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Magnesium in PDB 5sjo: Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,4-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- (2,4-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- (2,4-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- (2,4-Difluorophenyl)Pyrazol-3-Yl]-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One, PDB code: 5sjo 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 / 2.10
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.15, 135.15, 234.92, 90, 90, 120
R / Rfree (%) 19.3 / 23.7

Other elements in 5sjo:

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

Fluorine (F) 20 atoms
Chlorine (Cl) 1 atom
Zinc (Zn) 4 atoms
Praseodymium (Pr) 8 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 4 in 5sjo

Go back to Magnesium Binding Sites List in 5sjo
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,4-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- (2,4-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:23.5
occ:1.00
 O A:HOH983 1.8 24.9 1.0
OD1 A:ASP564 1.9 25.1 1.0
O A:HOH919 2.0 24.6 1.0
O A:HOH963 2.1 20.6 1.0
O A:HOH925 2.1 24.9 1.0
O A:HOH936 2.2 29.5 1.0
CG A:ASP564 3.0 24.8 1.0
OD2 A:ASP564 3.3 29.9 1.0
ZN A:ZN801 3.8 30.8 1.0
NE2 A:HIS595 4.0 28.8 1.0
O A:HOH998 4.0 22.0 1.0
OE2 A:GLU592 4.1 36.3 1.0
CD2 A:HIS567 4.2 29.7 1.0
O A:HOH987 4.2 41.7 1.0
CD2 A:HIS595 4.2 28.2 1.0
OG1 A:THR633 4.2 29.6 1.0
CD2 A:HIS563 4.3 24.6 1.0
O A:HIS563 4.3 26.6 1.0
CB A:ASP564 4.3 23.6 1.0
NE2 A:HIS567 4.4 31.4 1.0
OD2 A:ASP674 4.5 33.8 1.0
O A:THR633 4.5 28.6 1.0
CD2 A:HIS525 4.6 30.0 1.0
NE2 A:HIS563 4.6 24.8 1.0
NE2 A:HIS525 4.6 27.6 1.0
CA A:ASP564 4.7 24.4 1.0
CB A:THR633 4.8 28.2 1.0
CG A:GLU592 4.8 29.2 1.0
CD A:GLU592 4.9 31.9 1.0

Magnesium binding site 2 out of 4 in 5sjo

Go back to Magnesium Binding Sites List in 5sjo
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,4-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- (2,4-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:22.0
occ:1.00
 O B:HOH937 2.0 25.6 1.0
OD1 B:ASP564 2.0 25.3 1.0
O B:HOH932 2.1 24.2 1.0
O B:HOH981 2.1 18.6 1.0
O B:HOH924 2.1 15.7 1.0
O B:HOH947 2.2 22.2 1.0
CG B:ASP564 3.1 24.9 1.0
OD2 B:ASP564 3.5 23.9 1.0
ZN B:ZN801 3.8 29.8 1.0
OE2 B:GLU592 4.0 28.0 1.0
O B:HOH995 4.0 31.4 1.0
O B:HOH1023 4.1 51.9 1.0
NE2 B:HIS595 4.1 25.4 1.0
CD2 B:HIS563 4.2 21.5 1.0
OG1 B:THR633 4.2 28.4 1.0
O B:HOH992 4.3 27.4 1.0
CD2 B:HIS595 4.3 25.1 1.0
CD2 B:HIS567 4.3 26.7 1.0
OD2 B:ASP674 4.3 30.0 1.0
O B:HIS563 4.4 25.9 1.0
CB B:ASP564 4.4 23.8 1.0
NE2 B:HIS567 4.5 27.5 1.0
O B:THR633 4.5 27.6 1.0
NE2 B:HIS563 4.5 22.1 1.0
NE2 B:HIS525 4.6 30.2 1.0
CD2 B:HIS525 4.6 28.3 1.0
CB B:THR633 4.7 28.1 1.0
CG B:GLU592 4.8 28.2 1.0
CA B:ASP564 4.8 24.5 1.0
CD B:GLU592 4.8 28.8 1.0

Magnesium binding site 3 out of 4 in 5sjo

Go back to Magnesium Binding Sites List in 5sjo
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,4-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- (2,4-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:23.5
occ:1.00
 OD1 C:ASP564 2.1 25.4 1.0
O C:HOH986 2.1 28.1 1.0
O C:HOH918 2.1 24.6 1.0
O C:HOH943 2.1 27.3 1.0
O C:HOH945 2.1 25.3 1.0
O C:HOH1019 2.1 24.1 1.0
CG C:ASP564 3.1 25.0 1.0
OD2 C:ASP564 3.5 23.7 1.0
ZN C:ZN801 3.8 32.3 1.0
OE2 C:GLU592 4.0 34.6 1.0
O C:HOH999 4.1 36.0 1.0
NE2 C:HIS595 4.1 27.6 1.0
CD2 C:HIS563 4.1 24.1 1.0
OD2 C:ASP674 4.3 30.1 1.0
OG1 C:THR633 4.3 26.1 1.0
CD2 C:HIS567 4.3 28.5 1.0
O C:HIS563 4.3 26.2 1.0
O C:HOH983 4.3 37.6 1.0
NE2 C:HIS567 4.4 30.1 1.0
O C:THR633 4.4 30.4 1.0
CD2 C:HIS595 4.4 29.6 1.0
CB C:ASP564 4.5 23.0 1.0
NE2 C:HIS563 4.5 26.1 1.0
CB C:THR633 4.6 28.1 1.0
CG C:GLU592 4.7 31.2 1.0
CD C:GLU592 4.8 33.9 1.0
CA C:ASP564 4.8 24.6 1.0
CD2 C:HIS525 4.8 31.8 1.0
NE2 C:HIS525 4.8 31.4 1.0

Magnesium binding site 4 out of 4 in 5sjo

Go back to Magnesium Binding Sites List in 5sjo
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,4-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- (2,4-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:28.2
occ:1.00
 O D:HOH914 2.0 28.5 1.0
O D:HOH981 2.1 42.1 1.0
O D:HOH969 2.1 24.4 1.0
OD1 D:ASP564 2.1 28.9 1.0
O D:HOH911 2.1 29.1 1.0
O D:HOH929 2.2 20.9 1.0
CG D:ASP564 3.1 30.0 1.0
OD2 D:ASP564 3.5 33.7 1.0
ZN D:ZN801 3.9 37.5 1.0
O D:HOH974 3.9 34.5 1.0
OE2 D:GLU592 3.9 35.4 1.0
NE2 D:HIS595 4.0 36.9 1.0
O D:HOH980 4.1 28.8 1.0
CD2 D:HIS567 4.1 40.6 1.0
OG1 D:THR633 4.3 33.9 1.0
NE2 D:HIS567 4.3 40.3 1.0
CD2 D:HIS595 4.4 35.9 1.0
O D:HIS563 4.4 28.2 1.0
CB D:ASP564 4.5 30.6 1.0
CD2 D:HIS563 4.5 27.7 1.0
O D:THR633 4.5 34.6 1.0
OD2 D:ASP674 4.6 32.7 1.0
CD2 D:HIS525 4.7 37.9 1.0
NE2 D:HIS525 4.8 38.6 1.0
CD D:GLU592 4.8 36.3 1.0
CA D:ASP564 4.8 29.9 1.0
CG D:GLU592 4.8 37.2 1.0
NE2 D:HIS563 4.8 28.3 1.0
CB D:THR633 4.8 35.7 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 04:24:16 2024

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