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Magnesium 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:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 4 in 5sir

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

b:41.0
occ:1.00
 O A:HOH932 1.9 36.1 1.0
O A:HOH951 2.0 43.2 1.0
O A:HOH987 2.0 37.4 1.0
O A:HOH914 2.0 33.0 1.0
OD1 A:ASP564 2.1 34.2 1.0
O A:HOH929 2.1 41.3 1.0
CG A:ASP564 3.1 38.3 1.0
OD2 A:ASP564 3.4 41.6 1.0
ZN A:ZN801 3.8 43.3 1.0
NE2 A:HIS595 4.1 42.6 1.0
OE2 A:GLU592 4.2 47.0 1.0
O A:HOH925 4.2 38.2 1.0
OG1 A:THR633 4.2 40.1 1.0
CD2 A:HIS563 4.3 34.9 1.0
O A:THR633 4.3 40.1 1.0
CD2 A:HIS567 4.3 44.5 1.0
CD2 A:HIS595 4.4 41.7 1.0
CB A:ASP564 4.5 35.6 1.0
OD2 A:ASP674 4.5 44.5 1.0
NE2 A:HIS567 4.5 43.3 1.0
NE2 A:HIS563 4.6 37.4 1.0
CD2 A:HIS525 4.6 43.5 1.0
CB A:THR633 4.6 40.4 1.0
NE2 A:HIS525 4.6 45.5 1.0
O A:HIS563 4.7 35.8 1.0
CG A:GLU592 4.8 42.1 1.0
CA A:ASP564 4.9 37.2 1.0
CD A:GLU592 5.0 43.8 1.0
C A:THR633 5.0 41.0 1.0

Magnesium binding site 2 out of 4 in 5sir

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

b:33.0
occ:1.00
 O B:HOH933 2.0 36.2 1.0
O B:HOH981 2.0 29.1 1.0
O B:HOH919 2.1 34.4 1.0
O B:HOH913 2.1 31.4 1.0
O B:HOH954 2.2 29.0 1.0
OD1 B:ASP564 2.4 36.2 1.0
CG B:ASP564 3.4 35.7 1.0
OD2 B:ASP564 3.6 38.9 1.0
ZN B:ZN801 3.8 41.0 1.0
OE2 B:GLU592 4.1 34.6 1.0
NE2 B:HIS595 4.2 43.0 1.0
O B:THR633 4.3 41.3 1.0
CD2 B:HIS563 4.3 34.0 1.0
OD2 B:ASP674 4.3 41.4 1.0
OG1 B:THR633 4.3 42.2 1.0
O B:HOH950 4.3 31.4 1.0
CD2 B:HIS567 4.4 41.2 1.0
O B:HIS563 4.4 37.4 1.0
CD2 B:HIS595 4.4 41.7 1.0
NE2 B:HIS567 4.5 40.0 1.0
CB B:THR633 4.5 37.2 1.0
NE2 B:HIS563 4.6 34.8 1.0
CD2 B:HIS525 4.7 41.4 1.0
CB B:ASP564 4.7 34.5 1.0
NE2 B:HIS525 4.8 36.9 1.0
CG B:GLU592 4.9 35.3 1.0
CD B:GLU592 4.9 34.8 1.0
C B:THR633 4.9 36.8 1.0
CA B:ASP564 5.0 37.0 1.0

Magnesium binding site 3 out of 4 in 5sir

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

b:36.4
occ:1.00
 O C:HOH937 1.9 40.3 1.0
O C:HOH924 2.1 41.6 1.0
OD1 C:ASP564 2.2 35.7 1.0
O C:HOH921 2.2 38.6 1.0
O C:HOH915 2.3 36.6 1.0
O C:HOH920 2.3 35.3 1.0
CG C:ASP564 3.2 34.8 1.0
OD2 C:ASP564 3.5 37.7 1.0
OE2 C:GLU592 3.9 44.0 1.0
ZN C:ZN801 4.0 44.4 1.0
NE2 C:HIS595 4.0 46.1 1.0
O C:HOH916 4.0 35.9 1.0
CD2 C:HIS567 4.2 38.2 1.0
CD2 C:HIS595 4.3 46.9 1.0
NE2 C:HIS567 4.3 39.3 1.0
CD2 C:HIS563 4.4 35.5 1.0
OG1 C:THR633 4.5 39.7 1.0
O C:HIS563 4.5 34.9 1.0
OD2 C:ASP674 4.5 37.6 1.0
CB C:ASP564 4.5 34.4 1.0
O C:THR633 4.5 42.3 1.0
NE2 C:HIS525 4.6 40.4 1.0
CD2 C:HIS525 4.7 42.2 1.0
NE2 C:HIS563 4.7 34.9 1.0
CG C:GLU592 4.8 40.6 1.0
CD C:GLU592 4.8 42.1 1.0
CB C:THR633 4.9 36.4 1.0
CA C:ASP564 4.9 37.0 1.0

Magnesium binding site 4 out of 4 in 5sir

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

b:41.8
occ:1.00
 O D:HOH939 2.0 48.5 1.0
O D:HOH922 2.0 36.8 1.0
O D:HOH945 2.1 49.8 1.0
OD1 D:ASP564 2.1 46.6 1.0
O D:HOH917 2.2 39.8 1.0
O D:HOH904 2.4 41.3 1.0
CG D:ASP564 3.0 44.6 1.0
OD2 D:ASP564 3.3 46.6 1.0
O D:HOH954 3.7 47.0 1.0
ZN D:ZN801 3.7 47.4 1.0
NE2 D:HIS595 4.1 53.1 1.0
OE2 D:GLU592 4.1 46.2 1.0
O D:HOH958 4.2 56.6 1.0
CD2 D:HIS563 4.3 40.6 1.0
CD2 D:HIS567 4.3 48.1 1.0
OG1 D:THR633 4.3 40.8 1.0
CB D:ASP564 4.4 40.5 1.0
CD2 D:HIS595 4.4 51.9 1.0
O D:HIS563 4.4 43.8 1.0
CD2 D:HIS525 4.6 47.8 1.0
OD2 D:ASP674 4.6 37.1 1.0
NE2 D:HIS567 4.6 51.6 1.0
NE2 D:HIS525 4.6 44.8 1.0
NE2 D:HIS563 4.6 38.6 1.0
O D:THR633 4.7 43.8 1.0
CA D:ASP564 4.7 41.3 1.0
CB D:THR633 4.9 40.4 1.0
CG D:GLU592 4.9 44.4 1.0
CD D:GLU592 5.0 44.4 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: Tue Aug 12 20:00:21 2025

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