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Zinc in PDB 5sgd: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Methoxymethyl)-2-Methyl-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7- Yl)Pyrazole-3-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Methoxymethyl)-2-Methyl-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7- Yl)Pyrazole-3-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Methoxymethyl)-2-Methyl-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7- Yl)Pyrazole-3-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Methoxymethyl)-2-Methyl-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7- Yl)Pyrazole-3-Carboxamide, PDB code: 5sgd was solved by C.Joseph, J.Benz, A.Flohr, K.Groebke-Zbinden, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.56 / 2.54
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.391, 135.391, 236.173, 90, 90, 120
R / Rfree (%) 16.7 / 25.7

Other elements in 5sgd:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Methoxymethyl)-2-Methyl-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7- Yl)Pyrazole-3-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 4- (Methoxymethyl)-2-Methyl-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7- Yl)Pyrazole-3-Carboxamide (pdb code 5sgd). 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- (Methoxymethyl)-2-Methyl-N-(2-Phenyl-[1,2,4]Triazolo[1,5-A]Pyridin-7- Yl)Pyrazole-3-Carboxamide, PDB code: 5sgd:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sgd

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

b:53.2
occ:1.00
 OD2 A:ASP564 2.1 54.4 1.0
NE2 A:HIS563 2.1 41.0 1.0
NE2 A:HIS529 2.1 43.8 1.0
OD1 A:ASP674 2.2 57.9 1.0
O A:HOH919 2.2 45.2 1.0
O A:HOH908 2.3 58.8 1.0
CG A:ASP674 3.0 54.9 1.0
CD2 A:HIS563 3.1 39.6 1.0
CE1 A:HIS563 3.1 42.3 1.0
CE1 A:HIS529 3.1 50.5 1.0
CG A:ASP564 3.1 45.9 1.0
CD2 A:HIS529 3.1 43.5 1.0
OD2 A:ASP674 3.2 50.0 1.0
OD1 A:ASP564 3.6 55.4 1.0
MG A:MG802 3.7 52.5 1.0
CD2 A:HIS525 4.1 59.0 1.0
O A:HOH917 4.1 36.4 1.0
ND1 A:HIS563 4.2 38.5 1.0
NE2 A:HIS525 4.2 59.9 1.0
CG A:HIS563 4.2 42.7 1.0
ND1 A:HIS529 4.2 54.6 1.0
CG A:HIS529 4.3 41.6 1.0
CB A:ASP564 4.3 38.0 1.0
CB A:ASP674 4.4 49.4 1.0
O A:HOH903 4.6 42.1 1.0
CG2 A:VAL533 4.8 37.2 1.0
O A:ASP674 4.9 55.9 1.0
CA A:ASP674 4.9 48.2 1.0

Zinc binding site 2 out of 4 in 5sgd

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

b:50.4
occ:1.00
 NE2 B:HIS563 2.0 39.2 1.0
NE2 B:HIS529 2.1 42.9 1.0
OD2 B:ASP564 2.2 47.3 1.0
O B:HOH922 2.2 31.6 1.0
OD1 B:ASP674 2.3 49.1 1.0
O B:HOH919 2.3 47.3 1.0
CD2 B:HIS563 3.0 52.5 1.0
CE1 B:HIS563 3.0 48.2 1.0
CE1 B:HIS529 3.1 43.0 1.0
CG B:ASP674 3.1 45.8 1.0
CD2 B:HIS529 3.1 38.7 1.0
CG B:ASP564 3.2 44.2 1.0
OD2 B:ASP674 3.2 42.6 1.0
OD1 B:ASP564 3.6 47.4 1.0
MG B:MG802 3.8 44.0 1.0
O B:HOH924 3.9 44.9 1.0
O B:HOH939 4.0 31.8 1.0
CG B:HIS563 4.1 46.1 1.0
ND1 B:HIS563 4.1 45.8 1.0
ND1 B:HIS529 4.2 44.4 1.0
CD2 B:HIS525 4.2 50.3 1.0
CG B:HIS529 4.3 41.2 1.0
CB B:ASP564 4.4 42.5 1.0
CB B:ASP674 4.5 44.1 1.0
NE2 B:HIS525 4.5 37.3 1.0
CG2 B:VAL533 4.7 34.0 1.0
O B:HOH921 4.8 46.8 1.0
O B:ASP674 4.9 53.8 1.0
CA B:ASP674 4.9 43.4 1.0

