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Zinc in PDB 5skp: Crystal Structure of Human Phosphodiesterase 10 in Complex with [4-(2- Methoxyphenyl)Piperazin-1-Yl]-(3-Methyl-1-Phenylthieno[2,3-C]Pyrazol- 5-Yl)Methanone

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with [4-(2- Methoxyphenyl)Piperazin-1-Yl]-(3-Methyl-1-Phenylthieno[2,3-C]Pyrazol- 5-Yl)Methanone

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with [4-(2- Methoxyphenyl)Piperazin-1-Yl]-(3-Methyl-1-Phenylthieno[2,3-C]Pyrazol- 5-Yl)Methanone:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with [4-(2- Methoxyphenyl)Piperazin-1-Yl]-(3-Methyl-1-Phenylthieno[2,3-C]Pyrazol- 5-Yl)Methanone, PDB code: 5skp was solved by C.Joseph, J.Benz, A.Flohr, M.Brunner, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.94 / 2.00
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.91, 135.91, 236.75, 90, 90, 120
R / Rfree (%) 17.8 / 23

Other elements in 5skp:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with [4-(2- Methoxyphenyl)Piperazin-1-Yl]-(3-Methyl-1-Phenylthieno[2,3-C]Pyrazol- 5-Yl)Methanone also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with [4-(2- Methoxyphenyl)Piperazin-1-Yl]-(3-Methyl-1-Phenylthieno[2,3-C]Pyrazol- 5-Yl)Methanone (pdb code 5skp). 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 [4-(2- Methoxyphenyl)Piperazin-1-Yl]-(3-Methyl-1-Phenylthieno[2,3-C]Pyrazol- 5-Yl)Methanone, PDB code: 5skp:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5skp

Go back to Zinc Binding Sites List in 5skp
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with [4-(2- Methoxyphenyl)Piperazin-1-Yl]-(3-Methyl-1-Phenylthieno[2,3-C]Pyrazol- 5-Yl)Methanone


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 [4-(2- Methoxyphenyl)Piperazin-1-Yl]-(3-Methyl-1-Phenylthieno[2,3-C]Pyrazol- 5-Yl)Methanone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:28.9
occ:1.00
 NE2 A:HIS563 2.1 23.7 1.0
O A:HOH980 2.1 30.4 1.0
NE2 A:HIS529 2.2 28.1 1.0
OD1 A:ASP674 2.2 30.7 1.0
O A:HOH977 2.2 23.0 1.0
OD2 A:ASP564 2.2 22.9 1.0
CD2 A:HIS563 2.9 22.1 1.0
CD2 A:HIS529 3.0 25.9 1.0
CG A:ASP674 3.1 31.2 1.0
CG A:ASP564 3.2 25.5 1.0
CE1 A:HIS563 3.2 24.8 1.0
CE1 A:HIS529 3.3 27.2 1.0
OD2 A:ASP674 3.4 31.7 1.0
OD1 A:ASP564 3.7 21.9 1.0
MG A:MG802 3.9 23.4 1.0
CG A:HIS563 4.1 22.8 1.0
CG A:HIS529 4.2 27.3 1.0
ND1 A:HIS563 4.2 22.8 1.0
CD2 A:HIS525 4.3 25.4 1.0
O A:HOH1017 4.3 26.1 1.0
O A:HOH947 4.3 31.3 1.0
ND1 A:HIS529 4.3 23.3 1.0
CB A:ASP564 4.3 22.5 1.0
CB A:ASP674 4.4 27.9 1.0
O A:HOH908 4.5 17.4 1.0
O A:HOH1034 4.6 41.7 1.0
NE2 A:HIS525 4.6 27.7 1.0
CG2 A:VAL533 4.6 22.8 1.0
O A:ASP674 4.8 26.3 1.0
CA A:ASP674 4.9 26.6 1.0

Zinc binding site 2 out of 4 in 5skp

Go back to Zinc Binding Sites List in 5skp
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with [4-(2- Methoxyphenyl)Piperazin-1-Yl]-(3-Methyl-1-Phenylthieno[2,3-C]Pyrazol- 5-Yl)Methanone


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 [4-(2- Methoxyphenyl)Piperazin-1-Yl]-(3-Methyl-1-Phenylthieno[2,3-C]Pyrazol- 5-Yl)Methanone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:25.9
occ:1.00
 O B:HOH929 2.1 14.6 1.0
OD1 B:ASP674 2.1 23.6 1.0
NE2 B:HIS563 2.1 19.4 1.0
OD2 B:ASP564 2.2 21.1 1.0
NE2 B:HIS529 2.2 21.2 1.0
O B:HOH994 2.4 32.3 1.0
CG B:ASP674 3.0 24.4 1.0
CD2 B:HIS563 3.0 18.2 1.0
CG B:ASP564 3.1 22.4 1.0
OD2 B:ASP674 3.2 24.6 1.0
CD2 B:HIS529 3.2 20.4 1.0
CE1 B:HIS563 3.2 18.3 1.0
CE1 B:HIS529 3.3 20.1 1.0
OD1 B:ASP564 3.5 21.6 1.0
MG B:MG802 3.7 17.6 1.0
O B:HOH1009 4.0 17.0 1.0
CD2 B:HIS525 4.1 25.9 1.0
CG B:HIS563 4.2 19.3 1.0
O B:HOH972 4.2 28.2 1.0
ND1 B:HIS563 4.3 19.2 1.0
CB B:ASP564 4.3 19.4 1.0
CG B:HIS529 4.4 19.2 1.0
ND1 B:HIS529 4.4 18.2 1.0
CB B:ASP674 4.4 23.6 1.0
NE2 B:HIS525 4.5 25.2 1.0
O B:HOH963 4.5 19.4 1.0
O B:HOH1033 4.6 47.3 1.0
CG2 B:VAL533 4.8 21.5 1.0
CA B:ASP674 4.9 22.5 1.0
O B:ASP674 5.0 22.9 1.0

