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Magnesium in PDB 5si9: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- (2-Hydroxyethyl)-2-Methyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl) Pyrazole-3,4-Dicarboxamide

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

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

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- (2-Hydroxyethyl)-2-Methyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl) Pyrazole-3,4-Dicarboxamide, PDB code: 5si9 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) 43.91 / 2.01
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 136.254, 136.254, 236.528, 90, 90, 120
R / Rfree (%) 18.7 / 22.2

Other elements in 5si9:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- (2-Hydroxyethyl)-2-Methyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl) Pyrazole-3,4-Dicarboxamide 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-N- (2-Hydroxyethyl)-2-Methyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl) Pyrazole-3,4-Dicarboxamide (pdb code 5si9). 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-N- (2-Hydroxyethyl)-2-Methyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl) Pyrazole-3,4-Dicarboxamide, PDB code: 5si9:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5si9

Go back to Magnesium Binding Sites List in 5si9
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- (2-Hydroxyethyl)-2-Methyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl) Pyrazole-3,4-Dicarboxamide


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-N- (2-Hydroxyethyl)-2-Methyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl) Pyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:26.1
occ:1.00
 O A:HOH1016 1.9 24.4 1.0
O A:HOH924 2.0 25.8 1.0
OD1 A:ASP564 2.0 25.2 1.0
O A:HOH927 2.1 23.5 1.0
O A:HOH984 2.1 21.9 1.0
O A:HOH934 2.1 26.6 1.0
CG A:ASP564 3.0 27.1 1.0
OD2 A:ASP564 3.4 28.6 1.0
ZN A:ZN801 3.8 30.4 1.0
O A:HOH993 3.9 32.1 1.0
O A:HOH1034 4.0 51.4 1.0
OE2 A:GLU592 4.0 30.6 1.0
NE2 A:HIS595 4.1 27.7 1.0
O A:HIS563 4.3 25.7 1.0
OG1 A:THR633 4.3 26.1 1.0
CD2 A:HIS567 4.3 29.8 1.0
CD2 A:HIS563 4.3 24.7 1.0
CD2 A:HIS595 4.3 26.8 1.0
CB A:ASP564 4.4 25.9 1.0
OD2 A:ASP674 4.4 36.1 1.0
O A:HOH988 4.5 33.9 1.0
NE2 A:HIS567 4.5 30.2 1.0
O A:THR633 4.6 30.5 1.0
CD2 A:HIS525 4.6 32.2 1.0
NE2 A:HIS525 4.7 31.0 1.0
CB A:THR633 4.7 26.0 1.0
NE2 A:HIS563 4.7 26.1 1.0
CA A:ASP564 4.8 25.8 1.0
CG A:GLU592 4.8 30.1 1.0
CD A:GLU592 4.8 32.2 1.0

Magnesium binding site 2 out of 4 in 5si9

Go back to Magnesium Binding Sites List in 5si9
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- (2-Hydroxyethyl)-2-Methyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl) Pyrazole-3,4-Dicarboxamide


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-N- (2-Hydroxyethyl)-2-Methyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl) Pyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:26.4
occ:1.00
 O B:HOH974 1.9 23.9 1.0
O B:HOH940 2.0 19.5 1.0
O B:HOH1003 2.0 21.8 1.0
OD1 B:ASP564 2.1 25.9 1.0
O B:HOH1018 2.1 25.7 1.0
O B:HOH939 2.1 24.6 1.0
CG B:ASP564 3.1 25.3 1.0
OD2 B:ASP564 3.4 24.0 1.0
ZN B:ZN801 3.8 29.2 1.0
O B:HOH980 3.8 35.8 1.0
O B:HOH1049 3.9 48.1 1.0
NE2 B:HIS595 4.1 24.3 1.0
OE2 B:GLU592 4.1 31.5 1.0
CD2 B:HIS567 4.3 29.1 1.0
CD2 B:HIS563 4.3 22.9 1.0
OG1 B:THR633 4.3 27.4 1.0
O B:HIS563 4.3 29.2 1.0
CD2 B:HIS595 4.3 25.6 1.0
O B:HOH979 4.3 29.8 1.0
OD2 B:ASP674 4.4 30.1 1.0
CB B:ASP564 4.5 24.4 1.0
NE2 B:HIS567 4.5 27.8 1.0
O B:THR633 4.6 26.1 1.0
NE2 B:HIS563 4.6 22.6 1.0
CD2 B:HIS525 4.6 28.3 1.0
CB B:THR633 4.7 27.4 1.0
NE2 B:HIS525 4.7 29.2 1.0
CA B:ASP564 4.8 25.1 1.0
CG B:GLU592 4.9 30.1 1.0
CD B:GLU592 4.9 28.9 1.0

