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Magnesium 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:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sgd

Go back to Magnesium Binding Sites List in 5sgd
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg802

b:52.5
occ:1.00
 O A:HOH919 1.9 45.2 1.0
O A:HOH917 2.0 36.4 1.0
OD1 A:ASP564 2.0 55.4 1.0
O A:HOH931 2.1 43.6 1.0
O A:HOH903 2.1 42.1 1.0
O A:HOH918 2.2 49.7 1.0
CG A:ASP564 3.0 45.9 1.0
OD2 A:ASP564 3.3 54.4 1.0
ZN A:ZN801 3.7 53.2 1.0
O A:HOH908 3.8 58.8 1.0
O A:HOH924 4.0 42.7 1.0
NE2 A:HIS595 4.1 43.5 1.0
CD2 A:HIS567 4.2 48.6 1.0
NE2 A:HIS525 4.3 59.9 1.0
O A:HIS563 4.3 48.3 1.0
OE2 A:GLU592 4.3 53.5 1.0
CB A:ASP564 4.3 38.0 1.0
CD2 A:HIS525 4.4 59.0 1.0
CD2 A:HIS595 4.4 54.4 1.0
CD2 A:HIS563 4.4 39.6 1.0
OG1 A:THR633 4.4 53.9 1.0
NE2 A:HIS567 4.5 44.2 1.0
OD2 A:ASP674 4.6 50.0 1.0
NE2 A:HIS563 4.6 41.0 1.0
O A:THR633 4.7 48.2 1.0
CA A:ASP564 4.8 41.0 1.0
CB A:THR633 4.9 43.3 1.0
CG A:GLU592 4.9 49.3 1.0

Magnesium binding site 2 out of 4 in 5sgd

Go back to Magnesium Binding Sites List in 5sgd
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg802

b:44.0
occ:1.00
 O B:HOH922 1.8 31.6 1.0
O B:HOH921 1.9 46.8 1.0
O B:HOH905 2.0 39.5 1.0
O B:HOH939 2.0 31.8 1.0
O B:HOH913 2.0 37.6 1.0
OD1 B:ASP564 2.2 47.4 1.0
CG B:ASP564 3.2 44.2 1.0
OD2 B:ASP564 3.6 47.3 1.0
O B:HOH919 3.7 47.3 1.0
ZN B:ZN801 3.8 50.4 1.0
OE2 B:GLU592 4.0 53.5 1.0
NE2 B:HIS595 4.0 44.9 1.0
CD2 B:HIS563 4.1 52.5 1.0
O B:HOH917 4.2 44.8 1.0
OG1 B:THR633 4.2 43.1 1.0
CD2 B:HIS595 4.3 42.1 1.0
OD2 B:ASP674 4.4 42.6 1.0
O B:HIS563 4.4 45.9 1.0
NE2 B:HIS563 4.4 39.2 1.0
O B:THR633 4.5 45.2 1.0
CD2 B:HIS567 4.5 48.3 1.0
CB B:ASP564 4.5 42.5 1.0
CD2 B:HIS525 4.6 50.3 1.0
NE2 B:HIS567 4.6 45.7 1.0
CB B:THR633 4.7 36.1 1.0
CG B:GLU592 4.7 44.5 1.0
NE2 B:HIS525 4.7 37.3 1.0
CD B:GLU592 4.8 53.3 1.0
CA B:ASP564 4.8 44.0 1.0

Magnesium binding site 3 out of 4 in 5sgd

Go back to Magnesium Binding Sites List in 5sgd
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg802

b:43.6
occ:1.00
 O C:HOH909 1.9 49.1 1.0
O C:HOH918 1.9 40.0 1.0
O C:HOH935 2.0 35.1 1.0
O C:HOH922 2.1 38.6 1.0
O C:HOH914 2.2 36.2 1.0
OD1 C:ASP564 2.3 50.3 1.0
CG C:ASP564 3.1 42.9 1.0
OD2 C:ASP564 3.3 51.9 1.0
ZN C:ZN801 3.7 53.0 1.0
O C:HOH913 3.9 51.4 1.0
OG1 C:THR633 4.0 40.0 1.0
CD2 C:HIS563 4.1 45.5 1.0
OE2 C:GLU592 4.2 45.2 1.0
NE2 C:HIS595 4.2 46.0 1.0
O C:HIS563 4.3 41.6 1.0
CD2 C:HIS567 4.3 49.2 1.0
OD2 C:ASP674 4.4 47.6 1.0
O C:HOH924 4.4 41.4 1.0
CB C:THR633 4.4 50.8 1.0
NE2 C:HIS563 4.5 39.9 1.0
CB C:ASP564 4.5 36.1 1.0
O C:THR633 4.5 44.1 1.0
CD2 C:HIS595 4.6 48.3 1.0
NE2 C:HIS567 4.6 55.2 1.0
CD2 C:HIS525 4.8 56.9 1.0
CG C:GLU592 4.8 41.9 1.0
NE2 C:HIS525 4.8 50.2 1.0
CA C:ASP564 4.9 41.4 1.0
OD1 C:ASP674 4.9 58.5 1.0
CD C:GLU592 5.0 46.0 1.0

Magnesium binding site 4 out of 4 in 5sgd

Go back to Magnesium Binding Sites List in 5sgd
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg802

b:56.0
occ:1.00
 OD1 D:ASP564 1.9 76.5 1.0
O D:HOH911 2.0 60.8 1.0
O D:HOH909 2.0 57.4 1.0
O D:HOH906 2.1 53.4 1.0
O D:HOH903 2.2 53.9 1.0
O D:HOH905 2.2 60.3 1.0
CG D:ASP564 2.8 68.1 1.0
OD2 D:ASP564 3.1 86.3 1.0
O D:HOH902 3.7 54.8 1.0
NE2 D:HIS595 3.8 59.1 1.0
ZN D:ZN801 3.9 72.9 1.0
CD2 D:HIS567 4.0 58.8 1.0
CB D:ASP564 4.1 62.6 1.0
OE2 D:GLU592 4.2 66.0 1.0
NE2 D:HIS567 4.2 64.2 1.0
CD2 D:HIS563 4.2 58.8 1.0
CD2 D:HIS595 4.3 62.8 1.0
O D:HIS563 4.3 66.2 1.0
CD2 D:HIS525 4.4 77.1 1.0
OG1 D:THR633 4.4 72.4 1.0
CA D:ASP564 4.4 64.2 1.0
NE2 D:HIS525 4.5 70.7 1.0
OD2 D:ASP674 4.5 92.0 1.0
NE2 D:HIS563 4.6 53.0 1.0
CE1 D:HIS595 4.7 75.9 1.0
O D:THR633 4.8 57.1 1.0
CD D:GLU592 4.9 65.1 1.0
C D:HIS563 4.9 67.1 1.0
CB D:THR633 4.9 66.0 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 Sep 30 03:46:19 2024

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