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Zinc in PDB 5skf: Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile:
3.1.4.17;

Protein crystallography data

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

Resolution Low / High (Å) 39.07 / 2.10
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.05, 135.05, 234.4, 90, 90, 120
R / Rfree (%) 17.1 / 18.7

Other elements in 5skf:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Praseodymium (Pr) 8 atoms
Fluorine (F) 8 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 3-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile (pdb code 5skf). 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-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile, PDB code: 5skf:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5skf

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile


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-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:28.9
occ:1.00
 OD2 A:ASP564 2.1 25.7 1.0
NE2 A:HIS529 2.1 27.2 1.0
OD1 A:ASP674 2.2 30.5 1.0
NE2 A:HIS563 2.2 26.2 1.0
O A:HOH1002 2.3 23.4 1.0
O A:HOH938 2.3 30.5 1.0
CE1 A:HIS529 3.0 25.4 1.0
CG A:ASP564 3.1 25.5 1.0
CD2 A:HIS529 3.1 24.7 1.0
CG A:ASP674 3.1 28.0 1.0
CD2 A:HIS563 3.1 27.2 1.0
CE1 A:HIS563 3.2 27.6 1.0
OD2 A:ASP674 3.4 29.4 1.0
OD1 A:ASP564 3.6 26.1 1.0
MG A:MG802 3.8 22.3 1.0
O A:HOH1001 4.0 25.9 1.0
ND1 A:HIS529 4.1 26.0 1.0
O A:HOH966 4.2 28.7 1.0
CG A:HIS529 4.2 25.8 1.0
CD2 A:HIS525 4.2 27.2 1.0
CB A:ASP564 4.2 24.8 1.0
CG A:HIS563 4.3 26.8 1.0
ND1 A:HIS563 4.3 27.6 1.0
CB A:ASP674 4.4 27.8 1.0
NE2 A:HIS525 4.5 26.4 1.0
O A:HOH921 4.6 21.8 1.0
O A:ASP674 4.7 29.7 1.0
CG2 A:VAL533 4.8 24.5 1.0
CA A:ASP674 4.9 27.0 1.0

Zinc binding site 2 out of 4 in 5skf

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Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile


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-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:27.2
occ:1.00
 OD2 B:ASP564 2.0 22.8 1.0
NE2 B:HIS563 2.1 23.1 1.0
O B:HOH1002 2.1 28.1 1.0
OD1 B:ASP674 2.2 24.4 1.0
NE2 B:HIS529 2.2 24.1 1.0
O B:HOH927 2.3 18.3 1.0
CG B:ASP564 2.9 24.3 1.0
CD2 B:HIS563 3.0 22.7 1.0
CG B:ASP674 3.1 25.1 1.0
CE1 B:HIS563 3.1 24.0 1.0
CD2 B:HIS529 3.2 24.9 1.0
CE1 B:HIS529 3.2 27.0 1.0
OD2 B:ASP674 3.3 23.8 1.0
OD1 B:ASP564 3.4 26.2 1.0
O B:HOH996 3.9 17.2 1.0
MG B:MG802 4.0 22.0 1.0
O B:HOH931 4.1 27.3 1.0
CD2 B:HIS525 4.1 24.0 1.0
CG B:HIS563 4.1 23.9 1.0
CB B:ASP564 4.2 23.2 1.0
ND1 B:HIS563 4.2 23.8 1.0
ND1 B:HIS529 4.3 26.3 1.0
CG B:HIS529 4.3 26.1 1.0
NE2 B:HIS525 4.3 24.1 1.0
CB B:ASP674 4.5 25.2 1.0
O B:HOH947 4.6 30.4 1.0
CG2 B:VAL533 4.8 23.6 1.0
O B:ASP674 4.8 25.9 1.0
CA B:ASP674 4.9 25.1 1.0

Zinc binding site 3 out of 4 in 5skf

Go back to Zinc Binding Sites List in 5skf
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile


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-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:29.7
occ:1.00
 NE2 C:HIS563 2.1 22.6 1.0
O C:HOH994 2.1 28.1 1.0
NE2 C:HIS529 2.1 26.1 1.0
OD2 C:ASP564 2.2 24.6 1.0
O C:HOH933 2.2 25.3 1.0
OD1 C:ASP674 2.3 26.2 1.0
CD2 C:HIS563 3.0 22.7 1.0
CG C:ASP674 3.0 29.7 1.0
CG C:ASP564 3.1 24.8 1.0
CD2 C:HIS529 3.1 24.8 1.0
CE1 C:HIS563 3.2 22.4 1.0
CE1 C:HIS529 3.2 26.8 1.0
OD2 C:ASP674 3.2 31.2 1.0
OD1 C:ASP564 3.5 25.9 1.0
MG C:MG802 3.9 24.1 1.0
O C:HOH992 4.0 34.2 1.0
O C:HOH1014 4.1 26.9 1.0
CD2 C:HIS525 4.1 28.0 1.0
CG C:HIS563 4.1 23.2 1.0
ND1 C:HIS563 4.2 22.6 1.0
ND1 C:HIS529 4.3 27.1 1.0
CG C:HIS529 4.3 25.8 1.0
CB C:ASP564 4.3 23.5 1.0
CB C:ASP674 4.4 29.9 1.0
NE2 C:HIS525 4.4 28.6 1.0
O C:HOH941 4.5 27.3 1.0
CG2 C:VAL533 4.8 25.5 1.0
O C:ASP674 4.8 28.6 1.0
CA C:ASP674 4.8 29.7 1.0

Zinc binding site 4 out of 4 in 5skf

Go back to Zinc Binding Sites List in 5skf
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile


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-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:33.8
occ:1.00
 OD2 D:ASP564 2.0 30.0 1.0
NE2 D:HIS563 2.1 27.1 1.0
O D:HOH904 2.2 31.2 1.0
O D:HOH982 2.2 30.8 1.0
OD1 D:ASP674 2.2 24.4 1.0
NE2 D:HIS529 2.3 32.7 1.0
CD2 D:HIS563 3.0 27.1 1.0
CG D:ASP564 3.0 27.7 1.0
CG D:ASP674 3.0 26.2 1.0
CD2 D:HIS529 3.1 33.4 1.0
CE1 D:HIS563 3.1 27.3 1.0
OD2 D:ASP674 3.2 25.8 1.0
CE1 D:HIS529 3.4 32.6 1.0
OD1 D:ASP564 3.5 28.6 1.0
MG D:MG802 3.9 29.9 1.0
O D:HOH935 4.1 31.2 1.0
CG D:HIS563 4.2 27.7 1.0
CB D:ASP564 4.2 28.0 1.0
ND1 D:HIS563 4.2 27.4 1.0
CD2 D:HIS525 4.3 37.0 1.0
O D:HOH971 4.3 27.8 1.0
CG D:HIS529 4.3 33.2 1.0
ND1 D:HIS529 4.4 33.5 1.0
CB D:ASP674 4.4 26.9 1.0
O D:HOH924 4.5 26.3 1.0
NE2 D:HIS525 4.6 33.9 1.0
O D:ASP674 4.7 26.8 1.0
CG2 D:VAL533 4.8 29.0 1.0
CA D:ASP674 4.9 27.3 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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