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Magnesium in PDB 5sij: Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-[1,2, 4]Triazolo[1,5-A]Pyrazine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-[1,2, 4]Triazolo[1,5-A]Pyrazine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-[1,2, 4]Triazolo[1,5-A]Pyrazine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-[1,2, 4]Triazolo[1,5-A]Pyrazine, PDB code: 5sij 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) 43.74 / 2.55
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.711, 135.711, 235.6, 90, 90, 120
R / Rfree (%) 17.5 / 24.3

Other elements in 5sij:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-[1,2, 4]Triazolo[1,5-A]Pyrazine 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 5,8- Dimethyl-2-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-[1,2, 4]Triazolo[1,5-A]Pyrazine (pdb code 5sij). 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 5,8- Dimethyl-2-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-[1,2, 4]Triazolo[1,5-A]Pyrazine, PDB code: 5sij:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sij

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-[1,2, 4]Triazolo[1,5-A]Pyrazine


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 5,8- Dimethyl-2-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-[1,2, 4]Triazolo[1,5-A]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:48.4
occ:1.00
 O A:HOH912 1.8 49.9 1.0
O A:HOH916 1.9 43.5 1.0
O A:HOH908 1.9 46.3 1.0
OD1 A:ASP564 2.0 52.3 1.0
O A:HOH907 2.0 48.1 1.0
O A:HOH903 2.1 37.9 1.0
CG A:ASP564 3.1 52.5 1.0
OD2 A:ASP564 3.6 52.7 1.0
O A:HOH913 3.6 68.6 1.0
ZN A:ZN801 3.9 61.0 1.0
NE2 A:HIS595 4.0 51.8 1.0
CD2 A:HIS567 4.2 54.7 1.0
OE2 A:GLU592 4.2 55.7 1.0
CB A:ASP564 4.4 46.0 1.0
CD2 A:HIS595 4.4 52.3 1.0
CD2 A:HIS525 4.4 52.9 1.0
NE2 A:HIS567 4.5 53.9 1.0
CD2 A:HIS563 4.5 42.8 1.0
O A:THR633 4.5 43.1 1.0
O A:HIS563 4.5 51.7 1.0
NE2 A:HIS525 4.5 57.7 1.0
OD2 A:ASP674 4.5 69.2 1.0
OG1 A:THR633 4.6 45.9 1.0
NE2 A:HIS563 4.7 41.2 1.0
CA A:ASP564 4.8 49.9 1.0
CG A:GLU592 4.8 54.2 1.0
CB A:THR633 4.9 47.1 1.0
CD A:GLU592 4.9 52.6 1.0

Magnesium binding site 2 out of 4 in 5sij

Go back to Magnesium Binding Sites List in 5sij
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-[1,2, 4]Triazolo[1,5-A]Pyrazine


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 5,8- Dimethyl-2-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-[1,2, 4]Triazolo[1,5-A]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:47.0
occ:1.00
 O B:HOH914 1.9 42.5 1.0
O B:HOH921 1.9 45.5 1.0
O B:HOH909 1.9 42.2 1.0
O B:HOH923 2.1 36.5 1.0
OD1 B:ASP564 2.1 49.7 1.0
O B:HOH901 2.4 42.4 1.0
CG B:ASP564 3.2 48.9 1.0
OD2 B:ASP564 3.5 50.5 1.0
OE2 B:GLU592 3.9 56.6 1.0
ZN B:ZN801 3.9 55.5 1.0
NE2 B:HIS595 4.0 42.6 1.0
OG1 B:THR633 4.2 47.3 1.0
CD2 B:HIS563 4.2 47.2 1.0
CD2 B:HIS595 4.3 52.8 1.0
O B:HIS563 4.3 50.2 1.0
OD2 B:ASP674 4.4 46.3 1.0
CD2 B:HIS567 4.4 57.2 1.0
O B:THR633 4.5 41.7 1.0
CB B:ASP564 4.5 47.2 1.0
NE2 B:HIS567 4.6 55.7 1.0
CD2 B:HIS525 4.6 56.9 1.0
CB B:THR633 4.7 51.4 1.0
CG B:GLU592 4.7 49.5 1.0
NE2 B:HIS563 4.7 46.1 1.0
CD B:GLU592 4.7 53.5 1.0
NE2 B:HIS525 4.9 50.8 1.0
CA B:ASP564 4.9 52.6 1.0
O B:HOH927 5.0 43.6 1.0

