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Zinc in PDB 5sjd: Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (3,5-Dimethylpyrazol-1-Yl)Ethyl]-3-(2-Phenylpyrazol-3-Yl)Urea

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (3,5-Dimethylpyrazol-1-Yl)Ethyl]-3-(2-Phenylpyrazol-3-Yl)Urea

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (3,5-Dimethylpyrazol-1-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- (3,5-Dimethylpyrazol-1-Yl)Ethyl]-3-(2-Phenylpyrazol-3-Yl)Urea, PDB code: 5sjd 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) 43.73 / 2.16
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.859, 135.859, 235.544, 90, 90, 120
R / Rfree (%) 18.5 / 22.7

Other elements in 5sjd:

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

Zinc binding site 1 out of 4 in 5sjd

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (3,5-Dimethylpyrazol-1-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- (3,5-Dimethylpyrazol-1-Yl)Ethyl]-3-(2-Phenylpyrazol-3-Yl)Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:32.4
occ:1.00
 OD2 A:ASP564 2.1 27.6 1.0
NE2 A:HIS563 2.1 23.7 1.0
NE2 A:HIS529 2.2 27.3 1.0
O A:HOH958 2.2 26.6 1.0
OD1 A:ASP674 2.2 29.4 1.0
O A:HOH972 2.4 29.5 1.0
CD2 A:HIS563 3.0 23.5 1.0
CD2 A:HIS529 3.1 28.1 1.0
CG A:ASP674 3.1 30.5 1.0
CG A:ASP564 3.1 27.1 1.0
CE1 A:HIS563 3.2 24.7 1.0
CE1 A:HIS529 3.2 26.3 1.0
OD2 A:ASP674 3.4 35.0 1.0
OD1 A:ASP564 3.7 26.0 1.0
MG A:MG802 3.8 24.6 1.0
O A:HOH1009 4.1 23.7 1.0
CG A:HIS563 4.2 24.6 1.0
CD2 A:HIS525 4.2 26.8 1.0
O A:HOH947 4.2 33.3 1.0
ND1 A:HIS563 4.2 24.2 1.0
CG A:HIS529 4.2 26.6 1.0
CB A:ASP564 4.3 26.8 1.0
ND1 A:HIS529 4.3 26.2 1.0
CB A:ASP674 4.4 28.6 1.0
O A:HOH1015 4.5 42.3 1.0
NE2 A:HIS525 4.5 25.4 1.0
O A:HOH942 4.7 21.8 1.0
O A:ASP674 4.7 27.3 1.0
CG2 A:VAL533 4.7 24.6 1.0
CA A:ASP674 4.8 26.7 1.0

Zinc binding site 2 out of 4 in 5sjd

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Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (3,5-Dimethylpyrazol-1-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- (3,5-Dimethylpyrazol-1-Yl)Ethyl]-3-(2-Phenylpyrazol-3-Yl)Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:31.3
occ:1.00
 O B:HOH957 2.1 21.0 1.0
OD1 B:ASP674 2.1 28.7 1.0
OD2 B:ASP564 2.1 24.9 1.0
NE2 B:HIS563 2.2 23.7 1.0
NE2 B:HIS529 2.2 23.8 1.0
O B:HOH999 2.3 33.8 1.0
CG B:ASP674 3.0 26.7 1.0
CD2 B:HIS563 3.1 23.1 1.0
CD2 B:HIS529 3.1 25.6 1.0
CG B:ASP564 3.1 25.4 1.0
CE1 B:HIS563 3.2 23.2 1.0
CE1 B:HIS529 3.3 25.3 1.0
OD2 B:ASP674 3.3 28.7 1.0
OD1 B:ASP564 3.6 25.8 1.0
MG B:MG802 3.8 25.9 1.0
O B:HOH1015 4.1 22.5 1.0
O B:HOH966 4.2 32.3 1.0
CD2 B:HIS525 4.2 27.1 1.0
CG B:HIS563 4.3 23.5 1.0
ND1 B:HIS563 4.3 22.8 1.0
CG B:HIS529 4.3 25.0 1.0
CB B:ASP564 4.3 26.0 1.0
ND1 B:HIS529 4.3 24.9 1.0
O B:HOH1020 4.4 54.6 1.0
CB B:ASP674 4.4 26.2 1.0
NE2 B:HIS525 4.5 27.2 1.0
O B:HOH942 4.6 26.6 1.0
CG2 B:VAL533 4.7 23.1 1.0
O B:ASP674 4.8 25.6 1.0
CA B:ASP674 4.8 26.1 1.0

