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Zinc in PDB 5sg0: Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-3-(2-Phenylpyrazol-3-Yl) Imidazolidin-2-One

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-3-(2-Phenylpyrazol-3-Yl) Imidazolidin-2-One

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-3-(2-Phenylpyrazol-3-Yl) Imidazolidin-2-One:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-3-(2-Phenylpyrazol-3-Yl) Imidazolidin-2-One, PDB code: 5sg0 was solved by C.Joseph, J.Benz, A.Flohr, M.Koerner, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.57 / 2.06
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.456, 135.456, 235.611, 90, 90, 120
R / Rfree (%) 18.9 / 22.3

Other elements in 5sg0:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-3-(2-Phenylpyrazol-3-Yl) Imidazolidin-2-One 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 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-3-(2-Phenylpyrazol-3-Yl) Imidazolidin-2-One (pdb code 5sg0). 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 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-3-(2-Phenylpyrazol-3-Yl) Imidazolidin-2-One, PDB code: 5sg0:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sg0

Go back to Zinc Binding Sites List in 5sg0
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-3-(2-Phenylpyrazol-3-Yl) Imidazolidin-2-One


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 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-3-(2-Phenylpyrazol-3-Yl) Imidazolidin-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:27.0
occ:1.00
 OD2 A:ASP564 2.1 23.6 1.0
OD1 A:ASP674 2.1 23.4 1.0
NE2 A:HIS563 2.2 20.1 1.0
NE2 A:HIS529 2.2 23.2 1.0
O A:HOH969 2.2 21.2 1.0
O A:HOH993 2.3 21.6 1.0
CD2 A:HIS563 3.0 20.4 1.0
CG A:ASP674 3.0 24.2 1.0
CG A:ASP564 3.1 22.3 1.0
CD2 A:HIS529 3.1 23.3 1.0
CE1 A:HIS529 3.1 23.3 1.0
CE1 A:HIS563 3.3 22.2 1.0
OD2 A:ASP674 3.3 27.2 1.0
OD1 A:ASP564 3.6 20.8 1.0
MG A:MG802 3.8 20.2 1.0
O A:HOH1024 4.0 20.0 1.0
CD2 A:HIS525 4.2 23.8 1.0
CG A:HIS563 4.2 20.4 1.0
O A:HOH943 4.2 24.2 1.0
ND1 A:HIS529 4.3 22.2 1.0
CG A:HIS529 4.3 23.6 1.0
O A:HOH1008 4.3 46.3 1.0
CB A:ASP564 4.3 21.8 1.0
ND1 A:HIS563 4.3 21.2 1.0
CB A:ASP674 4.4 24.2 1.0
NE2 A:HIS525 4.5 22.9 1.0
O A:HOH928 4.5 18.8 1.0
CG2 A:VAL533 4.8 20.8 1.0
O A:ASP674 4.8 21.6 1.0
CA A:ASP674 4.8 22.7 1.0

Zinc binding site 2 out of 4 in 5sg0

Go back to Zinc Binding Sites List in 5sg0
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-3-(2-Phenylpyrazol-3-Yl) Imidazolidin-2-One


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 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-3-(2-Phenylpyrazol-3-Yl) Imidazolidin-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:27.3
occ:1.00
 O B:HOH936 2.0 15.8 1.0
OD1 B:ASP674 2.1 22.3 1.0
OD2 B:ASP564 2.2 20.8 1.0
NE2 B:HIS529 2.2 19.9 1.0
NE2 B:HIS563 2.2 18.7 1.0
O B:HOH1013 2.3 22.5 1.0
CG B:ASP674 3.0 22.4 1.0
CD2 B:HIS563 3.1 20.2 1.0
CD2 B:HIS529 3.1 20.8 1.0
CG B:ASP564 3.2 21.0 1.0
CE1 B:HIS529 3.2 20.6 1.0
OD2 B:ASP674 3.2 23.4 1.0
CE1 B:HIS563 3.3 19.2 1.0
OD1 B:ASP564 3.6 20.6 1.0
MG B:MG802 3.8 17.8 1.0
O B:HOH1007 4.0 18.4 1.0
CD2 B:HIS525 4.1 21.9 1.0
O B:HOH961 4.2 27.5 1.0
O B:HOH1003 4.2 40.4 1.0
CG B:HIS563 4.3 19.6 1.0
CG B:HIS529 4.3 20.7 1.0
ND1 B:HIS529 4.3 20.1 1.0
ND1 B:HIS563 4.3 19.3 1.0
CB B:ASP564 4.3 20.0 1.0
CB B:ASP674 4.4 21.8 1.0
NE2 B:HIS525 4.4 21.9 1.0
O B:HOH955 4.6 19.8 1.0
CG2 B:VAL533 4.7 20.7 1.0
CA B:ASP674 4.8 21.0 1.0
O B:ASP674 4.8 19.6 1.0

