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Zinc in PDB 5skn: Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[3- [3-[2-(2-Fluorophenyl)Pyrazol-3-Yl]-4-Oxopyridazin-1- Yl]Phenyl]Acetamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[3- [3-[2-(2-Fluorophenyl)Pyrazol-3-Yl]-4-Oxopyridazin-1- Yl]Phenyl]Acetamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[3- [3-[2-(2-Fluorophenyl)Pyrazol-3-Yl]-4-Oxopyridazin-1- Yl]Phenyl]Acetamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[3- [3-[2-(2-Fluorophenyl)Pyrazol-3-Yl]-4-Oxopyridazin-1- Yl]Phenyl]Acetamide, PDB code: 5skn was solved by C.Joseph, J.Benz, A.Flohr, M.Koerner, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.03 / 1.90
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.48, 135.48, 235.361, 90, 90, 120
R / Rfree (%) 19.1 / 22.2

Other elements in 5skn:

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

Chlorine (Cl) 2 atoms
Fluorine (F) 6 atoms
Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[3- [3-[2-(2-Fluorophenyl)Pyrazol-3-Yl]-4-Oxopyridazin-1- Yl]Phenyl]Acetamide (pdb code 5skn). 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 N-[3- [3-[2-(2-Fluorophenyl)Pyrazol-3-Yl]-4-Oxopyridazin-1- Yl]Phenyl]Acetamide, PDB code: 5skn:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5skn

Go back to Zinc Binding Sites List in 5skn
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[3- [3-[2-(2-Fluorophenyl)Pyrazol-3-Yl]-4-Oxopyridazin-1- Yl]Phenyl]Acetamide


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 N-[3- [3-[2-(2-Fluorophenyl)Pyrazol-3-Yl]-4-Oxopyridazin-1- Yl]Phenyl]Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:25.4
occ:1.00
 OD2 A:ASP564 2.1 21.3 1.0
OD1 A:ASP674 2.1 21.6 1.0
O A:HOH936 2.2 21.9 1.0
NE2 A:HIS529 2.2 20.7 1.0
NE2 A:HIS563 2.2 21.1 1.0
O A:HOH1010 2.3 26.0 1.0
CD2 A:HIS563 3.0 20.8 1.0
CG A:ASP674 3.0 22.3 1.0
CG A:ASP564 3.1 21.1 1.0
CD2 A:HIS529 3.1 21.0 1.0
CE1 A:HIS529 3.2 21.2 1.0
CE1 A:HIS563 3.3 20.9 1.0
OD2 A:ASP674 3.3 26.9 1.0
OD1 A:ASP564 3.5 20.6 1.0
MG A:MG802 3.8 20.0 1.0
O A:HOH1028 4.0 22.2 1.0
CD2 A:HIS525 4.2 23.8 1.0
CG A:HIS563 4.2 21.2 1.0
O A:HOH985 4.3 22.8 1.0
CG A:HIS529 4.3 20.6 1.0
CB A:ASP564 4.3 20.8 1.0
ND1 A:HIS529 4.3 20.6 1.0
ND1 A:HIS563 4.3 20.8 1.0
O A:HOH1027 4.4 41.5 1.0
NE2 A:HIS525 4.4 23.3 1.0
CB A:ASP674 4.4 22.8 1.0
O A:HOH946 4.6 19.4 1.0
CG2 A:VAL533 4.8 20.8 1.0
O A:ASP674 4.8 22.8 1.0
CA A:ASP674 4.8 22.3 1.0

Zinc binding site 2 out of 4 in 5skn

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Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[3- [3-[2-(2-Fluorophenyl)Pyrazol-3-Yl]-4-Oxopyridazin-1- Yl]Phenyl]Acetamide


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 N-[3- [3-[2-(2-Fluorophenyl)Pyrazol-3-Yl]-4-Oxopyridazin-1- Yl]Phenyl]Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:24.6
occ:1.00
 NE2 B:HIS563 2.1 20.0 1.0
O B:HOH920 2.1 17.9 1.0
OD1 B:ASP674 2.1 18.9 1.0
OD2 B:ASP564 2.2 17.7 1.0
NE2 B:HIS529 2.2 20.4 1.0
O B:HOH1004 2.3 26.0 1.0
CG B:ASP674 3.0 21.4 1.0
CD2 B:HIS563 3.1 20.5 1.0
CE1 B:HIS563 3.1 20.2 1.0
CD2 B:HIS529 3.1 22.3 1.0
CG B:ASP564 3.1 18.6 1.0
CE1 B:HIS529 3.3 22.4 1.0
OD2 B:ASP674 3.3 23.1 1.0
OD1 B:ASP564 3.6 19.1 1.0
MG B:MG802 3.8 17.0 1.0
O B:HOH1027 4.0 19.7 1.0
CD2 B:HIS525 4.2 23.9 1.0
ND1 B:HIS563 4.2 19.6 1.0
CG B:HIS563 4.2 20.8 1.0
O B:HOH976 4.2 23.4 1.0
CG B:HIS529 4.3 21.6 1.0
CB B:ASP564 4.3 18.6 1.0
ND1 B:HIS529 4.3 21.3 1.0
CB B:ASP674 4.4 21.1 1.0
O B:HOH1039 4.4 33.4 1.0
NE2 B:HIS525 4.4 24.8 1.0
O B:HOH959 4.6 19.9 1.0
CG2 B:VAL533 4.7 20.9 1.0
CA B:ASP674 4.8 21.5 1.0
O B:ASP674 4.8 22.3 1.0

