Atomistry » Magnesium » PDB 5skf-5t2v » 5sku
Atomistry »
  Magnesium »
    PDB 5skf-5t2v »
      5sku »

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

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy