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Magnesium in PDB 5shn: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-N-(1,3-Oxazol-2-Ylmethyl)-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 2- Methyl-4-N-(1,3-Oxazol-2-Ylmethyl)-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 2- Methyl-4-N-(1,3-Oxazol-2-Ylmethyl)-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 2- Methyl-4-N-(1,3-Oxazol-2-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-7-Yl)Pyrazole-3,4-Dicarboxamide, PDB code: 5shn 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) 43.53 / 2.03
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.319, 135.319, 235.517, 90, 90, 120
R / Rfree (%) 18.2 / 23.4

Other elements in 5shn:

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

Magnesium binding site 1 out of 4 in 5shn

Go back to Magnesium Binding Sites List in 5shn
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-N-(1,3-Oxazol-2-Ylmethyl)-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 2- Methyl-4-N-(1,3-Oxazol-2-Ylmethyl)-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:23.1
occ:1.00
 O A:HOH1009 1.9 23.0 1.0
OD1 A:ASP564 1.9 22.1 1.0
O A:HOH953 2.0 22.6 1.0
O A:HOH962 2.1 23.4 1.0
O A:HOH973 2.1 19.4 1.0
O A:HOH954 2.2 24.5 1.0
CG A:ASP564 3.0 25.7 1.0
OD2 A:ASP564 3.4 27.6 1.0
ZN A:ZN801 3.8 29.2 1.0
OE2 A:GLU592 4.0 28.8 1.0
O A:HOH997 4.0 30.8 1.0
NE2 A:HIS595 4.1 25.5 1.0
CD2 A:HIS563 4.2 20.6 1.0
CD2 A:HIS567 4.3 27.9 1.0
CD2 A:HIS595 4.3 22.1 1.0
O A:HIS563 4.3 24.3 1.0
OG1 A:THR633 4.3 25.7 1.0
CB A:ASP564 4.3 22.2 1.0
O A:HOH1011 4.3 36.2 1.0
NE2 A:HIS567 4.4 28.3 1.0
OD2 A:ASP674 4.4 35.7 1.0
NE2 A:HIS563 4.6 24.4 1.0
O A:THR633 4.6 27.8 1.0
CD2 A:HIS525 4.7 31.9 1.0
NE2 A:HIS525 4.7 30.2 1.0
CB A:THR633 4.7 25.5 1.0
CA A:ASP564 4.8 22.9 1.0
CG A:GLU592 4.8 28.8 1.0
CD A:GLU592 4.8 30.0 1.0

Magnesium binding site 2 out of 4 in 5shn

Go back to Magnesium Binding Sites List in 5shn
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-N-(1,3-Oxazol-2-Ylmethyl)-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 2- Methyl-4-N-(1,3-Oxazol-2-Ylmethyl)-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:21.3
occ:1.00
 O B:HOH979 1.9 19.3 1.0
O B:HOH926 2.0 18.8 1.0
OD1 B:ASP564 2.0 22.8 1.0
O B:HOH993 2.1 21.5 1.0
O B:HOH992 2.1 22.2 1.0
O B:HOH1003 2.1 26.8 1.0
CG B:ASP564 3.0 22.4 1.0
OD2 B:ASP564 3.3 22.0 1.0
ZN B:ZN801 3.7 27.7 1.0
O B:HOH1029 3.8 53.0 1.0
O B:HOH952 3.9 29.1 1.0
NE2 B:HIS595 4.1 22.4 1.0
CD2 B:HIS563 4.2 22.0 1.0
OE2 B:GLU592 4.2 28.2 1.0
O B:HIS563 4.2 24.9 1.0
OG1 B:THR633 4.3 27.7 1.0
CD2 B:HIS567 4.3 27.0 1.0
OD2 B:ASP674 4.3 26.0 1.0
CB B:ASP564 4.4 21.0 1.0
O B:HOH985 4.4 34.2 1.0
CD2 B:HIS595 4.4 24.1 1.0
NE2 B:HIS567 4.4 23.4 1.0
CD2 B:HIS525 4.5 27.2 1.0
NE2 B:HIS563 4.6 20.9 1.0
O B:THR633 4.6 20.8 1.0
NE2 B:HIS525 4.6 30.8 1.0
CA B:ASP564 4.7 23.5 1.0
CB B:THR633 4.7 24.9 1.0
CG B:GLU592 4.8 26.4 1.0
CD B:GLU592 5.0 24.9 1.0
C B:HIS563 5.0 21.3 1.0

