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Zinc in PDB 5sg8: Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- Butoxy-4-Ethoxypyrimidin-2-Amine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- Butoxy-4-Ethoxypyrimidin-2-Amine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- Butoxy-4-Ethoxypyrimidin-2-Amine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- Butoxy-4-Ethoxypyrimidin-2-Amine, PDB code: 5sg8 was solved by C.Joseph, J.Benz, A.Flohr, A.Gruessner, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.65 / 2.16
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.073, 135.073, 235.251, 90, 90, 120
R / Rfree (%) 21.7 / 27.1

Other elements in 5sg8:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- Butoxy-4-Ethoxypyrimidin-2-Amine 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 5- Butoxy-4-Ethoxypyrimidin-2-Amine (pdb code 5sg8). 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 5- Butoxy-4-Ethoxypyrimidin-2-Amine, PDB code: 5sg8:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sg8

Go back to Zinc Binding Sites List in 5sg8
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- Butoxy-4-Ethoxypyrimidin-2-Amine


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 5- Butoxy-4-Ethoxypyrimidin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:33.6
occ:1.00
 O A:HOH974 2.0 40.1 1.0
OD1 A:ASP674 2.1 33.8 1.0
NE2 A:HIS563 2.1 28.8 1.0
OD2 A:ASP564 2.2 32.4 1.0
NE2 A:HIS529 2.2 32.1 1.0
O A:HOH917 2.3 24.8 1.0
CD2 A:HIS563 3.0 28.9 1.0
CG A:ASP674 3.0 32.9 1.0
CD2 A:HIS529 3.1 33.6 1.0
CG A:ASP564 3.1 29.6 1.0
OD2 A:ASP674 3.2 37.4 1.0
CE1 A:HIS563 3.3 32.0 1.0
CE1 A:HIS529 3.3 32.8 1.0
OD1 A:ASP564 3.5 28.0 1.0
MG A:MG802 3.8 27.9 1.0
O A:HOH983 3.8 33.7 1.0
CD2 A:HIS525 4.2 29.3 1.0
CG A:HIS563 4.2 29.0 1.0
CB A:ASP564 4.3 28.4 1.0
CG A:HIS529 4.3 30.4 1.0
ND1 A:HIS563 4.3 30.7 1.0
ND1 A:HIS529 4.3 31.3 1.0
CB A:ASP674 4.4 32.7 1.0
NE2 A:HIS525 4.5 29.2 1.0
O A:HOH986 4.6 42.2 1.0
O A:HOH927 4.6 22.7 1.0
CG2 A:VAL533 4.7 25.2 1.0
O A:ASP674 4.8 33.7 1.0
CA A:ASP674 4.8 30.9 1.0
O A:HOH959 5.0 27.6 1.0

Zinc binding site 2 out of 4 in 5sg8

Go back to Zinc Binding Sites List in 5sg8
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- Butoxy-4-Ethoxypyrimidin-2-Amine


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 5- Butoxy-4-Ethoxypyrimidin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:34.4
occ:1.00
 OD1 B:ASP674 2.1 28.7 1.0
NE2 B:HIS529 2.1 26.8 1.0
OD2 B:ASP564 2.1 27.8 1.0
NE2 B:HIS563 2.2 24.5 1.0
O B:HOH931 2.2 17.5 1.0
O B:HOH953 2.4 42.5 1.0
CG B:ASP674 3.0 30.8 1.0
CD2 B:HIS529 3.1 30.2 1.0
CG B:ASP564 3.1 25.9 1.0
CD2 B:HIS563 3.1 26.8 1.0
CE1 B:HIS529 3.1 27.5 1.0
CE1 B:HIS563 3.2 26.4 1.0
OD2 B:ASP674 3.3 31.4 1.0
OD1 B:ASP564 3.5 27.3 1.0
MG B:MG802 3.9 29.1 1.0
O B:HOH977 4.0 27.0 1.0
CD2 B:HIS525 4.1 29.6 1.0
ND1 B:HIS529 4.2 29.1 1.0
CG B:HIS529 4.2 30.2 1.0
O B:HOH986 4.2 43.9 1.0
CG B:HIS563 4.3 26.0 1.0
ND1 B:HIS563 4.3 23.8 1.0
CB B:ASP564 4.3 26.2 1.0
CB B:ASP674 4.3 29.7 1.0
NE2 B:HIS525 4.4 31.7 1.0
O B:HOH918 4.4 18.7 1.0
O B:HOH1000 4.5 59.1 1.0
CG2 B:VAL533 4.7 28.6 1.0
O B:ASP674 4.7 31.8 1.0
CA B:ASP674 4.8 30.6 1.0

Zinc binding site 3 out of 4 in 5sg8

Go back to Zinc Binding Sites List in 5sg8
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- Butoxy-4-Ethoxypyrimidin-2-Amine


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 5- Butoxy-4-Ethoxypyrimidin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:39.4
occ:1.00
 O C:HOH930 1.9 32.0 1.0
OD1 C:ASP674 2.1 38.0 1.0
NE2 C:HIS563 2.1 28.7 1.0
OD2 C:ASP564 2.2 30.9 1.0
NE2 C:HIS529 2.2 32.1 1.0
O C:HOH975 2.3 29.5 1.0
CG C:ASP674 3.0 37.9 1.0
CD2 C:HIS563 3.1 32.8 1.0
CD2 C:HIS529 3.1 32.2 1.0
CE1 C:HIS563 3.1 32.5 1.0
CG C:ASP564 3.2 29.6 1.0
CE1 C:HIS529 3.3 32.5 1.0
OD2 C:ASP674 3.3 39.6 1.0
OD1 C:ASP564 3.7 28.0 1.0
MG C:MG802 4.0 30.2 1.0
CD2 C:HIS525 4.1 37.5 1.0
ND1 C:HIS563 4.2 27.8 1.0
CG C:HIS563 4.2 29.5 1.0
O C:HOH994 4.3 26.4 1.0
CB C:ASP564 4.3 28.1 1.0
CG C:HIS529 4.3 32.9 1.0
ND1 C:HIS529 4.3 31.4 1.0
CB C:ASP674 4.4 39.9 1.0
NE2 C:HIS525 4.5 35.7 1.0
CA C:ASP674 4.7 37.9 1.0
O C:HOH940 4.7 35.3 1.0
O C:ASP674 4.7 36.0 1.0
CG2 C:VAL533 4.7 29.2 1.0
O C:HOH966 4.9 30.1 1.0

Zinc binding site 4 out of 4 in 5sg8

Go back to Zinc Binding Sites List in 5sg8
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- Butoxy-4-Ethoxypyrimidin-2-Amine


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 5- Butoxy-4-Ethoxypyrimidin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:42.5
occ:1.00
 O D:HOH951 1.9 35.5 1.0
NE2 D:HIS563 2.1 32.6 1.0
OD1 D:ASP674 2.2 37.4 1.0
OD2 D:ASP564 2.2 43.0 1.0
NE2 D:HIS529 2.3 45.6 1.0
O D:HOH938 2.4 39.1 1.0
CD2 D:HIS563 2.9 36.8 1.0
CG D:ASP564 3.1 35.7 1.0
CG D:ASP674 3.1 35.1 1.0
CD2 D:HIS529 3.2 45.8 1.0
CE1 D:HIS563 3.3 38.1 1.0
CE1 D:HIS529 3.3 48.5 1.0
OD2 D:ASP674 3.4 40.7 1.0
OD1 D:ASP564 3.5 34.4 1.0
MG D:MG802 3.9 42.9 1.0
O D:HOH978 4.0 54.5 1.0
CD2 D:HIS525 4.1 39.8 1.0
CG D:HIS563 4.2 34.5 1.0
CB D:ASP564 4.3 37.1 1.0
ND1 D:HIS563 4.3 34.0 1.0
O D:HOH943 4.3 31.7 1.0
O D:HOH929 4.4 41.6 1.0
CG D:HIS529 4.4 42.0 1.0
ND1 D:HIS529 4.4 43.2 1.0
NE2 D:HIS525 4.5 38.1 1.0
CB D:ASP674 4.5 36.0 1.0
O D:ASP674 4.8 36.9 1.0
CG2 D:VAL533 4.8 39.2 1.0
CA D:ASP674 4.9 38.3 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 05:09:09 2024

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