Zinc binding site 3 out of 4 in 5sgd

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

b:53.0
occ:1.00
 OD2 C:ASP564 2.0 51.9 1.0
OD1 C:ASP674 2.0 58.5 1.0
O C:HOH918 2.0 40.0 1.0
NE2 C:HIS529 2.1 46.5 1.0
NE2 C:HIS563 2.1 39.9 1.0
O C:HOH913 2.4 51.4 1.0
CG C:ASP674 3.0 39.0 1.0
CD2 C:HIS563 3.1 45.5 1.0
CD2 C:HIS529 3.1 44.1 1.0
CG C:ASP564 3.1 42.9 1.0
CE1 C:HIS529 3.1 48.8 1.0
CE1 C:HIS563 3.2 43.2 1.0
OD2 C:ASP674 3.3 47.6 1.0
MG C:MG802 3.7 43.6 1.0
OD1 C:ASP564 3.7 50.3 1.0
CD2 C:HIS525 4.1 56.9 1.0
O C:HOH935 4.1 35.1 1.0
CB C:ASP564 4.3 36.1 1.0
ND1 C:HIS529 4.3 38.4 1.0
CG C:HIS563 4.3 38.6 1.0
CG C:HIS529 4.3 37.5 1.0
ND1 C:HIS563 4.3 35.5 1.0
CB C:ASP674 4.4 44.6 1.0
NE2 C:HIS525 4.4 50.2 1.0
O C:HOH909 4.5 49.1 1.0
O C:ASP674 4.8 45.1 1.0
CA C:ASP674 4.8 44.7 1.0
CG2 C:VAL533 5.0 44.1 1.0

Zinc binding site 4 out of 4 in 5sgd

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

b:72.9
occ:1.00
 OD2 D:ASP564 2.0 86.3 1.0
NE2 D:HIS563 2.2 53.0 1.0
O D:HOH903 2.2 53.9 1.0
OD1 D:ASP674 2.2 71.9 1.0
NE2 D:HIS529 2.3 53.1 1.0
O D:HOH902 2.4 54.8 1.0
CG D:ASP674 3.1 72.5 1.0
CD2 D:HIS563 3.1 58.8 1.0
CD2 D:HIS529 3.1 61.1 1.0
CG D:ASP564 3.2 68.1 1.0
CE1 D:HIS563 3.2 67.4 1.0
OD2 D:ASP674 3.3 92.0 1.0
CE1 D:HIS529 3.4 61.7 1.0
OD1 D:ASP564 3.9 76.5 1.0
MG D:MG802 3.9 56.0 1.0
O D:HOH911 4.1 60.8 1.0
CD2 D:HIS525 4.1 77.1 1.0
CG D:HIS563 4.3 66.8 1.0
CB D:ASP564 4.3 62.6 1.0
ND1 D:HIS563 4.3 60.7 1.0
CG D:HIS529 4.3 55.8 1.0
CB D:ASP674 4.4 82.9 1.0
ND1 D:HIS529 4.4 59.0 1.0
NE2 D:HIS525 4.4 70.7 1.0
CG2 D:VAL533 4.5 70.1 1.0
O D:HOH905 4.6 60.3 1.0
O D:ASP674 4.7 92.5 1.0
CA D:ASP674 4.7 77.4 1.0
O D:HOH906 5.0 53.4 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 05:11:59 2024

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