Zinc binding site 3 out of 4 in 5sg0

Go back to Zinc Binding Sites List in 5sg0
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-3-(2-Phenylpyrazol-3-Yl) Imidazolidin-2-One


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 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-3-(2-Phenylpyrazol-3-Yl) Imidazolidin-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:27.1
occ:1.00
 O C:HOH970 2.0 19.5 1.0
OD1 C:ASP674 2.1 22.9 1.0
OD2 C:ASP564 2.2 18.9 1.0
NE2 C:HIS529 2.2 20.8 1.0
O C:HOH1024 2.2 25.9 1.0
NE2 C:HIS563 2.3 22.0 1.0
CG C:ASP674 3.0 22.6 1.0
CD2 C:HIS563 3.0 21.6 1.0
CG C:ASP564 3.1 20.2 1.0
CE1 C:HIS529 3.2 23.6 1.0
CD2 C:HIS529 3.2 21.6 1.0
OD2 C:ASP674 3.3 22.9 1.0
CE1 C:HIS563 3.4 21.8 1.0
OD1 C:ASP564 3.6 20.3 1.0
MG C:MG802 3.8 21.0 1.0
CD2 C:HIS525 4.1 27.2 1.0
O C:HOH1031 4.2 19.1 1.0
CG C:HIS563 4.3 21.0 1.0
O C:HOH965 4.3 30.2 1.0
ND1 C:HIS529 4.3 21.7 1.0
O C:HOH1034 4.3 54.6 1.0
CB C:ASP564 4.3 20.3 1.0
CG C:HIS529 4.3 23.0 1.0
NE2 C:HIS525 4.4 28.8 1.0
ND1 C:HIS563 4.4 21.1 1.0
CB C:ASP674 4.4 23.0 1.0
O C:HOH922 4.6 26.2 1.0
CA C:ASP674 4.7 23.7 1.0
CG2 C:VAL533 4.8 21.4 1.0
O C:ASP674 4.8 24.3 1.0

Zinc binding site 4 out of 4 in 5sg0

Go back to Zinc Binding Sites List in 5sg0
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-3-(2-Phenylpyrazol-3-Yl) Imidazolidin-2-One


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 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-3-(2-Phenylpyrazol-3-Yl) Imidazolidin-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:35.3
occ:1.00
 O D:HOH929 2.0 18.2 1.0
NE2 D:HIS563 2.2 26.7 1.0
NE2 D:HIS529 2.2 34.7 1.0
OD2 D:ASP564 2.2 30.7 1.0
OD1 D:ASP674 2.3 30.1 1.0
O D:HOH971 2.3 34.0 1.0
CD2 D:HIS563 3.0 28.2 1.0
CG D:ASP674 3.1 31.9 1.0
CD2 D:HIS529 3.1 36.5 1.0
CE1 D:HIS529 3.2 34.4 1.0
CG D:ASP564 3.2 28.9 1.0
CE1 D:HIS563 3.3 26.4 1.0
OD2 D:ASP674 3.3 31.7 1.0
OD1 D:ASP564 3.7 29.9 1.0
MG D:MG802 3.8 28.5 1.0
O D:HOH984 4.0 29.6 1.0
O D:HOH961 4.2 35.3 1.0
CG D:HIS563 4.2 26.5 1.0
CD2 D:HIS525 4.2 33.5 1.0
ND1 D:HIS529 4.3 33.7 1.0
CG D:HIS529 4.3 34.8 1.0
ND1 D:HIS563 4.3 26.6 1.0
CB D:ASP564 4.3 28.2 1.0
CB D:ASP674 4.5 31.0 1.0
NE2 D:HIS525 4.5 34.4 1.0
O D:HOH932 4.6 30.4 1.0
CG2 D:VAL533 4.7 33.4 1.0
O D:ASP674 4.8 29.9 1.0
CA D:ASP674 4.9 29.8 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 05:04:36 2024

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