Zinc binding site 3 out of 4 in 5skn

Go back to Zinc Binding Sites List in 5skn
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[3- [3-[2-(2-Fluorophenyl)Pyrazol-3-Yl]-4-Oxopyridazin-1- Yl]Phenyl]Acetamide


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 N-[3- [3-[2-(2-Fluorophenyl)Pyrazol-3-Yl]-4-Oxopyridazin-1- Yl]Phenyl]Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:27.1
occ:1.00
 O C:HOH917 2.1 21.8 1.0
NE2 C:HIS529 2.1 24.6 1.0
OD2 C:ASP564 2.2 22.8 1.0
NE2 C:HIS563 2.2 21.8 1.0
OD1 C:ASP674 2.2 22.5 1.0
O C:HOH1040 2.2 28.1 1.0
CD2 C:HIS563 3.1 21.0 1.0
CG C:ASP674 3.1 23.9 1.0
CG C:ASP564 3.1 22.2 1.0
CE1 C:HIS529 3.1 25.1 1.0
CD2 C:HIS529 3.1 26.0 1.0
CE1 C:HIS563 3.3 21.9 1.0
OD2 C:ASP674 3.3 27.3 1.0
OD1 C:ASP564 3.5 23.1 1.0
MG C:MG802 3.8 24.5 1.0
O C:HOH1047 4.1 23.1 1.0
CD2 C:HIS525 4.2 28.7 1.0
ND1 C:HIS529 4.2 26.3 1.0
CG C:HIS563 4.2 21.2 1.0
O C:HOH995 4.3 28.8 1.0
CG C:HIS529 4.3 25.6 1.0
ND1 C:HIS563 4.3 20.6 1.0
CB C:ASP564 4.3 21.5 1.0
CB C:ASP674 4.4 24.4 1.0
O C:HOH1062 4.4 38.6 1.0
NE2 C:HIS525 4.5 29.8 1.0
O C:HOH977 4.6 23.9 1.0
CG2 C:VAL533 4.8 22.6 1.0
O C:ASP674 4.8 24.5 1.0
CA C:ASP674 4.8 23.1 1.0

Zinc binding site 4 out of 4 in 5skn

Go back to Zinc Binding Sites List in 5skn
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[3- [3-[2-(2-Fluorophenyl)Pyrazol-3-Yl]-4-Oxopyridazin-1- Yl]Phenyl]Acetamide


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 N-[3- [3-[2-(2-Fluorophenyl)Pyrazol-3-Yl]-4-Oxopyridazin-1- Yl]Phenyl]Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:33.7
occ:1.00
 O D:HOH929 2.1 25.3 1.0
NE2 D:HIS529 2.2 32.7 1.0
OD2 D:ASP564 2.2 28.6 1.0
NE2 D:HIS563 2.2 28.9 1.0
O D:HOH991 2.2 28.9 1.0
OD1 D:ASP674 2.3 30.7 1.0
CD2 D:HIS563 3.0 30.1 1.0
CD2 D:HIS529 3.1 34.6 1.0
CG D:ASP674 3.1 32.5 1.0
CG D:ASP564 3.1 27.4 1.0
CE1 D:HIS529 3.2 33.6 1.0
CE1 D:HIS563 3.3 29.1 1.0
OD2 D:ASP674 3.3 33.0 1.0
OD1 D:ASP564 3.6 27.9 1.0
MG D:MG802 3.8 31.2 1.0
O D:HOH977 4.0 31.3 1.0
CD2 D:HIS525 4.1 35.4 1.0
O D:HOH953 4.2 32.4 1.0
CG D:HIS563 4.2 27.7 1.0
CG D:HIS529 4.3 32.5 1.0
ND1 D:HIS529 4.3 32.6 1.0
CB D:ASP564 4.3 27.4 1.0
ND1 D:HIS563 4.3 28.9 1.0
NE2 D:HIS525 4.4 37.0 1.0
CB D:ASP674 4.5 31.3 1.0
O D:HOH927 4.6 30.8 1.0
CG2 D:VAL533 4.7 30.5 1.0
O D:ASP674 4.8 31.1 1.0
CA D:ASP674 4.9 31.0 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 07:38:47 2024

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