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Zinc 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:

Magnesium (Mg) 4 atoms
Fluorine (F) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc 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 Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sku

Go back to Zinc Binding Sites List in 5sku
Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:30.8
occ:1.00
 OD2 A:ASP564 2.0 28.6 1.0
NE2 A:HIS563 2.1 24.8 1.0
NE2 A:HIS529 2.2 30.2 1.0
OD1 A:ASP674 2.2 32.5 1.0
O A:HOH921 2.2 25.3 1.0
O A:HOH981 2.3 33.1 1.0
CD2 A:HIS563 3.0 24.8 1.0
CG A:ASP674 3.0 31.0 1.0
CD2 A:HIS529 3.1 27.3 1.0
CE1 A:HIS563 3.1 25.2 1.0
CG A:ASP564 3.1 25.7 1.0
CE1 A:HIS529 3.2 28.3 1.0
OD2 A:ASP674 3.2 34.0 1.0
OD1 A:ASP564 3.6 22.7 1.0
MG A:MG802 3.8 23.3 1.0
CG A:HIS563 4.1 26.0 1.0
O A:HOH1007 4.1 24.2 1.0
CD2 A:HIS525 4.1 32.1 1.0
ND1 A:HIS563 4.2 25.0 1.0
O A:HOH1000 4.2 40.1 1.0
CG A:HIS529 4.2 27.8 1.0
ND1 A:HIS529 4.3 29.8 1.0
CB A:ASP564 4.3 24.0 1.0
CB A:ASP674 4.4 29.4 1.0
NE2 A:HIS525 4.5 31.6 1.0
O A:HOH938 4.6 23.2 1.0
CG2 A:VAL533 4.7 24.1 1.0
CA A:ASP674 4.8 26.8 1.0
O A:ASP674 4.9 27.8 1.0

Zinc binding site 2 out of 4 in 5sku

Go back to Zinc Binding Sites List in 5sku
Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:29.0
occ:1.00
 O B:HOH964 2.1 19.5 1.0
NE2 B:HIS563 2.1 24.1 1.0
OD2 B:ASP564 2.1 24.5 1.0
NE2 B:HIS529 2.2 23.3 1.0
OD1 B:ASP674 2.2 24.2 1.0
O B:HOH987 2.5 31.8 1.0
CG B:ASP674 3.1 23.8 1.0
CD2 B:HIS563 3.1 23.1 1.0
CD2 B:HIS529 3.1 24.2 1.0
CE1 B:HIS563 3.1 24.9 1.0
CG B:ASP564 3.1 24.1 1.0
CE1 B:HIS529 3.2 22.8 1.0
OD2 B:ASP674 3.3 27.6 1.0
OD1 B:ASP564 3.6 23.7 1.0
MG B:MG802 3.7 20.0 1.0
O B:HOH1010 4.0 17.7 1.0
CD2 B:HIS525 4.1 25.6 1.0
O B:HOH1008 4.2 39.6 1.0
ND1 B:HIS563 4.2 23.1 1.0
CG B:HIS563 4.2 22.6 1.0
ND1 B:HIS529 4.2 25.0 1.0
CG B:HIS529 4.2 24.1 1.0
CB B:ASP564 4.3 23.0 1.0
CB B:ASP674 4.4 24.6 1.0
NE2 B:HIS525 4.5 25.6 1.0
O B:HOH965 4.7 21.3 1.0
O B:ASP674 4.7 21.7 1.0
CG2 B:VAL533 4.7 21.0 1.0
CA B:ASP674 4.8 23.4 1.0

Zinc binding site 3 out of 4 in 5sku

Go back to Zinc Binding Sites List in 5sku
Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:29.5
occ:1.00
 O C:HOH920 2.1 20.1 1.0
NE2 C:HIS529 2.1 24.8 1.0
OD2 C:ASP564 2.2 25.0 1.0
OD1 C:ASP674 2.2 22.6 1.0
NE2 C:HIS563 2.2 25.1 1.0
O C:HOH982 2.3 33.7 1.0
CG C:ASP674 3.0 23.6 1.0
CD2 C:HIS563 3.0 24.2 1.0
CD2 C:HIS529 3.1 24.6 1.0
OD2 C:ASP674 3.1 23.6 1.0
CE1 C:HIS529 3.1 27.2 1.0
CG C:ASP564 3.2 24.6 1.0
CE1 C:HIS563 3.3 24.8 1.0
OD1 C:ASP564 3.6 22.4 1.0
MG C:MG802 3.8 22.5 1.0
CD2 C:HIS525 4.1 27.1 1.0
O C:HOH1016 4.2 22.5 1.0
CG C:HIS529 4.2 24.4 1.0
O C:HOH1009 4.2 38.1 1.0
ND1 C:HIS529 4.2 26.2 1.0
CG C:HIS563 4.2 23.2 1.0
ND1 C:HIS563 4.3 23.5 1.0
CB C:ASP564 4.4 24.6 1.0
CB C:ASP674 4.4 25.2 1.0
NE2 C:HIS525 4.4 28.1 1.0
O C:HOH945 4.6 26.4 1.0
CA C:ASP674 4.8 26.3 1.0
CG2 C:VAL533 4.8 23.7 1.0
O C:ASP674 4.8 26.9 1.0

Zinc binding site 4 out of 4 in 5sku

Go back to Zinc Binding Sites List in 5sku
Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:40.1
occ:1.00
 OD2 D:ASP564 2.1 36.2 1.0
O D:HOH950 2.2 31.4 1.0
OD1 D:ASP674 2.2 39.4 1.0
NE2 D:HIS563 2.3 26.9 1.0
NE2 D:HIS529 2.3 36.8 1.0
O D:HOH958 2.4 38.0 1.0
CD2 D:HIS563 3.0 29.4 1.0
CG D:ASP674 3.1 36.7 1.0
CG D:ASP564 3.1 32.3 1.0
CD2 D:HIS529 3.2 36.7 1.0
OD2 D:ASP674 3.3 37.7 1.0
CE1 D:HIS529 3.3 36.0 1.0
CE1 D:HIS563 3.5 30.7 1.0
OD1 D:ASP564 3.6 30.4 1.0
MG D:MG802 3.8 36.7 1.0
O D:HOH962 4.0 47.9 1.0
CD2 D:HIS525 4.1 40.9 1.0
O D:HOH959 4.1 25.9 1.0
CG D:HIS563 4.2 28.9 1.0
CB D:ASP564 4.3 32.0 1.0
CG D:HIS529 4.4 35.0 1.0
ND1 D:HIS529 4.4 37.4 1.0
CB D:ASP674 4.4 36.6 1.0
ND1 D:HIS563 4.4 28.2 1.0
NE2 D:HIS525 4.5 42.2 1.0
O D:HOH914 4.6 28.9 1.0
CG2 D:VAL533 4.8 32.3 1.0
O D:ASP674 4.9 38.0 1.0
CA D:ASP674 4.9 37.2 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 Oct 28 07:42:27 2024

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