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Magnesium in PDB 5sjd: Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (3,5-Dimethylpyrazol-1-Yl)Ethyl]-3-(2-Phenylpyrazol-3-Yl)Urea

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (3,5-Dimethylpyrazol-1-Yl)Ethyl]-3-(2-Phenylpyrazol-3-Yl)Urea

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (3,5-Dimethylpyrazol-1-Yl)Ethyl]-3-(2-Phenylpyrazol-3-Yl)Urea:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (3,5-Dimethylpyrazol-1-Yl)Ethyl]-3-(2-Phenylpyrazol-3-Yl)Urea, PDB code: 5sjd 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) 43.73 / 2.16
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.859, 135.859, 235.544, 90, 90, 120
R / Rfree (%) 18.5 / 22.7

Other elements in 5sjd:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (3,5-Dimethylpyrazol-1-Yl)Ethyl]-3-(2-Phenylpyrazol-3-Yl)Urea 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 1-[2- (3,5-Dimethylpyrazol-1-Yl)Ethyl]-3-(2-Phenylpyrazol-3-Yl)Urea (pdb code 5sjd). 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 1-[2- (3,5-Dimethylpyrazol-1-Yl)Ethyl]-3-(2-Phenylpyrazol-3-Yl)Urea, PDB code: 5sjd:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sjd

Go back to Magnesium Binding Sites List in 5sjd
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (3,5-Dimethylpyrazol-1-Yl)Ethyl]-3-(2-Phenylpyrazol-3-Yl)Urea


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 1-[2- (3,5-Dimethylpyrazol-1-Yl)Ethyl]-3-(2-Phenylpyrazol-3-Yl)Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:24.6
occ:1.00
 O A:HOH958 2.0 26.6 1.0
O A:HOH942 2.0 21.8 1.0
OD1 A:ASP564 2.0 26.0 1.0
O A:HOH1009 2.0 23.7 1.0
O A:HOH968 2.1 20.4 1.0
O A:HOH923 2.1 28.1 1.0
CG A:ASP564 3.0 27.1 1.0
OD2 A:ASP564 3.3 27.6 1.0
ZN A:ZN801 3.8 32.4 1.0
O A:HOH1015 3.8 42.3 1.0
OE2 A:GLU592 4.0 32.1 1.0
O A:HOH972 4.0 29.5 1.0
NE2 A:HIS595 4.0 26.8 1.0
OG1 A:THR633 4.2 28.1 1.0
CD2 A:HIS567 4.2 31.6 1.0
CD2 A:HIS563 4.3 23.5 1.0
CD2 A:HIS595 4.3 26.9 1.0
CB A:ASP564 4.4 26.8 1.0
O A:HOH977 4.4 34.4 1.0
NE2 A:HIS567 4.4 31.7 1.0
O A:HIS563 4.5 28.8 1.0
O A:THR633 4.5 28.3 1.0
OD2 A:ASP674 4.5 35.0 1.0
NE2 A:HIS563 4.6 23.7 1.0
CD2 A:HIS525 4.7 26.8 1.0
CB A:THR633 4.7 29.6 1.0
NE2 A:HIS525 4.8 25.4 1.0
CA A:ASP564 4.8 26.5 1.0
CG A:GLU592 4.8 29.1 1.0
CD A:GLU592 4.8 31.7 1.0

Magnesium binding site 2 out of 4 in 5sjd

Go back to Magnesium Binding Sites List in 5sjd
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (3,5-Dimethylpyrazol-1-Yl)Ethyl]-3-(2-Phenylpyrazol-3-Yl)Urea


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 1-[2- (3,5-Dimethylpyrazol-1-Yl)Ethyl]-3-(2-Phenylpyrazol-3-Yl)Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:25.9
occ:1.00
 O B:HOH957 2.0 21.0 1.0
O B:HOH942 2.0 26.6 1.0
O B:HOH988 2.1 19.8 1.0
OD1 B:ASP564 2.1 25.8 1.0
O B:HOH1015 2.2 22.5 1.0
O B:HOH933 2.2 21.3 1.0
CG B:ASP564 3.1 25.4 1.0
OD2 B:ASP564 3.4 24.9 1.0
ZN B:ZN801 3.8 31.3 1.0
O B:HOH1020 3.8 54.6 1.0
NE2 B:HIS595 4.0 28.6 1.0
O B:HOH999 4.0 33.8 1.0
OE2 B:GLU592 4.2 29.6 1.0
CD2 B:HIS563 4.2 23.1 1.0
OG1 B:THR633 4.2 27.3 1.0
CD2 B:HIS595 4.3 31.4 1.0
O B:HIS563 4.3 28.5 1.0
O B:HOH993 4.3 33.7 1.0
CD2 B:HIS567 4.4 23.5 1.0
OD2 B:ASP674 4.4 28.7 1.0
CB B:ASP564 4.4 26.0 1.0
NE2 B:HIS567 4.5 23.6 1.0
O B:THR633 4.5 26.6 1.0
NE2 B:HIS563 4.6 23.7 1.0
CD2 B:HIS525 4.7 27.1 1.0
CB B:THR633 4.7 28.7 1.0
CA B:ASP564 4.8 26.7 1.0
CG B:GLU592 4.8 28.1 1.0
NE2 B:HIS525 4.8 27.2 1.0
CD B:GLU592 4.9 27.3 1.0

