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Zinc in PDB 5sgp: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- (2-Methoxyethyl)-4-N,2-Dimethyl-3-N-(2-Phenylimidazo[1,2-A]Pyridin-7- Yl)Pyrazole-3,4-Dicarboxamide

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

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- (2-Methoxyethyl)-4-N,2-Dimethyl-3-N-(2-Phenylimidazo[1,2-A]Pyridin-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-Methoxyethyl)-4-N,2-Dimethyl-3-N-(2-Phenylimidazo[1,2-A]Pyridin-7- Yl)Pyrazole-3,4-Dicarboxamide, PDB code: 5sgp 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) 43.56 / 1.95
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.398, 135.398, 235.64, 90, 90, 120
R / Rfree (%) 17.2 / 21.4

Other elements in 5sgp:

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

Zinc binding site 1 out of 4 in 5sgp

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

b:27.0
occ:1.00
 OD2 A:ASP564 2.1 21.4 1.0
NE2 A:HIS529 2.1 25.9 1.0
OD1 A:ASP674 2.2 25.7 1.0
NE2 A:HIS563 2.2 22.6 1.0
O A:HOH974 2.2 21.2 1.0
O A:HOH1008 2.2 27.9 1.0
CD2 A:HIS529 3.1 26.8 1.0
CG A:ASP564 3.1 23.3 1.0
CD2 A:HIS563 3.1 19.7 1.0
CG A:ASP674 3.1 27.6 1.0
CE1 A:HIS529 3.1 25.0 1.0
CE1 A:HIS563 3.3 22.7 1.0
OD2 A:ASP674 3.4 28.5 1.0
OD1 A:ASP564 3.5 19.7 1.0
MG A:MG802 3.8 21.2 1.0
CD2 A:HIS525 4.1 26.0 1.0
O A:HOH1011 4.1 21.7 1.0
O A:HOH972 4.2 23.0 1.0
CG A:HIS529 4.2 24.8 1.0
CG A:HIS563 4.2 22.1 1.0
ND1 A:HIS529 4.2 23.2 1.0
CB A:ASP564 4.3 22.7 1.0
ND1 A:HIS563 4.3 25.7 1.0
NE2 A:HIS525 4.3 27.4 1.0
CB A:ASP674 4.5 25.8 1.0
O A:HOH921 4.6 20.6 1.0
CG2 A:VAL533 4.7 19.6 1.0
CA A:ASP674 4.8 24.3 1.0
O A:ASP674 4.9 23.4 1.0

Zinc binding site 2 out of 4 in 5sgp

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

b:25.2
occ:1.00
 OD1 B:ASP674 2.1 19.2 1.0
O B:HOH947 2.1 17.0 1.0
NE2 B:HIS563 2.1 18.6 1.0
NE2 B:HIS529 2.2 21.5 1.0
OD2 B:ASP564 2.2 21.3 1.0
O B:HOH1015 2.2 28.6 1.0
CG B:ASP674 3.0 21.9 1.0
CD2 B:HIS563 3.0 19.6 1.0
CD2 B:HIS529 3.1 22.1 1.0
CE1 B:HIS563 3.1 20.0 1.0
CG B:ASP564 3.1 21.0 1.0
CE1 B:HIS529 3.2 22.2 1.0
OD2 B:ASP674 3.3 23.7 1.0
OD1 B:ASP564 3.7 20.5 1.0
MG B:MG802 3.8 17.7 1.0
O B:HOH995 4.0 19.4 1.0
CD2 B:HIS525 4.0 21.2 1.0
CG B:HIS563 4.2 19.8 1.0
ND1 B:HIS563 4.2 18.1 1.0
O B:HOH986 4.2 25.1 1.0
CG B:HIS529 4.3 20.4 1.0
ND1 B:HIS529 4.3 19.7 1.0
CB B:ASP564 4.3 18.3 1.0
NE2 B:HIS525 4.3 23.5 1.0
CB B:ASP674 4.4 21.6 1.0
O B:HOH958 4.6 19.1 1.0
CG2 B:VAL533 4.7 22.1 1.0
CA B:ASP674 4.8 21.0 1.0
O B:ASP674 4.9 21.9 1.0

Zinc binding site 3 out of 4 in 5sgp

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

b:26.5
occ:1.00
 O C:HOH930 2.1 17.1 1.0
OD2 C:ASP564 2.1 21.5 1.0
NE2 C:HIS529 2.1 21.9 1.0
NE2 C:HIS563 2.2 22.0 1.0
OD1 C:ASP674 2.2 21.8 1.0
O C:HOH1046 2.3 29.6 1.0
CD2 C:HIS563 3.0 22.1 1.0
CG C:ASP674 3.0 23.1 1.0
CG C:ASP564 3.1 22.0 1.0
CD2 C:HIS529 3.1 22.0 1.0
CE1 C:HIS529 3.1 23.9 1.0
CE1 C:HIS563 3.2 20.8 1.0
OD2 C:ASP674 3.3 30.4 1.0
OD1 C:ASP564 3.6 22.7 1.0
MG C:MG802 3.8 23.4 1.0
CD2 C:HIS525 4.1 22.9 1.0
O C:HOH1038 4.1 22.8 1.0
CG C:HIS563 4.2 18.3 1.0
ND1 C:HIS529 4.2 21.0 1.0
CG C:HIS529 4.3 22.9 1.0
CB C:ASP564 4.3 20.4 1.0
ND1 C:HIS563 4.3 22.7 1.0
O C:HOH983 4.3 24.8 1.0
NE2 C:HIS525 4.4 22.9 1.0
CB C:ASP674 4.4 21.7 1.0
O C:HOH928 4.7 22.1 1.0
CG2 C:VAL533 4.7 22.9 1.0
CA C:ASP674 4.8 24.5 1.0
O C:ASP674 4.9 23.7 1.0

Zinc binding site 4 out of 4 in 5sgp

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

b:31.8
occ:1.00
 O D:HOH942 2.0 25.1 1.0
NE2 D:HIS529 2.1 28.8 1.0
NE2 D:HIS563 2.1 22.7 1.0
O D:HOH975 2.2 36.7 1.0
OD2 D:ASP564 2.2 24.7 1.0
OD1 D:ASP674 2.3 24.8 1.0
CD2 D:HIS563 3.0 24.9 1.0
CD2 D:HIS529 3.1 34.4 1.0
CE1 D:HIS529 3.1 29.2 1.0
CG D:ASP674 3.1 28.1 1.0
CG D:ASP564 3.2 28.0 1.0
CE1 D:HIS563 3.2 23.8 1.0
OD2 D:ASP674 3.3 30.2 1.0
OD1 D:ASP564 3.7 27.8 1.0
MG D:MG802 3.9 30.9 1.0
CD2 D:HIS525 4.1 29.3 1.0
O D:HOH984 4.2 27.6 1.0
CG D:HIS563 4.2 22.5 1.0
ND1 D:HIS529 4.2 26.2 1.0
CG D:HIS529 4.2 30.1 1.0
ND1 D:HIS563 4.3 25.2 1.0
O D:HOH916 4.3 28.9 1.0
CB D:ASP564 4.3 24.1 1.0
NE2 D:HIS525 4.5 35.1 1.0
CB D:ASP674 4.5 25.9 1.0
CG2 D:VAL533 4.6 29.6 1.0
O D:HOH926 4.7 27.7 1.0
O D:ASP674 4.8 25.9 1.0
CA D:ASP674 4.8 25.7 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 05:16:30 2024

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