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Magnesium in PDB 5sj4: Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-5H-Pyrazolo[3,4- D]Pyrimidin-4-One

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-5H-Pyrazolo[3,4- D]Pyrimidin-4-One

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-5H-Pyrazolo[3,4- D]Pyrimidin-4-One:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-5H-Pyrazolo[3,4- D]Pyrimidin-4-One, PDB code: 5sj4 was solved by C.Joseph, J.Benz, A.Flohr, K.Groebke-Zbinden, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.48 / 2.77
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.14, 135.14, 235.843, 90, 90, 120
R / Rfree (%) 19.5 / 27.8

Other elements in 5sj4:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-5H-Pyrazolo[3,4- D]Pyrimidin-4-One 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- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-5H-Pyrazolo[3,4- D]Pyrimidin-4-One (pdb code 5sj4). 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- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-5H-Pyrazolo[3,4- D]Pyrimidin-4-One, PDB code: 5sj4:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sj4

Go back to Magnesium Binding Sites List in 5sj4
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-5H-Pyrazolo[3,4- D]Pyrimidin-4-One


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- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-5H-Pyrazolo[3,4- D]Pyrimidin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:90.3
occ:1.00
 O A:HOH903 1.5 47.4 1.0
O A:HOH913 1.8 33.5 1.0
O A:HOH926 1.9 53.5 1.0
OD1 A:ASP564 1.9 37.4 1.0
O A:HOH909 2.0 34.6 1.0
O A:HOH919 2.0 29.2 1.0
CG A:ASP564 3.0 44.3 1.0
OD2 A:ASP564 3.4 38.0 1.0
OE2 A:GLU592 3.8 54.9 1.0
NE2 A:HIS595 3.9 50.9 1.0
O A:HOH925 4.0 47.6 1.0
ZN A:ZN801 4.1 51.1 1.0
OG1 A:THR633 4.1 43.3 1.0
CD2 A:HIS567 4.3 47.7 1.0
OD2 A:ASP674 4.3 66.9 1.0
CG A:GLU592 4.3 68.8 1.0
CD2 A:HIS595 4.3 45.2 1.0
CB A:ASP564 4.3 40.4 1.0
O A:HOH924 4.4 46.4 1.0
O A:HIS563 4.4 34.8 1.0
CD A:GLU592 4.4 69.4 1.0
O A:THR633 4.5 60.4 1.0
NE2 A:HIS525 4.6 53.5 1.0
CD2 A:HIS525 4.6 51.5 1.0
NE2 A:HIS567 4.6 56.6 1.0
CB A:THR633 4.6 44.0 1.0
CD2 A:HIS563 4.6 48.2 1.0
CA A:ASP564 4.8 44.5 1.0
NE2 A:HIS563 4.8 47.7 1.0

Magnesium binding site 2 out of 4 in 5sj4

Go back to Magnesium Binding Sites List in 5sj4
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-5H-Pyrazolo[3,4- D]Pyrimidin-4-One


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- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-5H-Pyrazolo[3,4- D]Pyrimidin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:58.5
occ:1.00
 OD1 B:ASP564 2.0 41.0 1.0
O B:HOH902 2.0 43.5 1.0
O B:HOH915 2.1 33.8 1.0
O B:HOH904 2.5 43.3 1.0
O B:HOH928 2.5 25.0 1.0
CG B:ASP564 3.1 45.2 1.0
OG1 B:THR633 3.2 43.9 1.0
O B:HIS563 3.3 44.2 1.0
OE2 B:GLU592 3.4 47.9 1.0
OD2 B:ASP564 3.5 51.5 1.0
CD2 B:HIS563 3.6 47.4 1.0
CD2 B:HIS595 3.7 58.2 1.0
NE2 B:HIS595 3.7 57.4 1.0
CB B:THR633 4.0 44.5 1.0
ZN B:ZN801 4.0 51.5 1.0
CG B:GLU592 4.1 51.9 1.0
OD2 B:ASP674 4.2 63.1 1.0
CD B:GLU592 4.2 58.6 1.0
NE2 B:HIS563 4.2 46.8 1.0
C B:HIS563 4.3 41.3 1.0
CB B:ASP564 4.3 39.1 1.0
CA B:ASP564 4.4 41.7 1.0
CG B:HIS563 4.6 45.0 1.0
O B:THR633 4.6 36.6 1.0
N B:ASP564 4.8 46.0 1.0
CD2 B:HIS567 4.9 50.9 1.0
C B:THR633 4.9 42.0 1.0
CG2 B:THR633 4.9 41.3 1.0
CE1 B:HIS595 4.9 59.0 1.0
CG B:HIS595 4.9 56.4 1.0