Magnesium binding site 3 out of 4 in 5sjd

Go back to Magnesium Binding Sites List in 5sjd
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (3,5-Dimethylpyrazol-1-Yl)Ethyl]-3-(2-Phenylpyrazol-3-Yl)Urea


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 1-[2- (3,5-Dimethylpyrazol-1-Yl)Ethyl]-3-(2-Phenylpyrazol-3-Yl)Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:23.8
occ:1.00
 O C:HOH980 2.0 26.8 1.0
O C:HOH1015 2.0 25.4 1.0
O C:HOH951 2.1 27.7 1.0
OD1 C:ASP564 2.1 25.4 1.0
O C:HOH932 2.1 23.2 1.0
O C:HOH920 2.2 22.8 1.0
CG C:ASP564 3.1 27.2 1.0
OD2 C:ASP564 3.4 27.9 1.0
ZN C:ZN801 3.8 33.3 1.0
O C:HOH1000 3.9 37.8 1.0
NE2 C:HIS595 4.1 28.8 1.0
OE2 C:GLU592 4.2 34.2 1.0
CD2 C:HIS567 4.2 28.4 1.0
OG1 C:THR633 4.2 28.2 1.0
O C:HOH983 4.3 51.8 1.0
O C:HOH999 4.3 34.6 1.0
CD2 C:HIS563 4.3 25.4 1.0
NE2 C:HIS567 4.4 28.0 1.0
O C:THR633 4.4 30.4 1.0
OD2 C:ASP674 4.4 28.9 1.0
CD2 C:HIS595 4.4 28.4 1.0
O C:HIS563 4.5 24.9 1.0
CB C:ASP564 4.5 25.7 1.0
CD2 C:HIS525 4.6 31.6 1.0
CB C:THR633 4.7 29.7 1.0
NE2 C:HIS525 4.7 29.8 1.0
NE2 C:HIS563 4.7 27.4 1.0
CA C:ASP564 4.9 27.1 1.0
CG C:GLU592 4.9 29.6 1.0
CD C:GLU592 5.0 31.8 1.0

Magnesium binding site 4 out of 4 in 5sjd

Go back to Magnesium Binding Sites List in 5sjd
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (3,5-Dimethylpyrazol-1-Yl)Ethyl]-3-(2-Phenylpyrazol-3-Yl)Urea


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 1-[2- (3,5-Dimethylpyrazol-1-Yl)Ethyl]-3-(2-Phenylpyrazol-3-Yl)Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:33.5
occ:1.00
 O D:HOH970 2.1 34.3 1.0
O D:HOH947 2.1 26.1 1.0
OD1 D:ASP564 2.1 32.0 1.0
O D:HOH923 2.1 34.8 1.0
O D:HOH966 2.1 31.5 1.0
O D:HOH912 2.1 34.5 1.0
CG D:ASP564 3.1 31.4 1.0
OD2 D:ASP564 3.4 33.3 1.0
ZN D:ZN801 3.8 41.0 1.0
O D:HOH965 3.8 33.4 1.0
OE2 D:GLU592 4.0 36.0 1.0
NE2 D:HIS595 4.1 37.6 1.0
O D:HOH960 4.2 38.8 1.0
OG1 D:THR633 4.2 30.9 1.0
CD2 D:HIS563 4.3 31.1 1.0
CD2 D:HIS567 4.3 39.3 1.0
CD2 D:HIS595 4.4 36.1 1.0
OD2 D:ASP674 4.4 38.5 1.0
O D:HIS563 4.4 31.0 1.0
CB D:ASP564 4.5 33.5 1.0
NE2 D:HIS567 4.5 38.9 1.0
O D:THR633 4.6 41.2 1.0
CB D:THR633 4.7 37.5 1.0
CD2 D:HIS525 4.7 38.2 1.0
NE2 D:HIS563 4.7 29.5 1.0
NE2 D:HIS525 4.8 40.6 1.0
CA D:ASP564 4.8 32.5 1.0
CG D:GLU592 4.8 37.6 1.0
CD D:GLU592 4.9 37.7 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 04:21:22 2024

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