyridazin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:32.2
occ:1.00
 O D:HOH917 2.0 30.2 1.0
O D:HOH968 2.0 26.9 1.0
O D:HOH978 2.0 29.8 1.0
O D:HOH935 2.1 34.8 1.0
OD1 D:ASP564 2.1 31.0 1.0
O D:HOH909 2.4 39.2 1.0
CG D:ASP564 3.1 33.6 1.0
OD2 D:ASP564 3.5 35.8 1.0
ZN D:ZN801 3.9 39.3 1.0
NE2 D:HIS595 4.1 35.8 1.0
O D:HOH946 4.1 45.9 1.0
O D:HOH958 4.2 41.9 1.0
OE2 D:GLU592 4.2 39.7 1.0
CD2 D:HIS567 4.3 37.2 1.0
OG1 D:THR633 4.3 37.1 1.0
CD2 D:HIS563 4.3 30.8 1.0
O D:HIS563 4.4 33.5 1.0
CD2 D:HIS595 4.4 32.7 1.0
NE2 D:HIS567 4.4 43.2 1.0
CB D:ASP564 4.5 33.3 1.0
OD2 D:ASP674 4.5 33.9 1.0
O D:THR633 4.6 36.4 1.0
NE2 D:HIS525 4.7 41.1 1.0
CA D:ASP564 4.7 33.3 1.0
CB D:THR633 4.7 39.4 1.0
CD2 D:HIS525 4.8 39.8 1.0
NE2 D:HIS563 4.8 28.9 1.0
CD D:GLU592 5.0 37.9 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: Tue Aug 12 20:15:53 2025

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