Magnesium binding site 3 out of 4 in 5si9

Go back to Magnesium Binding Sites List in 5si9
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- (2-Hydroxyethyl)-2-Methyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl) Pyrazole-3,4-Dicarboxamide


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-N- (2-Hydroxyethyl)-2-Methyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl) Pyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:25.5
occ:1.00
 O C:HOH1002 2.0 25.8 1.0
O C:HOH970 2.0 24.0 1.0
O C:HOH1026 2.1 24.4 1.0
O C:HOH919 2.1 22.5 1.0
OD1 C:ASP564 2.1 24.5 1.0
O C:HOH933 2.2 21.5 1.0
CG C:ASP564 3.1 25.3 1.0
OD2 C:ASP564 3.5 24.7 1.0
ZN C:ZN801 3.8 30.3 1.0
O C:HOH1011 4.0 33.1 1.0
OE2 C:GLU592 4.0 32.0 1.0
NE2 C:HIS595 4.1 27.8 1.0
OG1 C:THR633 4.3 26.1 1.0
CD2 C:HIS567 4.3 29.6 1.0
OD2 C:ASP674 4.3 34.1 1.0
CD2 C:HIS563 4.3 26.3 1.0
O C:HOH1016 4.3 30.6 1.0
O C:HIS563 4.3 25.6 1.0
CD2 C:HIS595 4.4 26.7 1.0
CB C:ASP564 4.5 24.5 1.0
NE2 C:HIS567 4.5 29.4 1.0
O C:THR633 4.5 26.9 1.0
O C:HOH1034 4.7 53.4 1.0
CD2 C:HIS525 4.7 30.1 1.0
CB C:THR633 4.7 26.9 1.0
NE2 C:HIS563 4.7 27.6 1.0
NE2 C:HIS525 4.8 30.6 1.0
CG C:GLU592 4.8 28.4 1.0
CA C:ASP564 4.8 25.8 1.0
CD C:GLU592 4.8 29.7 1.0

Magnesium binding site 4 out of 4 in 5si9

Go back to Magnesium Binding Sites List in 5si9
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- (2-Hydroxyethyl)-2-Methyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl) Pyrazole-3,4-Dicarboxamide


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-N- (2-Hydroxyethyl)-2-Methyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl) Pyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:33.0
occ:1.00
 O D:HOH919 2.0 33.2 1.0
O D:HOH979 2.1 26.6 1.0
O D:HOH905 2.1 26.5 1.0
O D:HOH917 2.1 24.9 1.0
OD1 D:ASP564 2.2 32.3 1.0
O D:HOH980 2.2 30.5 1.0
CG D:ASP564 3.2 29.9 1.0
OD2 D:ASP564 3.6 30.7 1.0
ZN D:ZN801 3.9 35.3 1.0
OE2 D:GLU592 3.9 35.4 1.0
O D:HOH988 4.0 35.2 1.0
NE2 D:HIS595 4.1 33.5 1.0
OG1 D:THR633 4.2 31.0 1.0
O D:HOH974 4.3 36.8 1.0
CD2 D:HIS563 4.3 28.9 1.0
CD2 D:HIS567 4.3 36.3 1.0
CD2 D:HIS595 4.3 34.5 1.0
O D:HIS563 4.4 30.0 1.0
OD2 D:ASP674 4.4 38.4 1.0
O D:THR633 4.5 37.9 1.0
CB D:ASP564 4.5 29.4 1.0
NE2 D:HIS567 4.6 34.9 1.0
CB D:THR633 4.6 32.4 1.0
CD2 D:HIS525 4.7 36.2 1.0
NE2 D:HIS563 4.8 26.9 1.0
NE2 D:HIS525 4.8 39.5 1.0
CD D:GLU592 4.8 38.8 1.0
CA D:ASP564 4.9 30.0 1.0
CG D:GLU592 4.9 38.8 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 04:08:06 2024

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