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Magnesium in PDB 5sk4: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-3-(2-Phenylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-3-(2-Phenylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-3-(2-Phenylpyrazol-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 6- Methyl-3-(2-Phenylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One, PDB code: 5sk4 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) 35.02 / 2.00
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.407, 135.407, 235.581, 90, 90, 120
R / Rfree (%) 18.4 / 22.4

Other elements in 5sk4:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-3-(2-Phenylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Fluorine (F) 12 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-3-(2-Phenylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One (pdb code 5sk4). 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 6- Methyl-3-(2-Phenylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One, PDB code: 5sk4:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sk4

Go back to Magnesium Binding Sites List in 5sk4
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-3-(2-Phenylpyrazol-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 6- Methyl-3-(2-Phenylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:23.7
occ:1.00
 O A:HOH1032 2.0 25.2 1.0
OD1 A:ASP564 2.0 24.6 1.0
O A:HOH934 2.0 22.5 1.0
O A:HOH950 2.1 24.7 1.0
O A:HOH969 2.1 21.2 1.0
O A:HOH939 2.1 23.8 1.0
CG A:ASP564 3.1 25.0 1.0
OD2 A:ASP564 3.5 25.3 1.0
ZN A:ZN801 3.8 30.1 1.0
OE2 A:GLU592 4.0 31.1 1.0
NE2 A:HIS595 4.0 27.1 1.0
O A:HOH1023 4.1 27.0 1.0
OG1 A:THR633 4.2 27.6 1.0
O A:HOH990 4.2 33.7 1.0
CD2 A:HIS567 4.2 29.0 1.0
CD2 A:HIS563 4.3 24.4 1.0
O A:HIS563 4.3 27.6 1.0
CD2 A:HIS595 4.3 27.1 1.0
CB A:ASP564 4.4 24.6 1.0
NE2 A:HIS567 4.4 27.8 1.0
O A:THR633 4.5 28.0 1.0
OD2 A:ASP674 4.5 29.8 1.0
NE2 A:HIS563 4.7 24.9 1.0
CB A:THR633 4.7 26.9 1.0
CD2 A:HIS525 4.7 26.0 1.0
NE2 A:HIS525 4.7 26.2 1.0
CA A:ASP564 4.8 25.3 1.0
CG A:GLU592 4.8 28.2 1.0
CD A:GLU592 4.8 29.5 1.0

Magnesium binding site 2 out of 4 in 5sk4

Go back to Magnesium Binding Sites List in 5sk4
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-3-(2-Phenylpyrazol-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 6- Methyl-3-(2-Phenylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:21.5
occ:1.00
 O B:HOH943 1.9 22.9 1.0
O B:HOH932 2.0 18.9 1.0
OD1 B:ASP564 2.1 23.4 1.0
O B:HOH980 2.1 18.9 1.0
O B:HOH918 2.1 19.7 1.0
O B:HOH1009 2.1 24.6 1.0
CG B:ASP564 3.1 24.3 1.0
OD2 B:ASP564 3.5 24.3 1.0
ZN B:ZN801 3.8 28.6 1.0
NE2 B:HIS595 4.0 26.3 1.0
OE2 B:GLU592 4.1 30.6 1.0
O B:HOH1000 4.1 29.3 1.0
CD2 B:HIS563 4.2 23.6 1.0
CD2 B:HIS595 4.2 25.6 1.0
OG1 B:THR633 4.2 23.7 1.0
O B:HIS563 4.3 26.3 1.0
CD2 B:HIS567 4.3 25.1 1.0
OD2 B:ASP674 4.4 25.4 1.0
NE2 B:HIS567 4.4 25.1 1.0
O B:HOH996 4.4 32.2 1.0
CB B:ASP564 4.4 24.3 1.0
NE2 B:HIS563 4.5 24.0 1.0
O B:THR633 4.5 24.9 1.0
CB B:THR633 4.6 25.0 1.0
CD2 B:HIS525 4.7 26.7 1.0
NE2 B:HIS525 4.7 26.8 1.0
CG B:GLU592 4.8 27.2 1.0
CA B:ASP564 4.8 25.1 1.0
CD B:GLU592 4.8 26.9 1.0

Magnesium binding site 3 out of 4 in 5sk4

Go back to Magnesium Binding Sites List in 5sk4
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-3-(2-Phenylpyrazol-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 6- Methyl-3-(2-Phenylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:27.7
occ:1.00
 O C:HOH982 2.0 26.0 1.0
O C:HOH934 2.0 28.4 1.0
O C:HOH1026 2.1 26.0 1.0
O C:HOH930 2.1 21.6 1.0
OD1 C:ASP564 2.1 26.1 1.0
O C:HOH962 2.1 22.1 1.0
CG C:ASP564 3.1 25.6 1.0
OD2 C:ASP564 3.5 25.6 1.0
ZN C:ZN801 3.8 31.4 1.0
O C:HOH997 4.1 33.2 1.0
NE2 C:HIS595 4.1 28.6 1.0
OE2 C:GLU592 4.1 31.2 1.0
CD2 C:HIS567 4.2 29.0 1.0
OG1 C:THR633 4.3 29.7 1.0
CD2 C:HIS563 4.3 26.1 1.0
OD2 C:ASP674 4.3 32.6 1.0
CD2 C:HIS595 4.4 26.9 1.0
O C:HIS563 4.4 25.3 1.0
NE2 C:HIS567 4.4 28.0 1.0
O C:HOH1000 4.5 36.6 1.0
CB C:ASP564 4.5 24.1 1.0
O C:THR633 4.5 27.9 1.0
NE2 C:HIS563 4.7 26.7 1.0
CD2 C:HIS525 4.7 30.2 1.0
CB C:THR633 4.7 28.8 1.0
NE2 C:HIS525 4.7 32.2 1.0
CG C:GLU592 4.8 28.8 1.0
CA C:ASP564 4.8 24.1 1.0
CD C:GLU592 4.9 29.4 1.0

Magnesium binding site 4 out of 4 in 5sk4

Go back to Magnesium Binding Sites List in 5sk4
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-3-(2-Phenylpyrazol-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 6- Methyl-3-(2-Phenylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:33.4
occ:1.00
 O D:HOH978 2.0 29.3 1.0
O D:HOH932 2.0 35.1 1.0
O D:HOH911 2.1 29.5 1.0
O D:HOH920 2.1 32.9 1.0
O D:HOH979 2.2 34.7 1.0
OD1 D:ASP564 2.2 33.4 1.0
CG D:ASP564 3.2 34.4 1.0
OD2 D:ASP564 3.6 37.1 1.0
ZN D:ZN801 3.8 38.5 1.0
O D:HOH985 3.9 32.0 1.0
OE2 D:GLU592 4.0 36.7 1.0
O D:HOH989 4.1 39.2 1.0
OG1 D:THR633 4.2 36.2 1.0
NE2 D:HIS595 4.2 36.4 1.0
CD2 D:HIS567 4.3 43.7 1.0
CD2 D:HIS563 4.3 30.8 1.0
OD2 D:ASP674 4.3 35.7 1.0
NE2 D:HIS567 4.4 41.3 1.0
CD2 D:HIS595 4.4 36.1 1.0
O D:HIS563 4.4 34.6 1.0
CB D:ASP564 4.5 34.3 1.0
O D:THR633 4.5 35.5 1.0
CB D:THR633 4.6 36.2 1.0
NE2 D:HIS563 4.7 28.5 1.0
CD2 D:HIS525 4.8 40.9 1.0
NE2 D:HIS525 4.8 43.2 1.0
CA D:ASP564 4.9 33.2 1.0
CD D:GLU592 4.9 37.2 1.0
CG D:GLU592 5.0 36.8 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 04:30:05 2024

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