Magnesium binding site 3 out of 4 in 5sij

Go back to Magnesium Binding Sites List in 5sij
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-[1,2, 4]Triazolo[1,5-A]Pyrazine


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 5,8- Dimethyl-2-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-[1,2, 4]Triazolo[1,5-A]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:41.9
occ:1.00
 O C:HOH923 2.0 46.3 1.0
O C:HOH904 2.1 41.4 1.0
O C:HOH914 2.1 38.6 1.0
O C:HOH907 2.1 45.4 1.0
OD1 C:ASP564 2.1 42.0 1.0
O C:HOH912 2.2 39.4 1.0
CG C:ASP564 2.9 43.9 1.0
OD2 C:ASP564 3.1 51.6 1.0
ZN C:ZN801 3.6 56.5 1.0
O C:HOH918 3.8 57.9 1.0
CD2 C:HIS563 4.0 45.9 1.0
OE2 C:GLU592 4.1 50.3 1.0
OD2 C:ASP674 4.2 44.6 1.0
OG1 C:THR633 4.2 50.5 1.0
NE2 C:HIS595 4.3 56.0 1.0
CB C:ASP564 4.4 44.1 1.0
NE2 C:HIS563 4.4 45.1 1.0
CD2 C:HIS567 4.4 45.9 1.0
O C:HOH917 4.4 48.6 1.0
O C:HIS563 4.4 48.1 1.0
O C:THR633 4.5 49.4 1.0
CD2 C:HIS595 4.5 54.9 1.0
CD2 C:HIS525 4.6 57.8 1.0
NE2 C:HIS525 4.6 58.2 1.0
NE2 C:HIS567 4.6 47.6 1.0
CB C:THR633 4.7 52.1 1.0
CA C:ASP564 4.9 47.1 1.0
OD1 C:ASP674 4.9 49.1 1.0
CG C:ASP674 5.0 40.5 1.0
CG C:GLU592 5.0 49.9 1.0

Magnesium binding site 4 out of 4 in 5sij

Go back to Magnesium Binding Sites List in 5sij
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-[1,2, 4]Triazolo[1,5-A]Pyrazine


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 5,8- Dimethyl-2-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-[1,2, 4]Triazolo[1,5-A]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:68.8
occ:1.00
 O D:HOH901 2.0 62.5 1.0
O D:HOH902 2.1 75.0 1.0
OD1 D:ASP564 2.3 69.8 1.0
CG D:ASP564 3.2 77.8 1.0
OD2 D:ASP564 3.4 93.0 1.0
OE2 D:GLU592 3.9 73.5 1.0
ZN D:ZN801 4.0 78.8 1.0
CD2 D:HIS567 4.0 70.2 1.0
NE2 D:HIS525 4.1 81.2 1.0
CD2 D:HIS525 4.1 86.2 1.0
NE2 D:HIS595 4.2 73.7 1.0
NE2 D:HIS567 4.3 75.3 1.0
CB D:ASP564 4.6 82.7 1.0
CD2 D:HIS595 4.6 79.6 1.0
O D:THR633 4.7 82.0 1.0
CD2 D:HIS563 4.8 63.8 1.0
OG1 D:THR633 4.8 84.9 1.0
CD D:GLU592 4.8 77.2 1.0
O D:HIS563 4.9 77.0 1.0
OD2 D:ASP674 4.9 95.9 1.0
CA D:ASP564 5.0 77.9 1.0
NE2 D:HIS563 5.0 55.2 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 04:11:02 2024

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