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Magnesium in PDB 5sku: Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[4- [2-[2-(2-Ethoxy-4-Fluorophenyl)-5-Methyl-1,3-Oxazol-4- Yl]Ethoxy]Naphthalen-1-Yl]-2-Methoxypropanoic Acid

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[4- [2-[2-(2-Ethoxy-4-Fluorophenyl)-5-Methyl-1,3-Oxazol-4- Yl]Ethoxy]Naphthalen-1-Yl]-2-Methoxypropanoic Acid

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[4- [2-[2-(2-Ethoxy-4-Fluorophenyl)-5-Methyl-1,3-Oxazol-4- Yl]Ethoxy]Naphthalen-1-Yl]-2-Methoxypropanoic Acid:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[4- [2-[2-(2-Ethoxy-4-Fluorophenyl)-5-Methyl-1,3-Oxazol-4- Yl]Ethoxy]Naphthalen-1-Yl]-2-Methoxypropanoic Acid, PDB code: 5sku was solved by C.Joseph, J.Benz, A.Flohr, A.Binggeli, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.55 / 2.20
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.289, 135.289, 234.535, 90, 90, 120
R / Rfree (%) 18.1 / 22.5

Other elements in 5sku:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[4- [2-[2-(2-Ethoxy-4-Fluorophenyl)-5-Methyl-1,3-Oxazol-4- Yl]Ethoxy]Naphthalen-1-Yl]-2-Methoxypropanoic Acid also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Fluorine (F) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[4- [2-[2-(2-Ethoxy-4-Fluorophenyl)-5-Methyl-1,3-Oxazol-4- Yl]Ethoxy]Naphthalen-1-Yl]-2-Methoxypropanoic Acid (pdb code 5sku). 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 3-[4- [2-[2-(2-Ethoxy-4-Fluorophenyl)-5-Methyl-1,3-Oxazol-4- Yl]Ethoxy]Naphthalen-1-Yl]-2-Methoxypropanoic Acid, PDB code: 5sku:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sku

Go back to Magnesium Binding Sites List in 5sku
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[4- [2-[2-(2-Ethoxy-4-Fluorophenyl)-5-Methyl-1,3-Oxazol-4- Yl]Ethoxy]Naphthalen-1-Yl]-2-Methoxypropanoic Acid


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 3-[4- [2-[2-(2-Ethoxy-4-Fluorophenyl)-5-Methyl-1,3-Oxazol-4- Yl]Ethoxy]Naphthalen-1-Yl]-2-Methoxypropanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:23.3
occ:1.00
 OD1 A:ASP564 2.0 22.7 1.0
O A:HOH921 2.0 25.3 1.0
O A:HOH1007 2.0 24.2 1.0
O A:HOH938 2.1 23.2 1.0
O A:HOH924 2.1 25.4 1.0
O A:HOH944 2.2 19.7 1.0
CG A:ASP564 3.0 25.7 1.0
OD2 A:ASP564 3.4 28.6 1.0
ZN A:ZN801 3.8 30.8 1.0
NE2 A:HIS595 3.9 22.7 1.0
O A:HOH981 4.0 33.1 1.0
OE2 A:GLU592 4.1 32.0 1.0
CD2 A:HIS567 4.2 30.7 1.0
CD2 A:HIS595 4.2 24.9 1.0
CD2 A:HIS563 4.3 24.8 1.0
O A:HIS563 4.3 25.9 1.0
CB A:ASP564 4.3 24.0 1.0
OG1 A:THR633 4.4 30.8 1.0
OD2 A:ASP674 4.5 34.0 1.0
NE2 A:HIS567 4.5 31.7 1.0
O A:HOH972 4.5 32.7 1.0
O A:THR633 4.5 28.7 1.0
NE2 A:HIS563 4.6 24.8 1.0
CD2 A:HIS525 4.7 32.1 1.0
CA A:ASP564 4.7 26.5 1.0
NE2 A:HIS525 4.7 31.6 1.0
CB A:THR633 4.7 28.7 1.0
CG A:GLU592 4.9 29.6 1.0
CD A:GLU592 4.9 30.8 1.0

Magnesium binding site 2 out of 4 in 5sku

Go back to Magnesium Binding Sites List in 5sku
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[4- [2-[2-(2-Ethoxy-4-Fluorophenyl)-5-Methyl-1,3-Oxazol-4- Yl]Ethoxy]Naphthalen-1-Yl]-2-Methoxypropanoic Acid


