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Magnesium in PDB 5sjy: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 3-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 3-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 3-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 3-Carboxamide, PDB code: 5sjy was solved by C.Joseph, J.Benz, A.Flohr, J.Peters, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.81 / 2.20
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 136.053, 136.053, 235.986, 90, 90, 120
R / Rfree (%) 20.2 / 26.5

Other elements in 5sjy:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 3-Carboxamide also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Bromine (Br) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 3-Carboxamide (pdb code 5sjy). 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- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 3-Carboxamide, PDB code: 5sjy:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sjy

Go back to Magnesium Binding Sites List in 5sjy
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 3-Carboxamide


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- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:32.8
occ:1.00
 O A:HOH934 1.8 33.2 1.0
O A:HOH908 1.9 34.0 1.0
OD1 A:ASP564 1.9 34.2 1.0
O A:HOH909 2.0 34.2 1.0
O A:HOH918 2.2 33.7 1.0
O A:HOH931 2.2 30.9 1.0
CG A:ASP564 2.9 34.3 1.0
OD2 A:ASP564 3.3 41.0 1.0
ZN A:ZN801 3.7 42.2 1.0
O A:HOH929 3.8 45.5 1.0
NE2 A:HIS595 4.0 30.2 1.0
OE2 A:GLU592 4.0 44.3 1.0
O A:HIS563 4.1 35.5 1.0
O A:HOH920 4.1 44.0 1.0
CD2 A:HIS563 4.1 40.7 1.0
OG1 A:THR633 4.2 41.0 1.0
CB A:ASP564 4.3 33.0 1.0
CD2 A:HIS595 4.3 37.2 1.0
CD2 A:HIS567 4.4 41.5 1.0
OD2 A:ASP674 4.4 38.9 1.0
O A:THR633 4.5 39.4 1.0
NE2 A:HIS567 4.5 36.1 1.0
CD2 A:HIS525 4.6 45.9 1.0
CB A:THR633 4.6 35.4 1.0
NE2 A:HIS563 4.6 37.9 1.0
NE2 A:HIS525 4.7 40.9 1.0
CA A:ASP564 4.7 33.0 1.0
CG A:GLU592 4.8 37.7 1.0
CD A:GLU592 4.9 43.2 1.0
C A:HIS563 4.9 34.5 1.0

Magnesium binding site 2 out of 4 in 5sjy

Go back to Magnesium Binding Sites List in 5sjy
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 3-Carboxamide


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- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:29.4
occ:1.00
 OD1 B:ASP564 2.0 36.8 1.0
O B:HOH924 2.0 28.7 1.0
O B:HOH933 2.1 32.6 1.0
O B:HOH929 2.2 29.9 1.0
O B:HOH945 2.2 34.4 1.0
O B:HOH909 2.3 31.5 1.0
CG B:ASP564 2.9 31.8 1.0
OD2 B:ASP564 3.2 30.5 1.0
ZN B:ZN801 3.7 39.3 1.0
O B:HOH947 4.0 42.9 1.0
OE2 B:GLU592 4.2 35.5 1.0
NE2 B:HIS595 4.2 36.8 1.0
CD2 B:HIS563 4.2 33.7 1.0
O B:HOH932 4.2 47.8 1.0
CD2 B:HIS567 4.3 39.5 1.0
O B:HIS563 4.3 42.5 1.0
CB B:ASP564 4.3 29.5 1.0
OG1 B:THR633 4.3 33.1 1.0
CD2 B:HIS595 4.4 38.4 1.0
OD2 B:ASP674 4.4 35.8 1.0
NE2 B:HIS563 4.5 30.1 1.0
NE2 B:HIS567 4.5 37.1 1.0
CD2 B:HIS525 4.5 36.1 1.0
O B:THR633 4.5 35.8 1.0
NE2 B:HIS525 4.6 39.8 1.0
CA B:ASP564 4.7 33.1 1.0
CB B:THR633 4.7 34.9 1.0
CG B:GLU592 5.0 41.3 1.0
CD B:GLU592 5.0 40.3 1.0

Magnesium binding site 3 out of 4 in 5sjy

Go back to Magnesium Binding Sites List in 5sjy
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 3-Carboxamide


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- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:33.6
occ:1.00
 O C:HOH937 1.9 39.9 1.0
O C:HOH939 2.0 29.6 1.0
OD1 C:ASP564 2.1 30.5 1.0
O C:HOH930 2.1 36.8 1.0
O C:HOH956 2.2 29.6 1.0
O C:HOH924 2.2 30.2 1.0
CG C:ASP564 3.1 33.8 1.0
OD2 C:ASP564 3.6 33.1 1.0
OE2 C:GLU592 3.9 37.8 1.0
ZN C:ZN801 3.9 38.5 1.0
NE2 C:HIS595 4.0 50.9 1.0
O C:HOH940 4.1 35.3 1.0
O C:HOH945 4.2 48.8 1.0
CD2 C:HIS567 4.2 32.0 1.0
O C:HIS563 4.3 37.4 1.0
CD2 C:HIS595 4.3 43.7 1.0
CD2 C:HIS563 4.3 32.5 1.0
OG1 C:THR633 4.3 40.8 1.0
NE2 C:HIS567 4.4 37.4 1.0
CB C:ASP564 4.4 30.4 1.0
OD2 C:ASP674 4.5 39.6 1.0
O C:THR633 4.6 36.6 1.0
CG C:GLU592 4.7 38.7 1.0
CB C:THR633 4.7 39.5 1.0
CD C:GLU592 4.7 40.5 1.0
CA C:ASP564 4.8 34.0 1.0
NE2 C:HIS563 4.8 38.8 1.0
CD2 C:HIS525 4.8 40.6 1.0
NE2 C:HIS525 4.8 47.9 1.0
CE1 C:HIS595 5.0 43.7 1.0

Magnesium binding site 4 out of 4 in 5sjy

Go back to Magnesium Binding Sites List in 5sjy
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 3-Carboxamide


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- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:47.7
occ:1.00
 O D:HOH917 2.0 41.4 1.0
O D:HOH909 2.0 37.1 1.0
O D:HOH902 2.1 45.9 1.0
O D:HOH907 2.1 31.2 1.0
OD1 D:ASP564 2.2 47.7 1.0
O D:HOH915 2.3 37.5 1.0
CG D:ASP564 3.1 42.2 1.0
OD2 D:ASP564 3.4 48.6 1.0
ZN D:ZN801 3.9 46.8 1.0
O D:HOH913 4.0 41.5 1.0
OE2 D:GLU592 4.1 49.4 1.0
NE2 D:HIS595 4.1 43.8 1.0
OG1 D:THR633 4.1 42.1 1.0
O D:THR633 4.3 55.3 1.0
CD2 D:HIS567 4.4 54.4 1.0
CD2 D:HIS563 4.4 39.0 1.0
OD2 D:ASP674 4.4 35.1 1.0
CB D:ASP564 4.4 43.0 1.0
CD2 D:HIS595 4.5 44.8 1.0
O D:HIS563 4.5 38.1 1.0
NE2 D:HIS567 4.5 49.2 1.0
CD2 D:HIS525 4.5 51.6 1.0
CB D:THR633 4.6 45.3 1.0
NE2 D:HIS525 4.6 47.6 1.0
NE2 D:HIS563 4.8 38.6 1.0
CG D:GLU592 4.9 47.3 1.0
CA D:ASP564 4.9 40.7 1.0
CD D:GLU592 4.9 46.9 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 04:27:49 2024

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