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Zinc 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:

Magnesium (Mg) 4 atoms
Fluorine (F) 12 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 4 in 5sk4

Go back to Zinc Binding Sites List in 5sk4
Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:30.1
occ:1.00
 NE2 A:HIS529 2.1 26.9 1.0
O A:HOH950 2.1 24.7 1.0
OD2 A:ASP564 2.1 25.3 1.0
NE2 A:HIS563 2.2 24.9 1.0
OD1 A:ASP674 2.2 26.2 1.0
O A:HOH1023 2.3 27.0 1.0
CD2 A:HIS563 3.0 24.4 1.0
CD2 A:HIS529 3.1 26.1 1.0
CG A:ASP674 3.1 26.6 1.0
CE1 A:HIS529 3.1 26.1 1.0
CG A:ASP564 3.1 25.0 1.0
CE1 A:HIS563 3.2 25.7 1.0
OD2 A:ASP674 3.4 29.8 1.0
OD1 A:ASP564 3.6 24.6 1.0
MG A:MG802 3.8 23.7 1.0
O A:HOH1032 4.1 25.2 1.0
O A:HOH971 4.2 34.4 1.0
CG A:HIS563 4.2 25.2 1.0
ND1 A:HIS529 4.2 24.7 1.0
CD2 A:HIS525 4.2 26.0 1.0
CG A:HIS529 4.2 25.9 1.0
ND1 A:HIS563 4.3 25.2 1.0
CB A:ASP564 4.3 24.6 1.0
CB A:ASP674 4.5 26.7 1.0
NE2 A:HIS525 4.5 26.2 1.0
O A:HOH934 4.6 22.5 1.0
CG2 A:VAL533 4.7 23.7 1.0
O A:ASP674 4.8 26.2 1.0
CA A:ASP674 4.9 25.6 1.0

Zinc binding site 2 out of 4 in 5sk4

Go back to Zinc Binding Sites List in 5sk4
Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:28.6
occ:1.00
 NE2 B:HIS563 2.1 24.0 1.0
O B:HOH932 2.1 18.9 1.0
OD2 B:ASP564 2.2 24.3 1.0
OD1 B:ASP674 2.2 24.0 1.0
NE2 B:HIS529 2.2 24.6 1.0
O B:HOH1000 2.3 29.3 1.0
CD2 B:HIS563 3.0 23.6 1.0
CG B:ASP674 3.0 25.7 1.0
CG B:ASP564 3.1 24.3 1.0
CD2 B:HIS529 3.1 25.5 1.0
CE1 B:HIS563 3.1 23.8 1.0
CE1 B:HIS529 3.2 26.4 1.0
OD2 B:ASP674 3.3 25.4 1.0
OD1 B:ASP564 3.5 23.4 1.0
MG B:MG802 3.8 21.5 1.0
O B:HOH1009 3.9 24.6 1.0
O B:HOH983 4.1 34.4 1.0
CD2 B:HIS525 4.2 26.7 1.0
CG B:HIS563 4.2 23.6 1.0
ND1 B:HIS563 4.2 23.8 1.0
CG B:HIS529 4.3 24.7 1.0
ND1 B:HIS529 4.3 24.5 1.0
CB B:ASP564 4.3 24.3 1.0
NE2 B:HIS525 4.4 26.8 1.0
CB B:ASP674 4.4 23.7 1.0
O B:HOH943 4.6 22.9 1.0
CG2 B:VAL533 4.8 24.3 1.0
CA B:ASP674 4.9 23.9 1.0
O B:ASP674 4.9 24.7 1.0

Zinc binding site 3 out of 4 in 5sk4

Go back to Zinc Binding Sites List in 5sk4
Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:31.4
occ:1.00
 NE2 C:HIS529 2.1 27.8 1.0
O C:HOH930 2.1 21.6 1.0
O C:HOH997 2.1 33.2 1.0
OD2 C:ASP564 2.1 25.6 1.0
NE2 C:HIS563 2.2 26.7 1.0
OD1 C:ASP674 2.2 28.6 1.0
CD2 C:HIS563 3.0 26.1 1.0
CE1 C:HIS529 3.1 30.2 1.0
CG C:ASP564 3.1 25.6 1.0
CD2 C:HIS529 3.1 29.0 1.0
CG C:ASP674 3.1 30.0 1.0
CE1 C:HIS563 3.3 25.7 1.0
OD2 C:ASP674 3.4 32.6 1.0
OD1 C:ASP564 3.6 26.1 1.0
MG C:MG802 3.8 27.7 1.0
CD2 C:HIS525 4.1 30.2 1.0
O C:HOH1026 4.2 26.0 1.0
O C:HOH956 4.2 37.1 1.0
ND1 C:HIS529 4.2 27.3 1.0
CG C:HIS529 4.2 28.6 1.0
CG C:HIS563 4.2 24.2 1.0
ND1 C:HIS563 4.3 24.4 1.0
CB C:ASP564 4.3 24.1 1.0
CB C:ASP674 4.5 28.7 1.0
NE2 C:HIS525 4.5 32.2 1.0
O C:HOH934 4.6 28.4 1.0
CG2 C:VAL533 4.8 27.1 1.0
O C:ASP674 4.8 27.9 1.0
CA C:ASP674 4.8 29.2 1.0

Zinc binding site 4 out of 4 in 5sk4

Go back to Zinc Binding Sites List in 5sk4
Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:38.5
occ:1.00
 O D:HOH911 2.1 29.5 1.0
NE2 D:HIS563 2.2 28.5 1.0
NE2 D:HIS529 2.2 37.7 1.0
O D:HOH985 2.2 32.0 1.0
OD2 D:ASP564 2.2 37.1 1.0
OD1 D:ASP674 2.3 30.7 1.0
CD2 D:HIS563 3.0 30.8 1.0
CG D:ASP674 3.1 34.3 1.0
CG D:ASP564 3.1 34.4 1.0
CD2 D:HIS529 3.2 37.2 1.0
CE1 D:HIS529 3.2 38.6 1.0
CE1 D:HIS563 3.2 29.0 1.0
OD2 D:ASP674 3.3 35.7 1.0
OD1 D:ASP564 3.5 33.4 1.0
MG D:MG802 3.8 33.4 1.0
O D:HOH979 4.0 34.7 1.0
O D:HOH940 4.1 43.2 1.0
CG D:HIS563 4.2 28.7 1.0
CD2 D:HIS525 4.2 40.9 1.0
ND1 D:HIS563 4.3 29.1 1.0
ND1 D:HIS529 4.3 37.0 1.0
CB D:ASP564 4.3 34.3 1.0
CG D:HIS529 4.3 37.4 1.0
CB D:ASP674 4.5 34.9 1.0
NE2 D:HIS525 4.6 43.2 1.0
O D:HOH932 4.6 35.1 1.0
CG2 D:VAL533 4.8 35.5 1.0
O D:ASP674 4.8 37.5 1.0
CA D:ASP674 4.9 34.5 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 06:12:07 2024

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