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

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (3-Fluorophenyl)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- (3-Fluorophenyl)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- (3-Fluorophenyl)Pyrazol-3-Yl]-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One, PDB code: 5skh 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) 41.38 / 2.10
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.11, 135.11, 234.43, 90, 90, 120
R / Rfree (%) 19.4 / 23.7

Other elements in 5skh:

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

Fluorine (F) 16 atoms
Zinc (Zn) 4 atoms
Chlorine (Cl) 1 atom
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- (3-Fluorophenyl)Pyrazol-3-Yl]-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One (pdb code 5skh). 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- (3-Fluorophenyl)Pyrazol-3-Yl]-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One, PDB code: 5skh:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5skh

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

b:20.7
occ:1.00
 O A:HOH929 1.8 23.7 1.0
OD1 A:ASP564 2.0 23.9 1.0
O A:HOH1006 2.0 21.9 1.0
O A:HOH940 2.0 21.9 1.0
O A:HOH980 2.0 18.2 1.0
O A:HOH943 2.2 23.9 1.0
CG A:ASP564 3.1 24.9 1.0
OD2 A:ASP564 3.5 25.2 1.0
NE2 A:HIS595 3.8 27.2 1.0
OE2 A:GLU592 3.9 29.4 1.0
ZN A:ZN801 3.9 28.6 1.0
CD2 A:HIS595 4.1 27.0 1.0
O A:HOH994 4.2 26.7 1.0
CD2 A:HIS567 4.2 28.9 1.0
O A:HOH997 4.2 35.2 1.0
OG1 A:THR633 4.2 27.5 1.0
O A:HIS563 4.2 25.6 1.0
CD2 A:HIS563 4.3 22.8 1.0
NE2 A:HIS567 4.4 27.6 1.0
CB A:ASP564 4.4 23.8 1.0
O A:THR633 4.4 31.7 1.0
OD2 A:ASP674 4.5 29.6 1.0
NE2 A:HIS563 4.7 23.9 1.0
CD A:GLU592 4.7 29.7 1.0
CG A:GLU592 4.7 28.1 1.0
CA A:ASP564 4.7 24.2 1.0
NE2 A:HIS525 4.8 27.7 1.0
CD2 A:HIS525 4.8 28.0 1.0
CB A:THR633 4.8 27.3 1.0
CE1 A:HIS595 5.0 23.7 1.0

Magnesium binding site 2 out of 4 in 5skh

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

b:18.2
occ:1.00
 O B:HOH948 1.9 23.3 1.0
O B:HOH950 2.0 18.7 1.0
O B:HOH920 2.0 17.9 1.0
O B:HOH988 2.0 14.3 1.0
OD1 B:ASP564 2.1 23.0 1.0
O B:HOH969 2.1 22.7 1.0
CG B:ASP564 3.1 23.2 1.0
OD2 B:ASP564 3.5 22.6 1.0
ZN B:ZN801 3.9 28.3 1.0
OE2 B:GLU592 3.9 30.3 1.0
NE2 B:HIS595 4.1 25.3 1.0
O B:HOH1002 4.1 26.6 1.0
CD2 B:HIS563 4.2 20.1 1.0
OG1 B:THR633 4.3 24.2 1.0
O B:HOH1012 4.3 29.0 1.0
CD2 B:HIS567 4.3 23.5 1.0
O B:HIS563 4.3 27.5 1.0
NE2 B:HIS567 4.3 23.6 1.0
CD2 B:HIS595 4.3 25.9 1.0
OD2 B:ASP674 4.4 24.6 1.0
O B:THR633 4.4 24.4 1.0
CB B:ASP564 4.5 23.3 1.0
NE2 B:HIS563 4.5 21.2 1.0
NE2 B:HIS525 4.6 23.8 1.0
CD2 B:HIS525 4.6 23.2 1.0
CG B:GLU592 4.7 26.8 1.0
CB B:THR633 4.7 24.4 1.0
CD B:GLU592 4.7 28.6 1.0
CA B:ASP564 4.8 24.0 1.0

Magnesium binding site 3 out of 4 in 5skh

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

b:20.8
occ:1.00
 OD1 C:ASP564 2.1 22.1 1.0
O C:HOH931 2.1 28.7 1.0
O C:HOH1018 2.1 22.2 1.0
O C:HOH1007 2.1 22.5 1.0
O C:HOH952 2.1 22.3 1.0
O C:HOH922 2.1 24.4 1.0
CG C:ASP564 3.1 22.8 1.0
OD2 C:ASP564 3.5 24.4 1.0
ZN C:ZN801 3.9 29.8 1.0
OE2 C:GLU592 4.0 32.0 1.0
NE2 C:HIS595 4.0 24.9 1.0
OG1 C:THR633 4.1 22.9 1.0
O C:HOH1008 4.1 29.5 1.0
CD2 C:HIS563 4.2 23.9 1.0
CD2 C:HIS567 4.2 24.7 1.0
O C:HIS563 4.2 22.8 1.0
NE2 C:HIS567 4.3 24.8 1.0
OD2 C:ASP674 4.3 26.7 1.0
O C:HOH977 4.3 34.0 1.0
CD2 C:HIS595 4.4 25.4 1.0
O C:THR633 4.4 29.7 1.0
CB C:ASP564 4.4 21.7 1.0
NE2 C:HIS563 4.6 25.8 1.0
CB C:THR633 4.7 25.8 1.0
NE2 C:HIS525 4.7 29.1 1.0
CD2 C:HIS525 4.7 29.3 1.0
CA C:ASP564 4.7 23.0 1.0
CG C:GLU592 4.7 27.9 1.0
CD C:GLU592 4.8 29.9 1.0
F30 C:KFO806 5.0 46.5 1.0
C C:HIS563 5.0 22.9 1.0

Magnesium binding site 4 out of 4 in 5skh

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

b:30.6
occ:1.00
 O D:HOH962 2.0 23.6 1.0
O D:HOH949 2.1 33.3 1.0
O D:HOH939 2.1 23.6 1.0
O D:HOH976 2.1 31.9 1.0
O D:HOH925 2.1 26.9 1.0
OD1 D:ASP564 2.1 28.4 1.0
CG D:ASP564 3.1 29.9 1.0
OD2 D:ASP564 3.4 33.1 1.0
O D:HOH985 3.9 28.0 1.0
ZN D:ZN801 3.9 35.4 1.0
OE2 D:GLU592 4.0 34.0 1.0
O D:HOH982 4.0 26.7 1.0
NE2 D:HIS595 4.0 34.6 1.0
CD2 D:HIS567 4.2 37.1 1.0
NE2 D:HIS567 4.3 35.5 1.0
CD2 D:HIS595 4.4 34.0 1.0
OG1 D:THR633 4.4 31.5 1.0
CB D:ASP564 4.5 30.6 1.0
CD2 D:HIS563 4.5 27.2 1.0
O D:HIS563 4.5 24.8 1.0
O D:THR633 4.5 35.4 1.0
OD2 D:ASP674 4.5 33.7 1.0
CD2 D:HIS525 4.6 36.2 1.0
NE2 D:HIS525 4.6 39.1 1.0
CG D:GLU592 4.8 34.1 1.0
CD D:GLU592 4.8 33.9 1.0
CA D:ASP564 4.8 29.8 1.0
NE2 D:HIS563 4.9 25.7 1.0
CB D:THR633 4.9 33.5 1.0
O D:HOH994 5.0 39.6 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 04:35:11 2024

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