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Zinc 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:

Magnesium (Mg) 4 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 4 in 5sks

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Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:31.7
occ:1.00
 OD2 A:ASP564 2.0 27.1 1.0
O A:HOH945 2.1 29.2 1.0
O A:HOH965 2.1 28.2 1.0
NE2 A:HIS529 2.1 28.7 1.0
NE2 A:HIS563 2.2 25.1 1.0
OD1 A:ASP674 2.3 29.2 1.0
CD2 A:HIS529 3.0 25.9 1.0
CG A:ASP564 3.1 24.4 1.0
CD2 A:HIS563 3.1 27.0 1.0
CG A:ASP674 3.1 32.4 1.0
CE1 A:HIS563 3.2 31.9 1.0
CE1 A:HIS529 3.2 25.9 1.0
OD2 A:ASP674 3.4 32.5 1.0
OD1 A:ASP564 3.6 22.7 1.0
MG A:MG802 3.8 24.2 1.0
O A:HOH915 4.0 44.3 1.0
CD2 A:HIS525 4.1 27.2 1.0
CG A:HIS529 4.2 28.3 1.0
CG A:HIS563 4.2 25.2 1.0
O A:HOH988 4.2 22.5 1.0
CB A:ASP564 4.3 22.2 1.0
ND1 A:HIS529 4.3 26.2 1.0
ND1 A:HIS563 4.3 24.2 1.0
NE2 A:HIS525 4.4 29.3 1.0
CB A:ASP674 4.5 30.2 1.0
O A:HOH911 4.6 20.3 1.0
CG2 A:VAL533 4.6 21.8 1.0
CA A:ASP674 4.9 27.8 1.0
O A:ASP674 4.9 29.2 1.0

Zinc binding site 2 out of 4 in 5sks

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

b:28.8
occ:1.00
 NE2 B:HIS529 2.1 22.8 1.0
OD2 B:ASP564 2.1 23.7 1.0
OD1 B:ASP674 2.1 28.7 1.0
NE2 B:HIS563 2.1 20.0 1.0
O B:HOH959 2.2 18.2 1.0
O B:HOH947 2.5 28.8 1.0
CG B:ASP674 3.0 27.2 1.0
CD2 B:HIS563 3.0 20.9 1.0
CD2 B:HIS529 3.0 24.9 1.0
CG B:ASP564 3.1 22.6 1.0
CE1 B:HIS529 3.1 24.1 1.0
CE1 B:HIS563 3.2 20.9 1.0
OD2 B:ASP674 3.3 25.0 1.0
OD1 B:ASP564 3.6 20.4 1.0
MG B:MG802 3.9 21.5 1.0
O B:HOH948 3.9 36.6 1.0
O B:HOH989 4.1 19.9 1.0
CD2 B:HIS525 4.1 28.6 1.0
CG B:HIS563 4.2 21.8 1.0
CG B:HIS529 4.2 23.2 1.0
ND1 B:HIS529 4.2 21.0 1.0
ND1 B:HIS563 4.3 22.4 1.0
CB B:ASP564 4.4 20.8 1.0
CB B:ASP674 4.4 25.9 1.0
NE2 B:HIS525 4.4 26.4 1.0
CG2 B:VAL533 4.6 21.6 1.0
O B:HOH950 4.8 23.4 1.0
CA B:ASP674 4.8 23.9 1.0
O B:ASP674 4.9 26.4 1.0

Zinc binding site 3 out of 4 in 5sks

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

b:30.2
occ:1.00
 O C:HOH957 2.1 24.2 1.0
OD1 C:ASP674 2.1 28.2 1.0
NE2 C:HIS529 2.2 29.9 1.0
NE2 C:HIS563 2.2 21.2 1.0
OD2 C:ASP564 2.3 25.1 1.0
O C:HOH933 2.6 31.2 1.0
CG C:ASP674 3.0 26.3 1.0
CD2 C:HIS563 3.0 19.5 1.0
OD2 C:ASP674 3.1 25.1 1.0
CD2 C:HIS529 3.2 24.1 1.0
CG C:ASP564 3.2 24.9 1.0
CE1 C:HIS529 3.2 26.2 1.0
CE1 C:HIS563 3.4 26.9 1.0
OD1 C:ASP564 3.6 23.8 1.0
MG C:MG802 3.9 21.2 1.0
CD2 C:HIS525 4.1 28.1 1.0
O C:HOH1001 4.1 21.6 1.0
O C:HOH956 4.2 35.0 1.0
CG C:HIS563 4.2 22.4 1.0
ND1 C:HIS529 4.3 26.6 1.0
CG C:HIS529 4.3 23.0 1.0
CB C:ASP674 4.4 28.5 1.0
CB C:ASP564 4.4 22.3 1.0
ND1 C:HIS563 4.4 22.5 1.0
NE2 C:HIS525 4.5 29.9 1.0
O C:HOH918 4.5 21.2 1.0
O C:HOH1025 4.7 60.4 1.0
CA C:ASP674 4.8 27.8 1.0
CG2 C:VAL533 4.8 22.9 1.0
O C:ASP674 4.9 27.7 1.0

Zinc binding site 4 out of 4 in 5sks

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

b:42.3
occ:1.00
 NE2 D:HIS563 2.1 31.7 1.0
O D:HOH927 2.1 28.9 1.0
NE2 D:HIS529 2.1 36.7 1.0
OD2 D:ASP564 2.2 45.6 1.0
OD1 D:ASP674 2.3 47.1 1.0
O D:HOH928 2.5 34.8 1.0
CD2 D:HIS563 2.9 35.2 1.0
CD2 D:HIS529 3.0 38.0 1.0
CG D:ASP564 3.1 38.6 1.0
CG D:ASP674 3.2 35.2 1.0
CE1 D:HIS563 3.2 40.3 1.0
CE1 D:HIS529 3.2 37.1 1.0
OD2 D:ASP674 3.4 39.3 1.0
OD1 D:ASP564 3.6 37.9 1.0
MG D:MG802 3.9 37.8 1.0
O D:HOH914 4.1 40.7 1.0
CD2 D:HIS525 4.1 44.8 1.0
O D:HOH937 4.1 29.8 1.0
CG D:HIS563 4.1 36.5 1.0
CB D:ASP564 4.1 37.3 1.0
CG D:HIS529 4.2 34.1 1.0
ND1 D:HIS563 4.2 40.7 1.0
ND1 D:HIS529 4.3 37.3 1.0
NE2 D:HIS525 4.4 44.0 1.0
O D:HOH908 4.5 34.0 1.0
CB D:ASP674 4.5 36.6 1.0
CG2 D:VAL533 4.8 36.8 1.0
O D:ASP674 4.9 43.7 1.0
CA D:ASP674 4.9 36.2 1.0
O D:HOH931 5.0 42.5 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 07:39:42 2024

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