Zinc binding site 3 out of 4 in 5sjd

Go back to Zinc Binding Sites List in 5sjd
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (3,5-Dimethylpyrazol-1-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- (3,5-Dimethylpyrazol-1-Yl)Ethyl]-3-(2-Phenylpyrazol-3-Yl)Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:33.3
occ:1.00
 O C:HOH932 2.0 23.2 1.0
OD1 C:ASP674 2.1 25.7 1.0
OD2 C:ASP564 2.2 27.9 1.0
NE2 C:HIS563 2.2 27.4 1.0
NE2 C:HIS529 2.2 28.3 1.0
O C:HOH1000 2.3 37.8 1.0
CD2 C:HIS563 3.0 25.4 1.0
CG C:ASP674 3.0 28.4 1.0
CD2 C:HIS529 3.1 28.5 1.0
CG C:ASP564 3.2 27.2 1.0
CE1 C:HIS529 3.2 30.2 1.0
CE1 C:HIS563 3.2 26.2 1.0
OD2 C:ASP674 3.3 28.9 1.0
OD1 C:ASP564 3.7 25.4 1.0
MG C:MG802 3.8 23.8 1.0
CD2 C:HIS525 4.1 31.6 1.0
O C:HOH1015 4.2 25.4 1.0
CG C:HIS563 4.2 25.4 1.0
ND1 C:HIS563 4.3 25.6 1.0
O C:HOH989 4.3 34.8 1.0
CG C:HIS529 4.3 28.1 1.0
ND1 C:HIS529 4.3 29.5 1.0
CB C:ASP564 4.3 25.7 1.0
CB C:ASP674 4.4 27.8 1.0
NE2 C:HIS525 4.5 29.8 1.0
O C:HOH983 4.5 51.8 1.0
O C:HOH951 4.6 27.7 1.0
O C:ASP674 4.8 29.5 1.0
CG2 C:VAL533 4.8 26.3 1.0
CA C:ASP674 4.8 27.6 1.0

Zinc binding site 4 out of 4 in 5sjd

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Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (3,5-Dimethylpyrazol-1-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- (3,5-Dimethylpyrazol-1-Yl)Ethyl]-3-(2-Phenylpyrazol-3-Yl)Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:41.0
occ:1.00
 O D:HOH947 2.0 26.1 1.0
NE2 D:HIS563 2.2 29.5 1.0
OD1 D:ASP674 2.2 36.2 1.0
OD2 D:ASP564 2.3 33.3 1.0
NE2 D:HIS529 2.3 38.2 1.0
O D:HOH965 2.3 33.4 1.0
CD2 D:HIS563 3.0 31.1 1.0
CD2 D:HIS529 3.1 39.2 1.0
CG D:ASP564 3.1 31.4 1.0
CG D:ASP674 3.2 38.2 1.0
CE1 D:HIS563 3.3 32.0 1.0
CE1 D:HIS529 3.4 37.9 1.0
OD2 D:ASP674 3.4 38.5 1.0
OD1 D:ASP564 3.6 32.0 1.0
MG D:MG802 3.8 33.5 1.0
O D:HOH922 4.0 35.9 1.0
O D:HOH970 4.0 34.3 1.0
CD2 D:HIS525 4.2 38.2 1.0
CG D:HIS563 4.2 30.1 1.0
CB D:ASP564 4.2 33.5 1.0
ND1 D:HIS563 4.3 29.6 1.0
CG D:HIS529 4.3 37.7 1.0
ND1 D:HIS529 4.4 38.6 1.0
CB D:ASP674 4.5 38.9 1.0
O D:HOH923 4.5 34.8 1.0
NE2 D:HIS525 4.6 40.6 1.0
CG2 D:VAL533 4.8 38.9 1.0
O D:ASP674 4.8 33.5 1.0
CA D:ASP674 4.9 36.6 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 05:58:45 2024

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