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Zinc in PDB 5sia: Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2, 3-Dimethylquinoxalin-6-Yl)-3-(3-Methoxyphenyl)Urea

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2, 3-Dimethylquinoxalin-6-Yl)-3-(3-Methoxyphenyl)Urea

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2, 3-Dimethylquinoxalin-6-Yl)-3-(3-Methoxyphenyl)Urea:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2, 3-Dimethylquinoxalin-6-Yl)-3-(3-Methoxyphenyl)Urea, PDB code: 5sia was solved by C.Joseph, J.Benz, A.Flohr, M.Brunner, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.50 / 2.27
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.242, 135.242, 235.107, 90, 90, 120
R / Rfree (%) 18.8 / 24

Other elements in 5sia:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2, 3-Dimethylquinoxalin-6-Yl)-3-(3-Methoxyphenyl)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-Dimethylquinoxalin-6-Yl)-3-(3-Methoxyphenyl)Urea (pdb code 5sia). 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-Dimethylquinoxalin-6-Yl)-3-(3-Methoxyphenyl)Urea, PDB code: 5sia:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sia

Go back to Zinc Binding Sites List in 5sia
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2, 3-Dimethylquinoxalin-6-Yl)-3-(3-Methoxyphenyl)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-Dimethylquinoxalin-6-Yl)-3-(3-Methoxyphenyl)Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:39.7
occ:1.00
 OD2 A:ASP564 2.1 31.6 1.0
NE2 A:HIS563 2.1 30.2 1.0
NE2 A:HIS529 2.1 39.4 1.0
OD1 A:ASP674 2.2 41.9 1.0
O A:HOH925 2.3 26.9 1.0
O A:HOH948 2.4 39.7 1.0
CD2 A:HIS563 2.9 31.6 1.0
CG A:ASP674 3.0 37.3 1.0
CD2 A:HIS529 3.0 37.7 1.0
CG A:ASP564 3.1 32.8 1.0
CE1 A:HIS529 3.1 36.4 1.0
OD2 A:ASP674 3.2 43.5 1.0
CE1 A:HIS563 3.2 32.1 1.0
OD1 A:ASP564 3.7 31.2 1.0
MG A:MG802 3.8 34.0 1.0
O A:HOH964 4.1 25.9 1.0
CG A:HIS563 4.1 32.1 1.0
CD2 A:HIS525 4.2 38.5 1.0
ND1 A:HIS529 4.2 35.8 1.0
ND1 A:HIS563 4.2 29.8 1.0
CG A:HIS529 4.2 34.4 1.0
O A:HOH957 4.3 53.4 1.0
CB A:ASP564 4.3 29.5 1.0
O A:HOH939 4.3 41.2 1.0
CB A:ASP674 4.4 36.3 1.0
NE2 A:HIS525 4.4 35.0 1.0
O A:HOH932 4.7 28.4 1.0
CG2 A:VAL533 4.7 27.8 1.0
O A:ASP674 4.8 38.1 1.0
CA A:ASP674 4.9 35.2 1.0

Zinc binding site 2 out of 4 in 5sia

Go back to Zinc Binding Sites List in 5sia
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2, 3-Dimethylquinoxalin-6-Yl)-3-(3-Methoxyphenyl)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-Dimethylquinoxalin-6-Yl)-3-(3-Methoxyphenyl)Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:37.8
occ:1.00
 OD2 B:ASP564 2.2 31.1 1.0
NE2 B:HIS563 2.2 28.6 1.0
O B:HOH922 2.2 24.3 1.0
OD1 B:ASP674 2.2 34.7 1.0
NE2 B:HIS529 2.2 30.8 1.0
O B:HOH961 2.3 42.5 1.0
CG B:ASP674 3.0 33.2 1.0
CD2 B:HIS563 3.0 28.7 1.0
CG B:ASP564 3.1 32.3 1.0
CD2 B:HIS529 3.2 32.2 1.0
OD2 B:ASP674 3.2 39.1 1.0
CE1 B:HIS529 3.2 33.8 1.0
CE1 B:HIS563 3.3 33.5 1.0
OD1 B:ASP564 3.6 28.7 1.0
MG B:MG802 3.9 31.9 1.0
O B:HOH967 4.1 28.1 1.0
O B:HOH930 4.2 36.5 1.0
CG B:HIS563 4.2 29.0 1.0
CD2 B:HIS525 4.2 34.0 1.0
ND1 B:HIS529 4.3 34.6 1.0
CB B:ASP564 4.3 29.8 1.0
ND1 B:HIS563 4.3 30.5 1.0
CG B:HIS529 4.3 34.2 1.0
CB B:ASP674 4.4 36.3 1.0
NE2 B:HIS525 4.5 35.2 1.0
O B:HOH929 4.6 34.3 1.0
CG2 B:VAL533 4.7 29.9 1.0
O B:ASP674 4.8 34.4 1.0
CA B:ASP674 4.8 34.4 1.0

Zinc binding site 3 out of 4 in 5sia

Go back to Zinc Binding Sites List in 5sia
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2, 3-Dimethylquinoxalin-6-Yl)-3-(3-Methoxyphenyl)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-Dimethylquinoxalin-6-Yl)-3-(3-Methoxyphenyl)Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:43.4
occ:1.00
 O C:HOH926 1.9 30.1 1.0
O C:HOH951 2.1 33.5 1.0
NE2 C:HIS529 2.1 36.0 1.0
OD2 C:ASP564 2.1 34.6 1.0
NE2 C:HIS563 2.1 35.8 1.0
OD1 C:ASP674 2.2 35.1 1.0
CE1 C:HIS529 3.1 40.9 1.0
CD2 C:HIS563 3.1 33.5 1.0
CG C:ASP674 3.1 36.9 1.0
CD2 C:HIS529 3.1 34.6 1.0
CG C:ASP564 3.1 35.6 1.0
CE1 C:HIS563 3.2 35.7 1.0
OD2 C:ASP674 3.4 40.8 1.0
OD1 C:ASP564 3.6 34.2 1.0
MG C:MG802 3.7 33.0 1.0
O C:HOH965 4.1 42.7 1.0
CD2 C:HIS525 4.1 44.0 1.0
ND1 C:HIS529 4.2 39.0 1.0
CG C:HIS529 4.2 35.3 1.0
CG C:HIS563 4.2 32.2 1.0
ND1 C:HIS563 4.3 32.9 1.0
CB C:ASP564 4.3 33.8 1.0
CB C:ASP674 4.4 40.2 1.0
NE2 C:HIS525 4.5 42.5 1.0
O C:HOH924 4.7 38.7 1.0
CG2 C:VAL533 4.8 35.4 1.0
CA C:ASP674 4.8 38.5 1.0
O C:ASP674 4.8 39.9 1.0

Zinc binding site 4 out of 4 in 5sia

Go back to Zinc Binding Sites List in 5sia
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2, 3-Dimethylquinoxalin-6-Yl)-3-(3-Methoxyphenyl)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-Dimethylquinoxalin-6-Yl)-3-(3-Methoxyphenyl)Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:46.6
occ:1.00
 NE2 D:HIS563 2.1 35.9 1.0
NE2 D:HIS529 2.1 40.6 1.0
OD1 D:ASP674 2.2 39.0 1.0
OD2 D:ASP564 2.2 45.7 1.0
O D:HOH928 2.2 38.8 1.0
O D:HOH937 2.3 40.8 1.0
CD2 D:HIS563 2.9 37.7 1.0
CG D:ASP674 3.1 41.1 1.0
CD2 D:HIS529 3.1 43.5 1.0
CG D:ASP564 3.1 39.7 1.0
CE1 D:HIS529 3.1 42.8 1.0
CE1 D:HIS563 3.2 38.4 1.0
OD2 D:ASP674 3.3 43.7 1.0
OD1 D:ASP564 3.7 46.2 1.0
MG D:MG802 3.7 45.7 1.0
CG D:HIS563 4.1 38.2 1.0
O D:HOH941 4.2 42.6 1.0
ND1 D:HIS563 4.2 39.2 1.0
CB D:ASP564 4.2 39.6 1.0
ND1 D:HIS529 4.3 40.6 1.0
CG D:HIS529 4.3 40.2 1.0
CD2 D:HIS525 4.3 52.6 1.0
O D:HOH921 4.4 46.8 1.0
CB D:ASP674 4.5 46.5 1.0
O D:HOH919 4.5 37.9 1.0
NE2 D:HIS525 4.7 52.6 1.0
O D:ASP674 4.8 50.3 1.0
CG2 D:VAL533 4.8 40.8 1.0
CA D:ASP674 4.9 45.7 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 05:41:13 2024

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