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 3-[4- [2-[2-(2-Ethoxy-4-Fluorophenyl)-5-Methyl-1,3-Oxazol-4- Yl]Ethoxy]Naphthalen-1-Yl]-2-Methoxypropanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:20.0
occ:1.00
 O B:HOH965 1.9 21.3 1.0
O B:HOH964 1.9 19.5 1.0
O B:HOH1005 2.1 19.6 1.0
OD1 B:ASP564 2.1 23.7 1.0
O B:HOH1010 2.1 17.7 1.0
O B:HOH932 2.1 16.7 1.0
CG B:ASP564 3.1 24.1 1.0
OD2 B:ASP564 3.5 24.5 1.0
ZN B:ZN801 3.7 29.0 1.0
O B:HOH987 3.9 31.8 1.0
CD2 B:HIS563 4.1 23.1 1.0
OG1 B:THR633 4.2 23.6 1.0
OE2 B:GLU592 4.2 23.4 1.0
NE2 B:HIS595 4.2 25.3 1.0
O B:HIS563 4.3 27.3 1.0
OD2 B:ASP674 4.3 27.6 1.0
CD2 B:HIS567 4.3 27.9 1.0
O B:HOH950 4.4 30.7 1.0
CD2 B:HIS595 4.4 27.5 1.0
NE2 B:HIS563 4.4 24.1 1.0
NE2 B:HIS567 4.5 27.9 1.0
CB B:ASP564 4.5 23.0 1.0
O B:THR633 4.5 23.8 1.0
CB B:THR633 4.7 24.0 1.0
CD2 B:HIS525 4.7 25.6 1.0
NE2 B:HIS525 4.8 25.6 1.0
CA B:ASP564 4.8 24.4 1.0
CG B:GLU592 4.8 22.9 1.0
CD B:GLU592 4.9 22.9 1.0

Magnesium binding site 3 out of 4 in 5sku

Go back to Magnesium Binding Sites List in 5sku
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[4- [2-[2-(2-Ethoxy-4-Fluorophenyl)-5-Methyl-1,3-Oxazol-4- Yl]Ethoxy]Naphthalen-1-Yl]-2-Methoxypropanoic Acid


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 3-[4- [2-[2-(2-Ethoxy-4-Fluorophenyl)-5-Methyl-1,3-Oxazol-4- Yl]Ethoxy]Naphthalen-1-Yl]-2-Methoxypropanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:22.5
occ:1.00
 O C:HOH991 2.0 25.7 1.0
OD1 C:ASP564 2.0 22.4 1.0
O C:HOH1016 2.0 22.5 1.0
O C:HOH920 2.1 20.1 1.0
O C:HOH945 2.1 26.4 1.0
O C:HOH930 2.2 19.3 1.0
CG C:ASP564 3.1 24.6 1.0
OD2 C:ASP564 3.5 25.0 1.0
ZN C:ZN801 3.8 29.5 1.0
OE2 C:GLU592 4.0 27.1 1.0
NE2 C:HIS595 4.0 27.0 1.0
CD2 C:HIS563 4.2 24.2 1.0
CD2 C:HIS567 4.2 29.4 1.0
OG1 C:THR633 4.2 23.8 1.0
O C:HOH982 4.2 33.7 1.0
O C:HOH943 4.2 32.4 1.0
CD2 C:HIS595 4.3 25.4 1.0
O C:HIS563 4.3 22.5 1.0
OD2 C:ASP674 4.4 23.6 1.0
CB C:ASP564 4.4 24.6 1.0
NE2 C:HIS567 4.4 29.6 1.0
O C:THR633 4.5 27.3 1.0
NE2 C:HIS563 4.6 25.1 1.0
CB C:THR633 4.6 24.4 1.0
CA C:ASP564 4.7 25.6 1.0
CG C:GLU592 4.7 26.1 1.0
CD2 C:HIS525 4.7 27.1 1.0
NE2 C:HIS525 4.8 28.1 1.0
CD C:GLU592 4.8 27.4 1.0

Magnesium binding site 4 out of 4 in 5sku

Go back to Magnesium Binding Sites List in 5sku
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[4- [2-[2-(2-Ethoxy-4-Fluorophenyl)-5-Methyl-1,3-Oxazol-4- Yl]Ethoxy]Naphthalen-1-Yl]-2-Methoxypropanoic Acid


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 3-[4- [2-[2-(2-Ethoxy-4-Fluorophenyl)-5-Methyl-1,3-Oxazol-4- Yl]Ethoxy]Naphthalen-1-Yl]-2-Methoxypropanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:36.7
occ:1.00
 O D:HOH950 2.0 31.4 1.0
OD1 D:ASP564 2.1 30.4 1.0
O D:HOH959 2.1 25.9 1.0
O D:HOH910 2.1 31.9 1.0
O D:HOH942 2.1 30.2 1.0
O D:HOH914 2.2 28.9 1.0
CG D:ASP564 3.1 32.3 1.0
OD2 D:ASP564 3.5 36.2 1.0
ZN D:ZN801 3.8 40.1 1.0
O D:HOH958 3.9 38.0 1.0
NE2 D:HIS595 3.9 38.0 1.0
OE2 D:GLU592 4.0 36.0 1.0
CD2 D:HIS567 4.1 36.7 1.0
O D:HOH961 4.2 42.3 1.0
OG1 D:THR633 4.2 32.6 1.0
CD2 D:HIS595 4.3 35.6 1.0
O D:HIS563 4.3 32.5 1.0
NE2 D:HIS567 4.3 37.0 1.0
CD2 D:HIS563 4.4 29.4 1.0
CB D:ASP564 4.4 32.0 1.0
OD2 D:ASP674 4.5 37.7 1.0
CD2 D:HIS525 4.5 40.9 1.0
O D:THR633 4.6 35.6 1.0
NE2 D:HIS525 4.7 42.2 1.0
CA D:ASP564 4.7 31.6 1.0
CB D:THR633 4.8 34.7 1.0
CD D:GLU592 4.8 36.3 1.0
NE2 D:HIS563 4.9 26.9 1.0
CG D:GLU592 4.9 38.0 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 04:39:50 2024

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