Atomistry » Zinc » PDB 5si3-5sj7 » 5si3
Atomistry »
  Zinc »
    PDB 5si3-5sj7 »
      5si3 »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy