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Zinc in PDB 5si9: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- (2-Hydroxyethyl)-2-Methyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl) Pyrazole-3,4-Dicarboxamide

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

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

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- (2-Hydroxyethyl)-2-Methyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl) Pyrazole-3,4-Dicarboxamide, PDB code: 5si9 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) 43.91 / 2.01
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 136.254, 136.254, 236.528, 90, 90, 120
R / Rfree (%) 18.7 / 22.2

Other elements in 5si9:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- (2-Hydroxyethyl)-2-Methyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl) Pyrazole-3,4-Dicarboxamide 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 4-N- (2-Hydroxyethyl)-2-Methyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl) Pyrazole-3,4-Dicarboxamide (pdb code 5si9). 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-N- (2-Hydroxyethyl)-2-Methyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl) Pyrazole-3,4-Dicarboxamide, PDB code: 5si9:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5si9

Go back to Zinc Binding Sites List in 5si9
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- (2-Hydroxyethyl)-2-Methyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl) Pyrazole-3,4-Dicarboxamide


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

b:30.4
occ:1.00
 OD2 A:ASP564 2.1 28.6 1.0
O A:HOH993 2.1 32.1 1.0
NE2 A:HIS563 2.1 26.1 1.0
NE2 A:HIS529 2.1 29.0 1.0
O A:HOH927 2.2 23.5 1.0
OD1 A:ASP674 2.2 29.4 1.0
CD2 A:HIS563 3.0 24.7 1.0
CD2 A:HIS529 3.1 27.3 1.0
CG A:ASP674 3.1 31.0 1.0
CG A:ASP564 3.1 27.1 1.0
CE1 A:HIS529 3.2 28.2 1.0
CE1 A:HIS563 3.2 27.5 1.0
OD2 A:ASP674 3.3 36.1 1.0
OD1 A:ASP564 3.6 25.2 1.0
MG A:MG802 3.8 26.1 1.0
O A:HOH1016 4.1 24.4 1.0
CD2 A:HIS525 4.2 32.2 1.0
CG A:HIS563 4.2 25.6 1.0
O A:HOH972 4.2 33.9 1.0
ND1 A:HIS563 4.2 25.9 1.0
CG A:HIS529 4.2 27.7 1.0
ND1 A:HIS529 4.3 27.2 1.0
CB A:ASP564 4.3 25.9 1.0
CB A:ASP674 4.5 29.0 1.0
NE2 A:HIS525 4.5 31.0 1.0
O A:HOH924 4.6 25.8 1.0
CG2 A:VAL533 4.7 23.6 1.0
O A:ASP674 4.8 28.0 1.0
CA A:ASP674 4.9 28.1 1.0

Zinc binding site 2 out of 4 in 5si9

Go back to Zinc Binding Sites List in 5si9
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- (2-Hydroxyethyl)-2-Methyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl) Pyrazole-3,4-Dicarboxamide


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

b:29.2
occ:1.00
 NE2 B:HIS563 2.1 22.6 1.0
OD2 B:ASP564 2.1 24.0 1.0
O B:HOH980 2.1 35.8 1.0
OD1 B:ASP674 2.2 25.0 1.0
NE2 B:HIS529 2.2 23.3 1.0
O B:HOH940 2.2 19.5 1.0
CD2 B:HIS563 3.0 22.9 1.0
CG B:ASP674 3.0 28.2 1.0
CD2 B:HIS529 3.1 25.2 1.0
CG B:ASP564 3.1 25.3 1.0
CE1 B:HIS563 3.1 23.6 1.0
CE1 B:HIS529 3.2 24.7 1.0
OD2 B:ASP674 3.2 30.1 1.0
OD1 B:ASP564 3.6 25.9 1.0
MG B:MG802 3.8 26.4 1.0
O B:HOH1018 4.1 25.7 1.0
CD2 B:HIS525 4.1 28.3 1.0
O B:HOH1019 4.1 35.4 1.0
CG B:HIS563 4.2 23.2 1.0
ND1 B:HIS563 4.2 22.9 1.0
CG B:HIS529 4.3 24.9 1.0
ND1 B:HIS529 4.3 22.8 1.0
CB B:ASP564 4.3 24.4 1.0
CB B:ASP674 4.4 27.8 1.0
NE2 B:HIS525 4.5 29.2 1.0
O B:HOH1049 4.6 48.1 1.0
O B:HOH974 4.7 23.9 1.0
CG2 B:VAL533 4.7 24.4 1.0
CA B:ASP674 4.8 25.6 1.0
O B:ASP674 4.9 25.3 1.0

