Zinc in PDB 5si3: Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Methyl-5-[(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Carbamoyl]Pyrazole-4- Carboxylic Acid

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Methyl-5-[(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Carbamoyl]Pyrazole-4- Carboxylic Acid

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Methyl-5-[(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Carbamoyl]Pyrazole-4- Carboxylic Acid:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Methyl-5-[(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Carbamoyl]Pyrazole-4- Carboxylic Acid, PDB code: 5si3 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) 43.55 / 2.40
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.405, 135.405, 234.686, 90, 90, 120
R / Rfree (%) 19.8 / 23.3

Other elements in 5si3:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Methyl-5-[(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Carbamoyl]Pyrazole-4- Carboxylic Acid 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- Methyl-5-[(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Carbamoyl]Pyrazole-4- Carboxylic Acid (pdb code 5si3). 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- Methyl-5-[(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Carbamoyl]Pyrazole-4- Carboxylic Acid, PDB code: 5si3:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5si3

Go back to Zinc Binding Sites List in 5si3
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Methyl-5-[(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Carbamoyl]Pyrazole-4- Carboxylic Acid


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- Methyl-5-[(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Carbamoyl]Pyrazole-4- Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn802

b:35.0
occ:1.00
 OD1 A:ASP674 2.0 40.3 1.0
OD2 A:ASP564 2.1 30.7 1.0
NE2 A:HIS529 2.1 32.6 1.0
NE2 A:HIS563 2.2 30.0 1.0
O A:HOH943 2.3 44.6 1.0
O A:HOH926 2.6 34.9 1.0
CG A:ASP674 2.9 39.6 1.0
CD2 A:HIS563 3.0 30.3 1.0
CD2 A:HIS529 3.0 32.8 1.0
CE1 A:HIS529 3.1 34.1 1.0
CG A:ASP564 3.1 30.6 1.0
CE1 A:HIS563 3.2 32.7 1.0
OD2 A:ASP674 3.3 40.8 1.0
OD1 A:ASP564 3.6 36.2 1.0
MG A:MG803 4.0 33.4 1.0
CD2 A:HIS525 4.1 32.0 1.0
CG A:HIS563 4.2 31.0 1.0
ND1 A:HIS529 4.2 35.8 1.0
CG A:HIS529 4.2 32.8 1.0
O A:HOH969 4.2 32.2 1.0
ND1 A:HIS563 4.3 30.1 1.0
O A:HOH950 4.3 35.7 1.0
CB A:ASP674 4.3 36.7 1.0
CB A:ASP564 4.3 29.6 1.0
O A:HOH972 4.4 37.8 1.0
NE2 A:HIS525 4.5 32.6 1.0
CG2 A:VAL533 4.7 33.1 1.0
O A:ASP674 4.8 34.1 1.0
CA A:ASP674 4.8 33.7 1.0
O A:HOH917 4.8 30.1 1.0

Zinc binding site 2 out of 4 in 5si3

Go back to Zinc Binding Sites List in 5si3
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Methyl-5-[(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Carbamoyl]Pyrazole-4- Carboxylic Acid


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- Methyl-5-[(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Carbamoyl]Pyrazole-4- Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn802

b:34.1
occ:1.00
 O B:HOH947 2.1 25.6 1.0
NE2 B:HIS529 2.1 26.8 1.0
OD1 B:ASP674 2.1 34.0 1.0
OD2 B:ASP564 2.2 28.4 1.0
NE2 B:HIS563 2.2 29.1 1.0
O B:HOH964 2.4 36.9 1.0
CD2 B:HIS529 3.0 28.4 1.0
CD2 B:HIS563 3.1 30.6 1.0
CG B:ASP674 3.1 31.9 1.0
CE1 B:HIS529 3.2 30.7 1.0
CG B:ASP564 3.2 31.1 1.0
CE1 B:HIS563 3.3 30.5 1.0
OD2 B:ASP674 3.4 39.0 1.0
OD1 B:ASP564 3.7 29.4 1.0
MG B:MG803 3.9 30.1 1.0
O B:HOH969 4.0 22.8 1.0
O B:HOH956 4.2 34.5 1.0
CG B:HIS529 4.2 27.8 1.0
CD2 B:HIS525 4.2 33.1 1.0
CG B:HIS563 4.3 30.2 1.0
ND1 B:HIS529 4.3 27.3 1.0
ND1 B:HIS563 4.3 30.4 1.0
CB B:ASP674 4.4 32.0 1.0
CB B:ASP564 4.4 30.2 1.0
NE2 B:HIS525 4.6 28.9 1.0
O B:ASP674 4.6 34.5 1.0
O B:HOH925 4.7 28.5 1.0
CG2 B:VAL533 4.7 28.5 1.0
CA B:ASP674 4.7 30.4 1.0

Zinc binding site 3 out of 4 in 5si3

Go back to Zinc Binding Sites List in 5si3
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Methyl-5-[(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Carbamoyl]Pyrazole-4- Carboxylic Acid


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- Methyl-5-[(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Carbamoyl]Pyrazole-4- Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn802

b:39.8
occ:1.00
 OD2 C:ASP564 2.0 32.2 1.0
OD1 C:ASP674 2.0 32.1 1.0
O C:HOH905 2.1 27.3 1.0
NE2 C:HIS529 2.1 31.3 1.0
NE2 C:HIS563 2.2 31.0 1.0
CG C:ASP674 3.0 30.8 1.0
CD2 C:HIS563 3.0 29.9 1.0
CG C:ASP564 3.1 32.9 1.0
CD2 C:HIS529 3.1 32.1 1.0
CE1 C:HIS529 3.2 36.0 1.0
OD2 C:ASP674 3.2 33.6 1.0
CE1 C:HIS563 3.3 31.6 1.0
OD1 C:ASP564 3.6 34.0 1.0
MG C:MG803 3.7 29.9 1.0
O C:HOH974 4.1 28.6 1.0
CD2 C:HIS525 4.1 35.7 1.0
CB C:ASP564 4.2 31.9 1.0
O C:HOH980 4.2 34.6 1.0
CG C:HIS563 4.2 31.2 1.0
CG C:HIS529 4.2 32.3 1.0
ND1 C:HIS529 4.3 36.6 1.0
ND1 C:HIS563 4.3 31.6 1.0
CB C:ASP674 4.4 31.2 1.0
NE2 C:HIS525 4.5 32.4 1.0
O C:HOH947 4.5 28.1 1.0
CA C:ASP674 4.8 31.0 1.0
O C:HOH941 4.9 26.4 1.0
CG2 C:VAL533 4.9 32.3 1.0
O C:ASP674 4.9 32.7 1.0

Zinc binding site 4 out of 4 in 5si3

Go back to Zinc Binding Sites List in 5si3
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Methyl-5-[(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Carbamoyl]Pyrazole-4- Carboxylic Acid


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- Methyl-5-[(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Carbamoyl]Pyrazole-4- Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn802

b:54.4
occ:1.00
 OD1 D:ASP674 2.1 56.8 1.0
OD2 D:ASP564 2.1 52.3 1.0
NE2 D:HIS563 2.2 45.7 1.0
NE2 D:HIS529 2.2 49.3 1.0
CD2 D:HIS563 3.0 44.7 1.0
CG D:ASP674 3.1 51.4 1.0
CD2 D:HIS529 3.1 49.9 1.0
CG D:ASP564 3.2 48.0 1.0
CE1 D:HIS563 3.3 48.6 1.0
CE1 D:HIS529 3.3 49.2 1.0
OD2 D:ASP674 3.4 53.2 1.0
MG D:MG803 3.6 53.9 1.0
OD1 D:ASP564 3.9 44.8 1.0
O D:HOH904 3.9 47.5 1.0
CD2 D:HIS525 4.2 53.6 1.0
CG D:HIS563 4.2 45.8 1.0
CB D:ASP564 4.3 45.4 1.0
CG D:HIS529 4.3 50.1 1.0
ND1 D:HIS563 4.3 46.4 1.0
ND1 D:HIS529 4.4 52.9 1.0
CB D:ASP674 4.4 52.5 1.0
O D:HOH923 4.4 38.5 1.0
O D:ASP674 4.5 45.6 1.0
O D:HOH917 4.5 40.5 1.0
NE2 D:HIS525 4.6 53.9 1.0
CA D:ASP674 4.8 52.4 1.0
CG2 D:VAL533 4.8 51.3 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 05:41:13 2024

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