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Zinc in PDB 5sjy: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 3-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 3-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 3-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 3-Carboxamide, PDB code: 5sjy was solved by C.Joseph, J.Benz, A.Flohr, J.Peters, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.81 / 2.20
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 136.053, 136.053, 235.986, 90, 90, 120
R / Rfree (%) 20.2 / 26.5

Other elements in 5sjy:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 3-Carboxamide also contains other interesting chemical elements:

Bromine (Br) 4 atoms
Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 3-Carboxamide (pdb code 5sjy). 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 4- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 3-Carboxamide, PDB code: 5sjy:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sjy

Go back to Zinc Binding Sites List in 5sjy
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 3-Carboxamide


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 4- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:42.2
occ:1.00
 OD2 A:ASP564 2.0 41.0 1.0
O A:HOH929 2.1 45.5 1.0
NE2 A:HIS563 2.1 37.9 1.0
NE2 A:HIS529 2.2 39.6 1.0
OD1 A:ASP674 2.2 43.8 1.0
O A:HOH909 2.2 34.2 1.0
CD2 A:HIS563 2.9 40.7 1.0
CG A:ASP674 3.0 35.5 1.0
CG A:ASP564 3.1 34.3 1.0
CD2 A:HIS529 3.1 36.1 1.0
OD2 A:ASP674 3.2 38.9 1.0
CE1 A:HIS563 3.2 39.4 1.0
CE1 A:HIS529 3.2 31.4 1.0
OD1 A:ASP564 3.6 34.2 1.0
MG A:MG802 3.7 32.8 1.0
CD2 A:HIS525 4.1 45.9 1.0
CG A:HIS563 4.1 34.9 1.0
O A:HOH934 4.1 33.2 1.0
ND1 A:HIS563 4.2 33.6 1.0
CB A:ASP564 4.2 33.0 1.0
CG A:HIS529 4.3 32.5 1.0
ND1 A:HIS529 4.3 33.0 1.0
CB A:ASP674 4.4 40.4 1.0
NE2 A:HIS525 4.5 40.9 1.0
O A:HOH908 4.5 34.0 1.0
CG2 A:VAL533 4.7 34.6 1.0
CA A:ASP674 4.9 38.5 1.0
O A:ASP674 4.9 37.9 1.0

Zinc binding site 2 out of 4 in 5sjy

Go back to Zinc Binding Sites List in 5sjy
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 3-Carboxamide


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 4- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:39.3
occ:1.00
 O B:HOH924 2.1 28.7 1.0
O B:HOH947 2.1 42.9 1.0
OD2 B:ASP564 2.1 30.5 1.0
OD1 B:ASP674 2.1 33.0 1.0
NE2 B:HIS563 2.1 30.1 1.0
NE2 B:HIS529 2.2 32.8 1.0
CG B:ASP674 3.0 32.8 1.0
CD2 B:HIS563 3.1 33.7 1.0
CE1 B:HIS563 3.2 32.4 1.0
CG B:ASP564 3.2 31.8 1.0
CD2 B:HIS529 3.2 34.1 1.0
CE1 B:HIS529 3.2 39.2 1.0
OD2 B:ASP674 3.3 35.8 1.0
OD1 B:ASP564 3.7 36.8 1.0
MG B:MG802 3.7 29.4 1.0
O B:HOH929 4.1 29.9 1.0
CD2 B:HIS525 4.1 36.1 1.0
CG B:HIS563 4.2 30.2 1.0
ND1 B:HIS563 4.2 30.1 1.0
CB B:ASP564 4.2 29.5 1.0
ND1 B:HIS529 4.3 33.4 1.0
CG B:HIS529 4.3 33.9 1.0
O B:HOH943 4.4 46.1 1.0
CB B:ASP674 4.5 37.1 1.0
NE2 B:HIS525 4.5 39.8 1.0
O B:HOH933 4.7 32.6 1.0
CG2 B:VAL533 4.8 32.6 1.0
O B:ASP674 4.9 33.7 1.0
CA B:ASP674 4.9 33.3 1.0

Zinc binding site 3 out of 4 in 5sjy

Go back to Zinc Binding Sites List in 5sjy
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 3-Carboxamide


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 4- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:38.5
occ:1.00
 O C:HOH945 2.0 48.8 1.0
O C:HOH939 2.1 29.6 1.0
OD2 C:ASP564 2.1 33.1 1.0
NE2 C:HIS529 2.1 36.3 1.0
NE2 C:HIS563 2.3 38.8 1.0
OD1 C:ASP674 2.3 32.8 1.0
CD2 C:HIS563 3.0 32.5 1.0
CD2 C:HIS529 3.1 37.6 1.0
CG C:ASP674 3.1 33.6 1.0
CG C:ASP564 3.1 33.8 1.0
CE1 C:HIS529 3.2 40.1 1.0
OD2 C:ASP674 3.2 39.6 1.0
CE1 C:HIS563 3.3 32.6 1.0
OD1 C:ASP564 3.7 30.5 1.0
MG C:MG802 3.9 33.6 1.0
CD2 C:HIS525 4.2 40.6 1.0
CG C:HIS529 4.2 31.1 1.0
CG C:HIS563 4.2 36.2 1.0
O C:HOH956 4.3 29.6 1.0
ND1 C:HIS529 4.3 33.7 1.0
CB C:ASP564 4.3 30.4 1.0
ND1 C:HIS563 4.4 34.8 1.0
O C:HOH937 4.4 39.9 1.0
NE2 C:HIS525 4.4 47.9 1.0
CB C:ASP674 4.5 42.0 1.0
CG2 C:VAL533 4.8 28.3 1.0
CA C:ASP674 4.8 38.2 1.0
O C:ASP674 4.9 34.1 1.0

Zinc binding site 4 out of 4 in 5sjy

Go back to Zinc Binding Sites List in 5sjy
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 3-Carboxamide


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 4- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:46.8
occ:1.00
 OD2 D:ASP564 2.1 48.6 1.0
NE2 D:HIS563 2.1 38.6 1.0
NE2 D:HIS529 2.1 44.4 1.0
OD1 D:ASP674 2.1 46.9 1.0
O D:HOH909 2.2 37.1 1.0
CD2 D:HIS563 3.0 39.0 1.0
CG D:ASP674 3.0 43.3 1.0
CD2 D:HIS529 3.0 52.7 1.0
CG D:ASP564 3.2 42.2 1.0
CE1 D:HIS529 3.2 42.2 1.0
OD2 D:ASP674 3.2 35.1 1.0
CE1 D:HIS563 3.2 36.8 1.0
OD1 D:ASP564 3.8 47.7 1.0
MG D:MG802 3.9 47.7 1.0
CG D:HIS563 4.2 37.1 1.0
O D:HOH917 4.2 41.4 1.0
CG D:HIS529 4.2 41.2 1.0
CB D:ASP564 4.3 43.0 1.0
ND1 D:HIS529 4.3 47.1 1.0
ND1 D:HIS563 4.3 39.5 1.0
CD2 D:HIS525 4.3 51.6 1.0
CB D:ASP674 4.4 42.6 1.0
NE2 D:HIS525 4.6 47.6 1.0
CG2 D:VAL533 4.7 38.6 1.0
O D:HOH902 4.7 45.9 1.0
CA D:ASP674 4.8 45.4 1.0
O D:ASP674 5.0 47.3 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 06:10:02 2024

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