Zinc binding site 3 out of 4 in 5skp

Go back to Zinc Binding Sites List in 5skp
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with [4-(2- Methoxyphenyl)Piperazin-1-Yl]-(3-Methyl-1-Phenylthieno[2,3-C]Pyrazol- 5-Yl)Methanone


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 [4-(2- Methoxyphenyl)Piperazin-1-Yl]-(3-Methyl-1-Phenylthieno[2,3-C]Pyrazol- 5-Yl)Methanone within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:27.9
occ:1.00
 NE2 C:HIS529 2.1 22.2 1.0
OD2 C:ASP564 2.1 21.2 1.0
O C:HOH942 2.2 19.8 1.0
OD1 C:ASP674 2.2 23.9 1.0
NE2 C:HIS563 2.3 22.9 1.0
O C:HOH992 2.3 38.6 1.0
CD2 C:HIS563 3.0 20.9 1.0
CD2 C:HIS529 3.1 26.1 1.0
CE1 C:HIS529 3.1 25.9 1.0
CG C:ASP674 3.1 24.9 1.0
CG C:ASP564 3.1 21.7 1.0
CE1 C:HIS563 3.3 19.7 1.0
OD2 C:ASP674 3.4 28.0 1.0
OD1 C:ASP564 3.6 20.6 1.0
MG C:MG802 3.8 24.5 1.0
CD2 C:HIS525 4.1 25.1 1.0
O C:HOH1013 4.2 23.6 1.0
CG C:HIS563 4.2 20.6 1.0
ND1 C:HIS529 4.2 23.1 1.0
CG C:HIS529 4.2 23.1 1.0
O C:HOH988 4.3 27.5 1.0
CB C:ASP564 4.3 20.5 1.0
ND1 C:HIS563 4.3 22.3 1.0
NE2 C:HIS525 4.4 28.5 1.0
CB C:ASP674 4.5 26.9 1.0
O C:HOH1038 4.6 43.5 1.0
O C:HOH937 4.6 21.3 1.0
CG2 C:VAL533 4.8 22.6 1.0
CA C:ASP674 4.9 25.0 1.0
O C:ASP674 4.9 28.3 1.0

Zinc binding site 4 out of 4 in 5skp

Go back to Zinc Binding Sites List in 5skp
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with [4-(2- Methoxyphenyl)Piperazin-1-Yl]-(3-Methyl-1-Phenylthieno[2,3-C]Pyrazol- 5-Yl)Methanone


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 [4-(2- Methoxyphenyl)Piperazin-1-Yl]-(3-Methyl-1-Phenylthieno[2,3-C]Pyrazol- 5-Yl)Methanone within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:35.5
occ:1.00
 O D:HOH927 2.1 26.6 1.0
O D:HOH930 2.1 41.6 1.0
NE2 D:HIS563 2.2 25.8 1.0
OD1 D:ASP674 2.2 36.4 1.0
NE2 D:HIS529 2.2 29.8 1.0
OD2 D:ASP564 2.3 29.7 1.0
CD2 D:HIS563 3.0 28.0 1.0
CG D:ASP674 3.1 35.4 1.0
CG D:ASP564 3.2 31.1 1.0
CD2 D:HIS529 3.2 32.8 1.0
OD2 D:ASP674 3.2 39.6 1.0
CE1 D:HIS529 3.2 31.0 1.0
CE1 D:HIS563 3.4 28.1 1.0
OD1 D:ASP564 3.7 30.8 1.0
MG D:MG802 3.8 33.3 1.0
CD2 D:HIS525 4.1 35.4 1.0
O D:HOH955 4.2 36.8 1.0
CG D:HIS563 4.2 26.9 1.0
O D:HOH966 4.3 27.2 1.0
NE2 D:HIS525 4.3 40.2 1.0
ND1 D:HIS529 4.4 33.3 1.0
CB D:ASP564 4.4 29.8 1.0
CG D:HIS529 4.4 30.9 1.0
ND1 D:HIS563 4.4 28.9 1.0
CB D:ASP674 4.5 35.3 1.0
O D:HOH914 4.7 30.4 1.0
O D:ASP674 4.8 33.2 1.0
CG2 D:VAL533 4.8 29.6 1.0
CA D:ASP674 4.9 33.4 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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