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Magnesium in PDB 5sks: Crystal Structure of Human Phosphodiesterase 10 in Complex with Ethyl 1-[3-[3-(4-Ethoxycarbonyl-5-Methyl-Imidazol-1-Yl)Phenoxy]Phenyl]-5- Methyl-Imidazole-4-Carboxylate

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with Ethyl 1-[3-[3-(4-Ethoxycarbonyl-5-Methyl-Imidazol-1-Yl)Phenoxy]Phenyl]-5- Methyl-Imidazole-4-Carboxylate

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with Ethyl 1-[3-[3-(4-Ethoxycarbonyl-5-Methyl-Imidazol-1-Yl)Phenoxy]Phenyl]-5- Methyl-Imidazole-4-Carboxylate:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with Ethyl 1-[3-[3-(4-Ethoxycarbonyl-5-Methyl-Imidazol-1-Yl)Phenoxy]Phenyl]-5- Methyl-Imidazole-4-Carboxylate, PDB code: 5sks was solved by C.Joseph, J.Benz, A.Flohr, H.Knust, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.64 / 2.31
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 134.92, 134.92, 235.24, 90, 90, 120
R / Rfree (%) 15.5 / 21.4

Other elements in 5sks:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with Ethyl 1-[3-[3-(4-Ethoxycarbonyl-5-Methyl-Imidazol-1-Yl)Phenoxy]Phenyl]-5- Methyl-Imidazole-4-Carboxylate 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 Ethyl 1-[3-[3-(4-Ethoxycarbonyl-5-Methyl-Imidazol-1-Yl)Phenoxy]Phenyl]-5- Methyl-Imidazole-4-Carboxylate (pdb code 5sks). 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 Ethyl 1-[3-[3-(4-Ethoxycarbonyl-5-Methyl-Imidazol-1-Yl)Phenoxy]Phenyl]-5- Methyl-Imidazole-4-Carboxylate, PDB code: 5sks:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sks

Go back to Magnesium Binding Sites List in 5sks
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with Ethyl 1-[3-[3-(4-Ethoxycarbonyl-5-Methyl-Imidazol-1-Yl)Phenoxy]Phenyl]-5- Methyl-Imidazole-4-Carboxylate


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 Ethyl 1-[3-[3-(4-Ethoxycarbonyl-5-Methyl-Imidazol-1-Yl)Phenoxy]Phenyl]-5- Methyl-Imidazole-4-Carboxylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:24.2
occ:1.00
 O A:HOH988 2.0 22.5 1.0
O A:HOH937 2.1 24.1 1.0
O A:HOH945 2.1 29.2 1.0
O A:HOH911 2.1 20.3 1.0
OD1 A:ASP564 2.1 22.7 1.0
O A:HOH936 2.1 24.6 1.0
CG A:ASP564 3.1 24.4 1.0
OD2 A:ASP564 3.4 27.1 1.0
O A:HOH965 3.8 28.2 1.0
ZN A:ZN801 3.8 31.7 1.0
O A:HOH963 4.0 34.4 1.0
NE2 A:HIS595 4.1 26.2 1.0
OE2 A:GLU592 4.1 28.7 1.0
CD2 A:HIS567 4.3 30.8 1.0
O A:HIS563 4.4 28.2 1.0
OG1 A:THR633 4.4 29.1 1.0
CD2 A:HIS563 4.4 27.0 1.0
CB A:ASP564 4.4 22.2 1.0
NE2 A:HIS567 4.5 32.5 1.0
NE2 A:HIS525 4.5 29.3 1.0
O A:THR633 4.5 28.1 1.0
CD2 A:HIS525 4.5 27.2 1.0
CD2 A:HIS595 4.5 27.8 1.0
OD2 A:ASP674 4.6 32.5 1.0
NE2 A:HIS563 4.7 25.1 1.0
CB A:THR633 4.8 27.8 1.0
CA A:ASP564 4.8 25.4 1.0
CG A:GLU592 4.9 26.8 1.0
CD A:GLU592 4.9 31.7 1.0

Magnesium binding site 2 out of 4 in 5sks

Go back to Magnesium Binding Sites List in 5sks
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with Ethyl 1-[3-[3-(4-Ethoxycarbonyl-5-Methyl-Imidazol-1-Yl)Phenoxy]Phenyl]-5- Methyl-Imidazole-4-Carboxylate


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 Ethyl 1-[3-[3-(4-Ethoxycarbonyl-5-Methyl-Imidazol-1-Yl)Phenoxy]Phenyl]-5- Methyl-Imidazole-4-Carboxylate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:21.5
occ:1.00
 O B:HOH950 2.0 23.4 1.0
O B:HOH931 2.0 20.9 1.0
O B:HOH959 2.1 18.2 1.0
OD1 B:ASP564 2.1 20.4 1.0
O B:HOH914 2.1 15.6 1.0
O B:HOH989 2.1 19.9 1.0
CG B:ASP564 3.2 22.6 1.0
OD2 B:ASP564 3.6 23.7 1.0
NE2 B:HIS595 3.9 24.5 1.0
ZN B:ZN801 3.9 28.8 1.0
OE2 B:GLU592 4.0 26.2 1.0
O B:HOH947 4.1 28.8 1.0
OG1 B:THR633 4.2 24.6 1.0
O B:HOH997 4.2 28.7 1.0
O B:HIS563 4.2 27.0 1.0
CD2 B:HIS595 4.2 24.3 1.0
CD2 B:HIS567 4.3 27.2 1.0
CD2 B:HIS563 4.3 20.9 1.0
O B:THR633 4.4 24.7 1.0
NE2 B:HIS567 4.5 26.7 1.0
CB B:ASP564 4.5 20.8 1.0
OD2 B:ASP674 4.5 25.0 1.0
CB B:THR633 4.6 26.4 1.0
CD2 B:HIS525 4.7 28.6 1.0
NE2 B:HIS563 4.7 20.0 1.0
CA B:ASP564 4.7 24.3 1.0
NE2 B:HIS525 4.7 26.4 1.0
CG B:GLU592 4.8 25.7 1.0
CD B:GLU592 4.8 26.6 1.0
O B:HOH998 4.9 28.8 1.0

Magnesium binding site 3 out of 4 in 5sks

Go back to Magnesium Binding Sites List in 5sks
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with Ethyl 1-[3-[3-(4-Ethoxycarbonyl-5-Methyl-Imidazol-1-Yl)Phenoxy]Phenyl]-5- Methyl-Imidazole-4-Carboxylate


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 Ethyl 1-[3-[3-(4-Ethoxycarbonyl-5-Methyl-Imidazol-1-Yl)Phenoxy]Phenyl]-5- Methyl-Imidazole-4-Carboxylate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:21.2
occ:1.00
 O C:HOH976 1.9 24.3 1.0
O C:HOH937 2.0 21.8 1.0
O C:HOH918 2.0 21.2 1.0
OD1 C:ASP564 2.1 23.8 1.0
O C:HOH957 2.1 24.2 1.0
O C:HOH1001 2.1 21.6 1.0
CG C:ASP564 3.1 24.9 1.0
OD2 C:ASP564 3.5 25.1 1.0
ZN C:ZN801 3.9 30.2 1.0
NE2 C:HIS595 3.9 25.9 1.0
OE2 C:GLU592 3.9 29.1 1.0
O C:HOH933 4.0 31.2 1.0
O C:HOH980 4.1 27.4 1.0
CD2 C:HIS567 4.2 26.1 1.0
O C:HIS563 4.3 24.2 1.0
OG1 C:THR633 4.3 25.5 1.0
CD2 C:HIS595 4.3 29.4 1.0
O C:HOH1025 4.3 60.4 1.0
NE2 C:HIS567 4.4 27.4 1.0
CD2 C:HIS563 4.4 19.5 1.0
O C:THR633 4.5 28.1 1.0
CB C:ASP564 4.5 22.3 1.0
OD2 C:ASP674 4.5 25.1 1.0
CB C:THR633 4.7 25.1 1.0
CD2 C:HIS525 4.7 28.1 1.0
CG C:GLU592 4.7 26.6 1.0
CD C:GLU592 4.8 29.1 1.0
NE2 C:HIS525 4.8 29.9 1.0
CA C:ASP564 4.8 25.3 1.0
NE2 C:HIS563 4.9 21.2 1.0
CE1 C:HIS595 5.0 27.4 1.0

Magnesium binding site 4 out of 4 in 5sks

Go back to Magnesium Binding Sites List in 5sks
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with Ethyl 1-[3-[3-(4-Ethoxycarbonyl-5-Methyl-Imidazol-1-Yl)Phenoxy]Phenyl]-5- Methyl-Imidazole-4-Carboxylate


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 Ethyl 1-[3-[3-(4-Ethoxycarbonyl-5-Methyl-Imidazol-1-Yl)Phenoxy]Phenyl]-5- Methyl-Imidazole-4-Carboxylate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:37.8
occ:1.00
 OD1 D:ASP564 2.0 37.9 1.0
O D:HOH939 2.0 38.6 1.0
O D:HOH931 2.1 42.5 1.0
O D:HOH937 2.1 29.8 1.0
O D:HOH927 2.2 28.9 1.0
O D:HOH908 2.3 34.0 1.0
CG D:ASP564 3.0 38.6 1.0
OD2 D:ASP564 3.3 45.6 1.0
O D:HOH950 3.8 36.2 1.0
ZN D:ZN801 3.9 42.3 1.0
NE2 D:HIS595 4.0 40.7 1.0
CD2 D:HIS567 4.0 37.0 1.0
OE2 D:GLU592 4.0 41.9 1.0
O D:HOH928 4.0 34.8 1.0
NE2 D:HIS567 4.2 40.5 1.0
OG1 D:THR633 4.3 36.1 1.0
CB D:ASP564 4.3 37.3 1.0
CD2 D:HIS595 4.3 43.4 1.0
CD2 D:HIS563 4.4 35.2 1.0
O D:HIS563 4.4 38.4 1.0
CD2 D:HIS525 4.5 44.8 1.0
NE2 D:HIS525 4.5 44.0 1.0
O D:THR633 4.6 45.9 1.0
OD2 D:ASP674 4.6 39.3 1.0
CA D:ASP564 4.7 35.7 1.0
NE2 D:HIS563 4.8 31.7 1.0
CD D:GLU592 4.8 38.0 1.0
CB D:THR633 4.9 38.0 1.0
CG D:GLU592 4.9 43.4 1.0
O D:HOH961 5.0 44.6 1.0
CE1 D:HIS595 5.0 42.1 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: Wed Apr 5 11:44:23 2023

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