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Zinc in PDB 5sir: Crystal Structure of Human Phosphodiesterase 10 in Complex with 3,6- Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyridine-2- Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3,6- Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyridine-2- Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3,6- Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyridine-2- Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3,6- Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyridine-2- Carboxamide, PDB code: 5sir was solved by C.Joseph, J.Benz, A.Flohr, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.77 / 2.50
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 136.063, 136.063, 236.111, 90, 90, 120
R / Rfree (%) 18.6 / 22.2

Other elements in 5sir:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3,6- Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyridine-2- Carboxamide 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 3,6- Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyridine-2- Carboxamide (pdb code 5sir). 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 3,6- Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyridine-2- Carboxamide, PDB code: 5sir:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sir

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3,6- Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyridine-2- 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 3,6- Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyridine-2- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:43.3
occ:1.00
 OD2 A:ASP564 1.9 41.6 1.0
NE2 A:HIS563 2.0 37.4 1.0
O A:HOH951 2.2 43.2 1.0
NE2 A:HIS529 2.2 44.5 1.0
OD1 A:ASP674 2.4 49.5 1.0
CD2 A:HIS563 2.9 34.9 1.0
CE1 A:HIS563 3.0 36.3 1.0
CG A:ASP564 3.0 38.3 1.0
CD2 A:HIS529 3.1 41.6 1.0
CG A:ASP674 3.1 47.8 1.0
CE1 A:HIS529 3.2 46.2 1.0
OD2 A:ASP674 3.4 44.5 1.0
OD1 A:ASP564 3.6 34.2 1.0
MG A:MG802 3.8 41.0 1.0
CG A:HIS563 4.0 35.7 1.0
ND1 A:HIS563 4.1 33.5 1.0
O A:HOH987 4.1 37.4 1.0
CD2 A:HIS525 4.1 43.5 1.0
CB A:ASP564 4.2 35.6 1.0
CG A:HIS529 4.3 39.3 1.0
ND1 A:HIS529 4.3 42.9 1.0
CB A:ASP674 4.4 42.4 1.0
NE2 A:HIS525 4.4 45.5 1.0
O A:HOH914 4.7 33.0 1.0
CG2 A:VAL533 4.7 37.9 1.0
CA A:ASP674 4.9 40.8 1.0

Zinc binding site 2 out of 4 in 5sir

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Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3,6- Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyridine-2- 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 3,6- Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyridine-2- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:41.0
occ:1.00
 OD2 B:ASP564 2.1 38.9 1.0
O B:HOH933 2.1 36.2 1.0
NE2 B:HIS563 2.1 34.8 1.0
OD1 B:ASP674 2.2 34.9 1.0
NE2 B:HIS529 2.3 39.1 1.0
CD2 B:HIS563 3.1 34.0 1.0
CG B:ASP564 3.1 35.7 1.0
CG B:ASP674 3.1 37.9 1.0
CE1 B:HIS563 3.1 40.0 1.0
CD2 B:HIS529 3.2 38.5 1.0
CE1 B:HIS529 3.3 43.2 1.0
OD2 B:ASP674 3.3 41.4 1.0
OD1 B:ASP564 3.6 36.2 1.0
MG B:MG802 3.8 33.0 1.0
O B:HOH954 4.0 29.0 1.0
CD2 B:HIS525 4.2 41.4 1.0
CG B:HIS563 4.2 33.8 1.0
ND1 B:HIS563 4.2 35.8 1.0
CB B:ASP564 4.3 34.5 1.0
CG B:HIS529 4.3 38.4 1.0
ND1 B:HIS529 4.4 40.6 1.0
CB B:ASP674 4.5 38.2 1.0
NE2 B:HIS525 4.6 36.9 1.0
O B:HOH919 4.6 34.4 1.0
O B:HOH998 4.6 50.3 1.0
CG2 B:VAL533 4.9 34.5 1.0
CA B:ASP674 4.9 36.0 1.0

Zinc binding site 3 out of 4 in 5sir

Go back to Zinc Binding Sites List in 5sir
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3,6- Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyridine-2- 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 3,6- Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyridine-2- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:44.4
occ:1.00
 NE2 C:HIS563 1.9 34.9 1.0
O C:HOH915 2.0 36.6 1.0
OD2 C:ASP564 2.0 37.7 1.0
NE2 C:HIS529 2.2 42.1 1.0
OD1 C:ASP674 2.2 43.4 1.0
CD2 C:HIS563 2.9 35.5 1.0
CE1 C:HIS563 3.0 36.6 1.0
CG C:ASP674 3.0 37.4 1.0
CG C:ASP564 3.1 34.8 1.0
CD2 C:HIS529 3.2 40.9 1.0
OD2 C:ASP674 3.2 37.6 1.0
CE1 C:HIS529 3.3 44.5 1.0
OD1 C:ASP564 3.7 35.7 1.0
O C:HOH921 3.9 38.6 1.0
MG C:MG802 4.0 36.4 1.0
CG C:HIS563 4.0 35.4 1.0
ND1 C:HIS563 4.1 35.6 1.0
CD2 C:HIS525 4.2 42.2 1.0
CB C:ASP564 4.3 34.4 1.0
CG C:HIS529 4.3 38.4 1.0
ND1 C:HIS529 4.4 39.7 1.0
CB C:ASP674 4.4 40.8 1.0
O C:HOH924 4.6 41.6 1.0
NE2 C:HIS525 4.6 40.4 1.0
O C:HOH981 4.6 53.2 1.0
CA C:ASP674 4.8 39.3 1.0
CG2 C:VAL533 4.9 38.6 1.0
O C:ASP674 5.0 42.5 1.0

Zinc binding site 4 out of 4 in 5sir

Go back to Zinc Binding Sites List in 5sir
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3,6- Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyridine-2- 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 3,6- Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyridine-2- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:47.4
occ:1.00
 NE2 D:HIS563 1.9 38.6 1.0
O D:HOH917 2.0 39.8 1.0
OD2 D:ASP564 2.1 46.6 1.0
OD1 D:ASP674 2.3 45.8 1.0
NE2 D:HIS529 2.3 48.3 1.0
O D:HOH954 2.4 47.0 1.0
CD2 D:HIS563 2.8 40.6 1.0
CE1 D:HIS563 3.0 40.3 1.0
CG D:ASP564 3.1 44.6 1.0
CG D:ASP674 3.2 42.5 1.0
CD2 D:HIS529 3.2 49.1 1.0
CE1 D:HIS529 3.4 48.6 1.0
OD2 D:ASP674 3.4 37.1 1.0
MG D:MG802 3.7 41.8 1.0
OD1 D:ASP564 3.8 46.6 1.0
CG D:HIS563 4.0 41.0 1.0
O D:HOH939 4.0 48.5 1.0
ND1 D:HIS563 4.1 38.8 1.0
O D:HOH932 4.2 53.0 1.0
CB D:ASP564 4.2 40.5 1.0
CD2 D:HIS525 4.3 47.8 1.0
CG D:HIS529 4.4 46.5 1.0
ND1 D:HIS529 4.4 50.7 1.0
O D:HOH922 4.5 36.8 1.0
CB D:ASP674 4.6 43.1 1.0
NE2 D:HIS525 4.7 44.8 1.0
CG2 D:VAL533 4.8 39.3 1.0
O D:ASP674 4.8 46.0 1.0
CA D:ASP674 5.0 43.1 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 05:49:46 2024

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