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Magnesium in PDB 5sjf: Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Quinolin-4-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin-4- One

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Quinolin-4-Ylpyrazol-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- Quinolin-4-Ylpyrazol-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- Quinolin-4-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin-4- One, PDB code: 5sjf 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) 43.95 / 2.05
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 136.77, 136.77, 236.65, 90, 90, 120
R / Rfree (%) 18.8 / 22.7

Other elements in 5sjf:

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

Fluorine (F) 12 atoms
Zinc (Zn) 4 atoms
Chlorine (Cl) 1 atom

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 4 in 5sjf

Go back to Magnesium Binding Sites List in 5sjf
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Quinolin-4-Ylpyrazol-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- Quinolin-4-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin-4- One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:29.8
occ:1.00
 O A:HOH929 1.9 34.1 1.0
OD1 A:ASP564 2.0 31.9 1.0
O A:HOH952 2.0 32.2 1.0
O A:HOH1001 2.1 34.8 1.0
O A:HOH955 2.1 28.9 1.0
O A:HOH967 2.1 32.8 1.0
CG A:ASP564 3.0 33.5 1.0
OD2 A:ASP564 3.3 34.2 1.0
ZN A:ZN801 3.9 36.7 1.0
NE2 A:HIS595 4.0 31.2 1.0
O A:HOH980 4.1 34.4 1.0
OE2 A:GLU592 4.1 35.9 1.0
O A:HOH999 4.2 44.2 1.0
CD2 A:HIS567 4.2 37.2 1.0
O A:HIS563 4.3 32.8 1.0
CD2 A:HIS563 4.3 32.2 1.0
OG1 A:THR633 4.3 36.2 1.0
CB A:ASP564 4.4 33.5 1.0
CD2 A:HIS595 4.4 30.9 1.0
NE2 A:HIS567 4.4 36.4 1.0
OD2 A:ASP674 4.6 35.7 1.0
CD2 A:HIS525 4.6 31.8 1.0
O A:THR633 4.6 33.8 1.0
NE2 A:HIS563 4.7 29.9 1.0
NE2 A:HIS525 4.7 35.6 1.0
CA A:ASP564 4.7 32.5 1.0
CB A:THR633 4.8 34.2 1.0
CG A:GLU592 4.9 36.6 1.0
CE1 A:HIS595 5.0 29.5 1.0
CD A:GLU592 5.0 38.1 1.0

Magnesium binding site 2 out of 4 in 5sjf

Go back to Magnesium Binding Sites List in 5sjf
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Quinolin-4-Ylpyrazol-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- Quinolin-4-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin-4- One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:28.7
occ:1.00
 O B:HOH962 2.0 29.3 1.0
O B:HOH959 2.0 31.0 1.0
OD1 B:ASP564 2.1 30.9 1.0
O B:HOH1008 2.1 31.3 1.0
O B:HOH980 2.2 25.9 1.0
O B:HOH920 2.2 32.8 1.0
CG B:ASP564 3.1 29.8 1.0
OD2 B:ASP564 3.5 32.7 1.0
ZN B:ZN801 3.9 35.0 1.0
NE2 B:HIS595 4.0 32.7 1.0
OE2 B:GLU592 4.1 32.3 1.0
O B:HOH995 4.2 33.0 1.0
CD2 B:HIS567 4.2 33.1 1.0
CD2 B:HIS563 4.2 28.9 1.0
CD2 B:HIS595 4.2 32.9 1.0
OG1 B:THR633 4.3 31.0 1.0
O B:HIS563 4.3 31.0 1.0
O B:HOH1025 4.3 36.0 1.0
NE2 B:HIS567 4.4 32.6 1.0
CB B:ASP564 4.4 30.7 1.0
OD2 B:ASP674 4.5 32.3 1.0
NE2 B:HIS563 4.6 27.7 1.0
O B:THR633 4.6 31.4 1.0
CD2 B:HIS525 4.7 32.6 1.0
CB B:THR633 4.7 30.0 1.0
CA B:ASP564 4.7 29.9 1.0
NE2 B:HIS525 4.8 33.0 1.0
CG B:GLU592 4.8 32.3 1.0
CD B:GLU592 4.9 33.8 1.0
C33 B:K1X804 5.0 46.9 1.0

Magnesium binding site 3 out of 4 in 5sjf

Go back to Magnesium Binding Sites List in 5sjf
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Quinolin-4-Ylpyrazol-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- Quinolin-4-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin-4- One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:30.4
occ:1.00
 O C:HOH940 2.0 31.1 1.0
OD1 C:ASP564 2.1 31.1 1.0
O C:HOH914 2.1 29.6 1.0
O C:HOH995 2.1 30.8 1.0
O C:HOH962 2.1 32.1 1.0
O C:HOH1024 2.2 32.9 1.0
CG C:ASP564 3.1 30.8 1.0
OD2 C:ASP564 3.5 28.6 1.0
ZN C:ZN801 3.9 34.4 1.0
O C:HOH988 4.0 34.5 1.0
NE2 C:HIS595 4.1 31.1 1.0
OE2 C:GLU592 4.1 36.5 1.0
OG1 C:THR633 4.2 32.9 1.0
CD2 C:HIS563 4.2 27.6 1.0
CD2 C:HIS567 4.2 32.8 1.0
CD2 C:HIS595 4.3 31.0 1.0
O C:HIS563 4.3 30.9 1.0
O C:HOH991 4.3 36.5 1.0
OD2 C:ASP674 4.4 33.7 1.0
NE2 C:HIS567 4.4 32.9 1.0
CB C:ASP564 4.4 31.2 1.0
O C:THR633 4.5 32.5 1.0
CB C:THR633 4.7 36.0 1.0
NE2 C:HIS563 4.7 29.0 1.0
CA C:ASP564 4.8 30.8 1.0
NE2 C:HIS525 4.8 34.6 1.0
CD2 C:HIS525 4.8 34.3 1.0
CG C:GLU592 4.9 32.9 1.0
C33 C:K1X803 4.9 44.8 1.0
CD C:GLU592 4.9 36.0 1.0
C29 C:K1X803 5.0 44.5 1.0

Magnesium binding site 4 out of 4 in 5sjf

Go back to Magnesium Binding Sites List in 5sjf
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Quinolin-4-Ylpyrazol-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- Quinolin-4-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin-4- One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:41.2
occ:1.00
 O D:HOH918 2.0 40.6 1.0
OD1 D:ASP564 2.1 39.5 1.0
O D:HOH950 2.1 36.9 1.0
O D:HOH909 2.2 36.3 1.0
O D:HOH942 2.2 40.1 1.0
O D:HOH961 2.2 38.4 1.0
CG D:ASP564 3.1 36.5 1.0
OD2 D:ASP564 3.5 41.2 1.0
OE2 D:GLU592 3.9 42.9 1.0
ZN D:ZN801 4.0 45.5 1.0
NE2 D:HIS595 4.0 42.5 1.0
O D:HOH972 4.1 44.1 1.0
O D:HOH966 4.2 45.4 1.0
OG1 D:THR633 4.2 37.9 1.0
CD2 D:HIS567 4.3 41.0 1.0
CD2 D:HIS595 4.3 42.1 1.0
O D:HIS563 4.3 38.8 1.0
CD2 D:HIS563 4.4 36.6 1.0
O D:THR633 4.4 45.4 1.0
CB D:ASP564 4.5 37.1 1.0
NE2 D:HIS567 4.5 43.2 1.0
OD2 D:ASP674 4.5 37.0 1.0
CB D:THR633 4.6 41.5 1.0
CD2 D:HIS525 4.7 44.5 1.0
CG D:GLU592 4.7 42.5 1.0
CA D:ASP564 4.8 36.5 1.0
CD D:GLU592 4.8 43.3 1.0
NE2 D:HIS525 4.8 48.0 1.0
NE2 D:HIS563 4.8 35.4 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 20:06:17 2025

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