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Zinc in PDB 5sfz: 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) Urea

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) Urea

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) Urea:
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) Urea, PDB code: 5sfz 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) 43.49 / 2.16
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.195, 135.195, 234.845, 90, 90, 120
R / Rfree (%) 19.1 / 23.5

Other elements in 5sfz:

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) Urea 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) Urea (pdb code 5sfz). 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) Urea, PDB code: 5sfz:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sfz

Go back to Zinc Binding Sites List in 5sfz
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) Urea


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) Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:30.5
occ:1.00
 NE2 A:HIS563 2.1 26.3 1.0
OD2 A:ASP564 2.1 26.8 1.0
NE2 A:HIS529 2.1 27.7 1.0
OD1 A:ASP674 2.2 29.9 1.0
O A:HOH953 2.2 22.4 1.0
O A:HOH970 2.3 30.2 1.0
CD2 A:HIS563 2.9 26.8 1.0
CG A:ASP674 3.0 30.2 1.0
CE1 A:HIS529 3.1 26.5 1.0
CG A:ASP564 3.1 24.7 1.0
CD2 A:HIS529 3.2 27.1 1.0
CE1 A:HIS563 3.2 27.3 1.0
OD2 A:ASP674 3.2 34.1 1.0
OD1 A:ASP564 3.5 23.3 1.0
MG A:MG802 3.8 27.9 1.0
CG A:HIS563 4.1 26.6 1.0
ND1 A:HIS529 4.2 25.9 1.0
ND1 A:HIS563 4.2 25.7 1.0
CD2 A:HIS525 4.2 29.0 1.0
O A:HOH1004 4.2 23.9 1.0
CB A:ASP564 4.3 24.7 1.0
CG A:HIS529 4.3 25.9 1.0
O A:HOH992 4.4 33.1 1.0
CB A:ASP674 4.4 28.8 1.0
NE2 A:HIS525 4.5 27.4 1.0
O A:HOH934 4.6 25.6 1.0
O A:HOH1010 4.7 49.8 1.0
CG2 A:VAL533 4.7 25.0 1.0
O A:ASP674 4.8 29.0 1.0
CA A:ASP674 4.9 27.9 1.0

Zinc binding site 2 out of 4 in 5sfz

Go back to Zinc Binding Sites List in 5sfz
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) Urea


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) Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:29.7
occ:1.00
 O B:HOH953 2.1 20.6 1.0
OD2 B:ASP564 2.1 24.9 1.0
NE2 B:HIS563 2.1 23.7 1.0
OD1 B:ASP674 2.2 26.2 1.0
NE2 B:HIS529 2.2 23.4 1.0
O B:HOH971 2.5 32.1 1.0
CD2 B:HIS563 3.0 23.6 1.0
CG B:ASP674 3.0 25.3 1.0
CG B:ASP564 3.1 23.9 1.0
CE1 B:HIS529 3.1 23.3 1.0
CE1 B:HIS563 3.2 22.8 1.0
CD2 B:HIS529 3.2 24.9 1.0
OD2 B:ASP674 3.2 28.3 1.0
OD1 B:ASP564 3.5 24.6 1.0
MG B:MG802 3.8 25.9 1.0
O B:HOH979 3.9 22.2 1.0
CD2 B:HIS525 4.1 24.5 1.0
CG B:HIS563 4.2 24.4 1.0
O B:HOH974 4.2 33.4 1.0
ND1 B:HIS563 4.2 22.8 1.0
CB B:ASP564 4.3 23.7 1.0
ND1 B:HIS529 4.3 22.9 1.0
CG B:HIS529 4.3 23.4 1.0
NE2 B:HIS525 4.3 24.4 1.0
CB B:ASP674 4.4 24.9 1.0
O B:HOH947 4.6 20.7 1.0
CG2 B:VAL533 4.7 25.3 1.0
CA B:ASP674 4.8 25.7 1.0
O B:ASP674 4.8 24.5 1.0

Zinc binding site 3 out of 4 in 5sfz

Go back to Zinc Binding Sites List in 5sfz
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) Urea


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) Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:32.7
occ:1.00
 O C:HOH968 1.9 26.0 1.0
OD1 C:ASP674 2.1 24.6 1.0
OD2 C:ASP564 2.2 28.8 1.0
NE2 C:HIS563 2.2 25.8 1.0
NE2 C:HIS529 2.2 26.8 1.0
O C:HOH994 2.3 27.8 1.0
CG C:ASP674 3.0 26.4 1.0
CD2 C:HIS563 3.1 23.8 1.0
CG C:ASP564 3.2 27.1 1.0
CD2 C:HIS529 3.2 24.6 1.0
CE1 C:HIS529 3.2 26.9 1.0
CE1 C:HIS563 3.3 26.7 1.0
OD2 C:ASP674 3.3 28.0 1.0
OD1 C:ASP564 3.7 26.3 1.0
MG C:MG802 3.7 23.6 1.0
CD2 C:HIS525 4.1 29.4 1.0
O C:HOH1022 4.1 25.5 1.0
CG C:HIS563 4.2 25.3 1.0
O C:HOH978 4.3 36.5 1.0
ND1 C:HIS529 4.3 26.4 1.0
ND1 C:HIS563 4.3 25.3 1.0
CG C:HIS529 4.3 24.4 1.0
CB C:ASP564 4.3 24.7 1.0
NE2 C:HIS525 4.4 29.8 1.0
CB C:ASP674 4.4 25.5 1.0
O C:HOH951 4.6 26.8 1.0
CG2 C:VAL533 4.7 28.8 1.0
CA C:ASP674 4.8 26.4 1.0
O C:ASP674 4.8 26.0 1.0

Zinc binding site 4 out of 4 in 5sfz

Go back to Zinc Binding Sites List in 5sfz
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) Urea


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) Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:40.1
occ:1.00
 O D:HOH936 2.0 25.2 1.0
NE2 D:HIS563 2.1 31.9 1.0
OD1 D:ASP674 2.2 39.0 1.0
OD2 D:ASP564 2.2 39.0 1.0
NE2 D:HIS529 2.3 39.0 1.0
O D:HOH956 2.3 33.0 1.0
CD2 D:HIS563 2.9 32.2 1.0
CG D:ASP674 3.1 36.0 1.0
CD2 D:HIS529 3.1 40.7 1.0
CG D:ASP564 3.1 32.2 1.0
CE1 D:HIS563 3.2 34.7 1.0
OD2 D:ASP674 3.3 37.5 1.0
CE1 D:HIS529 3.4 37.2 1.0
OD1 D:ASP564 3.7 34.0 1.0
MG D:MG802 3.8 34.5 1.0
O D:HOH951 4.0 32.1 1.0
O D:HOH934 4.1 41.3 1.0
CG D:HIS563 4.1 30.8 1.0
CB D:ASP564 4.2 32.4 1.0
CD2 D:HIS525 4.2 39.6 1.0
ND1 D:HIS563 4.3 32.5 1.0
CG D:HIS529 4.3 37.9 1.0
ND1 D:HIS529 4.4 37.0 1.0
CB D:ASP674 4.4 37.7 1.0
O D:HOH920 4.4 33.1 1.0
NE2 D:HIS525 4.6 42.1 1.0
CG2 D:VAL533 4.8 38.8 1.0
O D:ASP674 4.8 39.4 1.0
CA D:ASP674 4.9 35.7 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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