Magnesium binding site 3 out of 4 in 5sj4

Go back to Magnesium Binding Sites List in 5sj4
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-5H-Pyrazolo[3,4- D]Pyrimidin-4-One


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- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-5H-Pyrazolo[3,4- D]Pyrimidin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:44.7
occ:1.00
 O C:HOH934 1.8 35.1 1.0
O C:HOH915 1.9 56.5 1.0
O C:HOH918 2.0 36.8 1.0
O C:HOH914 2.3 17.2 1.0
OD1 C:ASP564 2.3 44.5 1.0
CG C:ASP564 3.4 49.3 1.0
OE2 C:GLU592 3.6 60.6 1.0
OD2 C:ASP564 3.8 56.3 1.0
CD2 C:HIS567 4.1 53.0 1.0
NE2 C:HIS567 4.1 55.1 1.0
O C:HOH917 4.1 52.5 1.0
NE2 C:HIS595 4.2 53.5 1.0
ZN C:ZN801 4.2 46.6 1.0
O C:HOH935 4.4 34.1 1.0
OD2 C:ASP674 4.4 55.8 1.0
CD2 C:HIS595 4.6 51.1 1.0
CD C:GLU592 4.6 54.8 1.0
CD2 C:HIS525 4.6 59.5 1.0
O C:HIS563 4.6 34.9 1.0
CD2 C:HIS563 4.6 43.1 1.0
O C:THR633 4.7 75.3 1.0
O C:HOH937 4.7 47.8 1.0
NE2 C:HIS525 4.7 64.4 1.0
CG C:GLU592 4.7 43.9 1.0
CB C:ASP564 4.7 43.1 1.0
OG1 C:THR633 4.9 67.7 1.0

Magnesium binding site 4 out of 4 in 5sj4

Go back to Magnesium Binding Sites List in 5sj4
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-5H-Pyrazolo[3,4- D]Pyrimidin-4-One


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- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-5H-Pyrazolo[3,4- D]Pyrimidin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:54.3
occ:1.00
 O D:HOH912 2.0 23.8 1.0
O D:HOH916 2.2 48.5 1.0
O D:HOH904 2.2 40.0 1.0
OD1 D:ASP564 2.4 60.7 1.0
CG D:ASP564 3.3 62.2 1.0
OG1 D:THR633 3.4 67.9 1.0
OE2 D:GLU592 3.5 72.5 1.0
O D:HIS563 3.7 66.3 1.0
OD2 D:ASP564 3.7 75.1 1.0
O D:THR633 3.9 54.1 1.0
CD2 D:HIS563 3.9 54.9 1.0
CB D:THR633 4.0 67.7 1.0
ZN D:ZN801 4.0 60.9 1.0
NE2 D:HIS595 4.0 57.7 1.0
CD2 D:HIS595 4.2 72.4 1.0
O D:HOH915 4.2 45.7 1.0
CD D:GLU592 4.3 82.7 1.0
OD2 D:ASP674 4.4 70.1 1.0
CG D:GLU592 4.4 80.5 1.0
C D:THR633 4.5 66.0 1.0
NE2 D:HIS563 4.6 50.8 1.0
CB D:ASP564 4.6 49.6 1.0
C D:HIS563 4.7 54.0 1.0
CA D:ASP564 4.7 50.2 1.0
OD1 D:ASP674 4.9 60.8 1.0
CD2 D:HIS567 4.9 59.0 1.0
CA D:THR633 4.9 60.0 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 04:18:19 2024

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