Zinc binding site 3 out of 4 in 5si9

Go back to Zinc Binding Sites List in 5si9
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- (2-Hydroxyethyl)-2-Methyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl) Pyrazole-3,4-Dicarboxamide


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

b:30.3
occ:1.00
 O C:HOH919 2.1 22.5 1.0
OD2 C:ASP564 2.1 24.7 1.0
NE2 C:HIS529 2.2 26.8 1.0
NE2 C:HIS563 2.2 27.6 1.0
OD1 C:ASP674 2.2 28.2 1.0
O C:HOH1011 2.2 33.1 1.0
CD2 C:HIS563 3.0 26.3 1.0
CG C:ASP674 3.0 29.3 1.0
CD2 C:HIS529 3.1 26.4 1.0
CG C:ASP564 3.1 25.3 1.0
CE1 C:HIS529 3.2 27.4 1.0
OD2 C:ASP674 3.2 34.1 1.0
CE1 C:HIS563 3.3 25.6 1.0
OD1 C:ASP564 3.6 24.5 1.0
MG C:MG802 3.8 25.5 1.0
CD2 C:HIS525 4.1 30.1 1.0
O C:HOH1026 4.2 24.4 1.0
CG C:HIS563 4.2 26.6 1.0
O C:HOH1015 4.2 38.5 1.0
CG C:HIS529 4.3 26.1 1.0
ND1 C:HIS529 4.3 25.9 1.0
ND1 C:HIS563 4.3 25.3 1.0
CB C:ASP564 4.3 24.5 1.0
CB C:ASP674 4.4 28.3 1.0
NE2 C:HIS525 4.5 30.6 1.0
O C:HOH970 4.6 24.0 1.0
CG2 C:VAL533 4.8 25.6 1.0
CA C:ASP674 4.8 28.6 1.0
O C:HOH1034 4.8 53.4 1.0
O C:ASP674 4.9 27.6 1.0

Zinc binding site 4 out of 4 in 5si9

Go back to Zinc Binding Sites List in 5si9
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- (2-Hydroxyethyl)-2-Methyl-3-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl) Pyrazole-3,4-Dicarboxamide


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

b:35.3
occ:1.00
 O D:HOH917 2.1 24.9 1.0
NE2 D:HIS563 2.1 26.9 1.0
O D:HOH988 2.1 35.2 1.0
NE2 D:HIS529 2.2 34.2 1.0
OD2 D:ASP564 2.2 30.7 1.0
OD1 D:ASP674 2.2 34.4 1.0
CD2 D:HIS563 2.9 28.9 1.0
CG D:ASP674 3.0 34.8 1.0
CD2 D:HIS529 3.1 35.7 1.0
CG D:ASP564 3.1 29.9 1.0
CE1 D:HIS529 3.2 34.8 1.0
CE1 D:HIS563 3.2 28.6 1.0
OD2 D:ASP674 3.2 38.4 1.0
OD1 D:ASP564 3.6 32.3 1.0
MG D:MG802 3.9 33.0 1.0
O D:HOH980 4.1 30.5 1.0
CG D:HIS563 4.1 29.2 1.0
CD2 D:HIS525 4.2 36.2 1.0
ND1 D:HIS563 4.3 27.4 1.0
CG D:HIS529 4.3 32.8 1.0
CB D:ASP564 4.3 29.4 1.0
ND1 D:HIS529 4.3 33.6 1.0
O D:HOH935 4.3 43.0 1.0
CB D:ASP674 4.4 34.4 1.0
O D:HOH919 4.5 33.2 1.0
CG2 D:VAL533 4.7 33.7 1.0
NE2 D:HIS525 4.7 39.5 1.0
O D:ASP674 4.8 33.3 1.0
CA D:ASP674 4.9 32.7 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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