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Zinc 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
Magnesium (Mg) 4 atoms
Chlorine (Cl) 1 atom
Praseodymium (Pr) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc 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 Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5skh

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Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:28.6
occ:1.00
 OD2 A:ASP564 2.0 25.2 1.0
NE2 A:HIS529 2.1 28.7 1.0
OD1 A:ASP674 2.2 29.0 1.0
NE2 A:HIS563 2.2 23.9 1.0
O A:HOH994 2.2 26.7 1.0
O A:HOH940 2.4 21.9 1.0
CG A:ASP564 3.1 24.9 1.0
CG A:ASP674 3.1 27.6 1.0
CD2 A:HIS529 3.1 28.6 1.0
CE1 A:HIS529 3.1 27.9 1.0
CD2 A:HIS563 3.1 22.8 1.0
CE1 A:HIS563 3.2 24.3 1.0
OD2 A:ASP674 3.3 29.6 1.0
OD1 A:ASP564 3.6 23.9 1.0
MG A:MG802 3.9 20.7 1.0
O A:HOH1006 4.0 21.9 1.0
CD2 A:HIS525 4.1 28.0 1.0
ND1 A:HIS529 4.2 26.3 1.0
CG A:HIS529 4.2 26.3 1.0
O A:HOH979 4.2 28.1 1.0
CG A:HIS563 4.3 24.5 1.0
CB A:ASP564 4.3 23.8 1.0
ND1 A:HIS563 4.3 23.6 1.0
NE2 A:HIS525 4.4 27.7 1.0
CB A:ASP674 4.4 27.9 1.0
O A:HOH929 4.6 23.7 1.0
CG2 A:VAL533 4.7 20.4 1.0
O A:ASP674 4.8 28.1 1.0
CA A:ASP674 4.9 26.2 1.0

Zinc binding site 2 out of 4 in 5skh

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Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:28.3
occ:1.00
 OD2 B:ASP564 2.1 22.6 1.0
NE2 B:HIS563 2.1 21.2 1.0
NE2 B:HIS529 2.1 21.1 1.0
O B:HOH950 2.2 18.7 1.0
OD1 B:ASP674 2.2 25.1 1.0
O B:HOH1002 2.3 26.6 1.0
CD2 B:HIS563 3.0 20.1 1.0
CG B:ASP674 3.1 24.9 1.0
CG B:ASP564 3.1 23.2 1.0
CE1 B:HIS563 3.1 21.6 1.0
CD2 B:HIS529 3.1 23.3 1.0
CE1 B:HIS529 3.2 23.8 1.0
OD2 B:ASP674 3.3 24.6 1.0
OD1 B:ASP564 3.6 23.0 1.0
MG B:MG802 3.9 18.2 1.0
O B:HOH969 4.0 22.7 1.0
CD2 B:HIS525 4.2 23.2 1.0
O B:HOH981 4.2 24.9 1.0
CG B:HIS563 4.2 22.2 1.0
ND1 B:HIS563 4.2 21.1 1.0
ND1 B:HIS529 4.3 22.4 1.0
CB B:ASP564 4.3 23.3 1.0
CG B:HIS529 4.3 22.4 1.0
NE2 B:HIS525 4.4 23.8 1.0
CB B:ASP674 4.4 25.4 1.0
O B:HOH948 4.6 23.3 1.0
CG2 B:VAL533 4.7 21.8 1.0
CA B:ASP674 4.8 25.3 1.0
O B:ASP674 4.8 23.7 1.0

Zinc binding site 3 out of 4 in 5skh

Go back to Zinc Binding Sites List in 5skh
Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:29.8
occ:1.00
 NE2 C:HIS529 2.1 24.1 1.0
O C:HOH922 2.1 24.4 1.0
OD1 C:ASP674 2.1 21.9 1.0
OD2 C:ASP564 2.1 24.4 1.0
NE2 C:HIS563 2.2 25.8 1.0
O C:HOH1008 2.2 29.5 1.0
CE1 C:HIS529 3.0 25.8 1.0
CG C:ASP674 3.0 25.6 1.0
CD2 C:HIS563 3.1 23.9 1.0
CD2 C:HIS529 3.1 24.8 1.0
CG C:ASP564 3.1 22.8 1.0
OD2 C:ASP674 3.2 26.7 1.0
CE1 C:HIS563 3.3 24.6 1.0
OD1 C:ASP564 3.6 22.1 1.0
MG C:MG802 3.9 20.8 1.0
O C:HOH1018 4.0 22.2 1.0
ND1 C:HIS529 4.1 24.7 1.0
CD2 C:HIS525 4.2 29.3 1.0
CG C:HIS529 4.2 24.1 1.0
O C:HOH965 4.2 30.0 1.0
CG C:HIS563 4.3 23.0 1.0
ND1 C:HIS563 4.3 23.1 1.0
CB C:ASP674 4.3 26.4 1.0
CB C:ASP564 4.3 21.7 1.0
NE2 C:HIS525 4.4 29.1 1.0
O C:HOH931 4.6 28.7 1.0
CA C:ASP674 4.7 26.1 1.0
CG2 C:VAL533 4.7 24.2 1.0
O C:ASP674 4.8 27.3 1.0

Zinc binding site 4 out of 4 in 5skh

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Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:35.4
occ:1.00
 OD2 D:ASP564 2.1 33.1 1.0
NE2 D:HIS529 2.1 33.3 1.0
NE2 D:HIS563 2.2 25.7 1.0
OD1 D:ASP674 2.2 34.9 1.0
O D:HOH939 2.2 23.6 1.0
O D:HOH982 2.2 26.7 1.0
CD2 D:HIS563 3.0 27.2 1.0
CG D:ASP674 3.1 33.1 1.0
CD2 D:HIS529 3.1 33.4 1.0
CG D:ASP564 3.1 29.9 1.0
CE1 D:HIS529 3.2 35.3 1.0
CE1 D:HIS563 3.3 28.7 1.0
OD2 D:ASP674 3.3 33.7 1.0
OD1 D:ASP564 3.7 28.4 1.0
MG D:MG802 3.9 30.6 1.0
O D:HOH943 4.1 28.6 1.0
CD2 D:HIS525 4.2 36.2 1.0
CG D:HIS563 4.2 26.9 1.0
O D:HOH976 4.2 31.9 1.0
CB D:ASP564 4.2 30.6 1.0
ND1 D:HIS529 4.2 32.8 1.0
CG D:HIS529 4.2 31.3 1.0
ND1 D:HIS563 4.3 26.8 1.0
CB D:ASP674 4.4 32.4 1.0
NE2 D:HIS525 4.5 39.1 1.0
O D:HOH949 4.5 33.3 1.0
CG2 D:VAL533 4.7 31.9 1.0
O D:ASP674 4.7 32.7 1.0
CA D:ASP674 4.9 31.8 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 Oct 28 07:35:36 2024

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