Magnesium binding site 3 out of 4 in 5shn

Go back to Magnesium Binding Sites List in 5shn
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-N-(1,3-Oxazol-2-Ylmethyl)-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 2- Methyl-4-N-(1,3-Oxazol-2-Ylmethyl)-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:26.7
occ:1.00
 O C:HOH932 1.9 30.0 1.0
O C:HOH993 2.0 25.3 1.0
O C:HOH1027 2.1 25.1 1.0
OD1 C:ASP564 2.1 20.9 1.0
O C:HOH969 2.1 22.6 1.0
O C:HOH931 2.2 23.5 1.0
CG C:ASP564 3.1 25.4 1.0
OD2 C:ASP564 3.4 24.2 1.0
ZN C:ZN801 3.8 30.6 1.0
O C:HOH963 4.1 49.5 1.0
O C:HOH1000 4.1 34.9 1.0
OE2 C:GLU592 4.1 31.4 1.0
NE2 C:HIS595 4.1 24.4 1.0
CD2 C:HIS567 4.2 28.3 1.0
NE2 C:HIS567 4.2 26.1 1.0
CD2 C:HIS563 4.3 23.7 1.0
OG1 C:THR633 4.3 29.3 1.0
O C:HOH1004 4.3 30.5 1.0
OD2 C:ASP674 4.4 31.9 1.0
CD2 C:HIS595 4.4 25.9 1.0
O C:HIS563 4.5 25.5 1.0
CB C:ASP564 4.5 22.7 1.0
O C:THR633 4.5 27.4 1.0
CD2 C:HIS525 4.7 34.4 1.0
NE2 C:HIS525 4.7 33.0 1.0
NE2 C:HIS563 4.7 25.8 1.0
CG C:GLU592 4.7 25.0 1.0
CB C:THR633 4.8 28.4 1.0
CA C:ASP564 4.8 23.5 1.0
CD C:GLU592 4.9 26.7 1.0

Magnesium binding site 4 out of 4 in 5shn

Go back to Magnesium Binding Sites List in 5shn
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-N-(1,3-Oxazol-2-Ylmethyl)-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 2- Methyl-4-N-(1,3-Oxazol-2-Ylmethyl)-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:31.2
occ:1.00
 O D:HOH980 2.0 29.2 1.0
O D:HOH930 2.0 30.2 1.0
O D:HOH974 2.0 28.8 1.0
O D:HOH919 2.2 28.9 1.0
O D:HOH918 2.2 21.1 1.0
OD1 D:ASP564 2.2 29.4 1.0
CG D:ASP564 3.2 29.7 1.0
OD2 D:ASP564 3.6 33.3 1.0
O D:HOH986 3.8 38.1 1.0
ZN D:ZN801 3.9 35.5 1.0
OE2 D:GLU592 4.0 36.0 1.0
O D:HOH982 4.1 38.7 1.0
NE2 D:HIS595 4.2 30.1 1.0
OG1 D:THR633 4.2 30.2 1.0
OD2 D:ASP674 4.3 35.6 1.0
CD2 D:HIS563 4.4 28.7 1.0
CD2 D:HIS595 4.4 30.7 1.0
CD2 D:HIS567 4.4 37.4 1.0
O D:HIS563 4.4 29.4 1.0
O D:THR633 4.5 38.5 1.0
CB D:ASP564 4.6 29.3 1.0
CD2 D:HIS525 4.6 34.4 1.0
CB D:THR633 4.7 33.2 1.0
NE2 D:HIS567 4.7 36.5 1.0
NE2 D:HIS525 4.7 40.4 1.0
NE2 D:HIS563 4.8 22.4 1.0
O D:HOH988 4.9 34.0 1.0
CA D:ASP564 4.9 26.3 1.0
CG D:GLU592 4.9 34.2 1.0
CD D:GLU592 4.9 35.2 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 04:00:22 2024

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