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Magnesium 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:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 4 in 5skp

Go back to Magnesium Binding Sites List in 5skp
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg802

b:23.4
occ:1.00
 OD1 A:ASP564 2.0 21.9 1.0
O A:HOH1017 2.0 26.1 1.0
O A:HOH908 2.0 17.4 1.0
O A:HOH977 2.1 23.0 1.0
O A:HOH943 2.1 23.3 1.0
O A:HOH956 2.3 22.7 1.0
CG A:ASP564 3.0 25.5 1.0
OD2 A:ASP564 3.4 22.9 1.0
O A:HOH980 3.9 30.4 1.0
ZN A:ZN801 3.9 28.9 1.0
O A:HOH1034 3.9 41.7 1.0
NE2 A:HIS595 4.0 22.3 1.0
OE2 A:GLU592 4.1 23.2 1.0
O A:HOH1004 4.1 26.4 1.0
OG1 A:THR633 4.2 22.9 1.0
O A:HIS563 4.3 22.8 1.0
CD2 A:HIS563 4.4 22.1 1.0
CD2 A:HIS567 4.4 24.7 1.0
CB A:ASP564 4.4 22.5 1.0
CD2 A:HIS595 4.4 20.4 1.0
CD2 A:HIS525 4.6 25.4 1.0
O A:THR633 4.6 24.6 1.0
NE2 A:HIS567 4.6 25.8 1.0
OD2 A:ASP674 4.7 31.7 1.0
NE2 A:HIS525 4.7 27.7 1.0
CB A:THR633 4.7 23.2 1.0
CA A:ASP564 4.8 23.1 1.0
NE2 A:HIS563 4.8 23.7 1.0
CG A:GLU592 4.8 25.6 1.0
CD A:GLU592 4.9 27.3 1.0

Magnesium binding site 2 out of 4 in 5skp

Go back to Magnesium Binding Sites List in 5skp
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg802

b:17.6
occ:1.00
 O B:HOH963 1.9 19.4 1.0
O B:HOH929 1.9 14.6 1.0
O B:HOH1009 2.0 17.0 1.0
O B:HOH931 2.1 20.4 1.0
OD1 B:ASP564 2.1 21.6 1.0
O B:HOH995 2.1 16.6 1.0
CG B:ASP564 3.1 22.4 1.0
OD2 B:ASP564 3.5 21.1 1.0
ZN B:ZN801 3.7 25.9 1.0
O B:HOH994 3.9 32.3 1.0
O B:HOH1033 4.0 47.3 1.0
OE2 B:GLU592 4.1 21.6 1.0
NE2 B:HIS595 4.1 18.2 1.0
O B:HOH978 4.2 24.5 1.0
CD2 B:HIS563 4.3 18.2 1.0
OD2 B:ASP674 4.3 24.6 1.0
O B:HIS563 4.3 22.8 1.0
CD2 B:HIS567 4.4 22.0 1.0
OG1 B:THR633 4.4 22.7 1.0
CD2 B:HIS595 4.4 20.2 1.0
CB B:ASP564 4.5 19.4 1.0
NE2 B:HIS567 4.5 19.7 1.0
CD2 B:HIS525 4.5 25.9 1.0
NE2 B:HIS563 4.6 19.4 1.0
O B:THR633 4.6 21.3 1.0
CB B:THR633 4.7 24.6 1.0
NE2 B:HIS525 4.7 25.2 1.0
CA B:ASP564 4.8 20.9 1.0
CG B:GLU592 4.8 23.0 1.0
CD B:GLU592 4.9 24.8 1.0

Magnesium binding site 3 out of 4 in 5skp

Go back to Magnesium Binding Sites List in 5skp
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg802

b:24.5
occ:1.00
 O C:HOH966 2.0 21.1 1.0
O C:HOH942 2.0 19.8 1.0
OD1 C:ASP564 2.1 20.6 1.0
O C:HOH937 2.1 21.3 1.0
O C:HOH959 2.1 23.2 1.0
O C:HOH1013 2.1 23.6 1.0
CG C:ASP564 3.1 21.7 1.0
OD2 C:ASP564 3.5 21.2 1.0
ZN C:ZN801 3.8 27.9 1.0
O C:HOH1038 3.9 43.5 1.0
OE2 C:GLU592 4.0 31.1 1.0
O C:HOH992 4.1 38.6 1.0
NE2 C:HIS595 4.1 27.6 1.0
OG1 C:THR633 4.1 23.0 1.0
CD2 C:HIS563 4.3 20.9 1.0
CD2 C:HIS567 4.3 24.9 1.0
O C:HIS563 4.3 22.6 1.0
O C:HOH967 4.4 29.0 1.0
CD2 C:HIS595 4.4 25.4 1.0
CB C:ASP564 4.4 20.5 1.0
OD2 C:ASP674 4.4 28.0 1.0
O C:THR633 4.5 23.3 1.0
NE2 C:HIS567 4.5 23.7 1.0
CB C:THR633 4.6 24.5 1.0
CD2 C:HIS525 4.7 25.1 1.0
NE2 C:HIS525 4.7 28.5 1.0
NE2 C:HIS563 4.8 22.9 1.0
CA C:ASP564 4.8 23.3 1.0
CG C:GLU592 4.8 25.1 1.0
CD C:GLU592 4.9 26.8 1.0

Magnesium binding site 4 out of 4 in 5skp

Go back to Magnesium Binding Sites List in 5skp
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg802

b:33.3
occ:1.00
 O D:HOH960 1.9 28.9 1.0
OD1 D:ASP564 2.0 30.8 1.0
O D:HOH927 2.0 26.6 1.0
O D:HOH926 2.1 23.2 1.0
O D:HOH914 2.2 30.4 1.0
O D:HOH966 2.2 27.2 1.0
CG D:ASP564 3.1 31.1 1.0
OD2 D:ASP564 3.5 29.7 1.0
O D:HOH930 3.7 41.6 1.0
ZN D:ZN801 3.8 35.5 1.0
NE2 D:HIS595 4.0 32.5 1.0
OE2 D:GLU592 4.1 32.7 1.0
O D:HOH967 4.1 32.0 1.0
OG1 D:THR633 4.2 30.1 1.0
CD2 D:HIS567 4.3 34.1 1.0
CD2 D:HIS563 4.3 28.0 1.0
CD2 D:HIS595 4.4 30.5 1.0
O D:HIS563 4.4 31.4 1.0
CB D:ASP564 4.4 29.8 1.0
NE2 D:HIS567 4.4 31.1 1.0
OD2 D:ASP674 4.4 39.6 1.0
O D:THR633 4.5 33.0 1.0
NE2 D:HIS525 4.5 40.2 1.0
CD2 D:HIS525 4.5 35.4 1.0
CA D:ASP564 4.8 29.3 1.0
CB D:THR633 4.8 33.1 1.0
NE2 D:HIS563 4.8 25.8 1.0
CD D:GLU592 4.9 33.4 1.0
CG D:GLU592 5.0 34.3 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 Sep 30 04:37:42 2024

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