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Magnesium in PDB 5sg6: Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-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-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-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-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-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-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-A]Pyrazine, PDB code: 5sg6 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) 43.72 / 1.96
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.437, 135.437, 235.568, 90, 90, 120
R / Rfree (%) 17.8 / 21.9

Other elements in 5sg6:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-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-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-A]Pyrazine (pdb code 5sg6). 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-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-A]Pyrazine, PDB code: 5sg6:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sg6

Go back to Magnesium Binding Sites List in 5sg6
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-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-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-A]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:28.5
occ:1.00
 O A:HOH1013 2.0 25.2 1.0
O A:HOH980 2.0 28.4 1.0
OD1 A:ASP564 2.0 26.9 1.0
O A:HOH928 2.1 26.9 1.0
O A:HOH930 2.2 26.8 1.0
O A:HOH968 2.2 28.2 1.0
CG A:ASP564 3.1 28.4 1.0
OD2 A:ASP564 3.4 30.8 1.0
ZN A:ZN801 3.7 33.9 1.0
O A:HOH998 3.8 40.7 1.0
OE2 A:GLU592 4.0 30.1 1.0
NE2 A:HIS595 4.1 29.9 1.0
OG1 A:THR633 4.2 28.9 1.0
O A:HOH993 4.3 29.7 1.0
O A:HIS563 4.4 30.6 1.0
O A:THR633 4.4 29.2 1.0
CD2 A:HIS563 4.4 27.5 1.0
CB A:ASP564 4.4 26.7 1.0
CD2 A:HIS595 4.4 27.1 1.0
CD2 A:HIS567 4.4 29.8 1.0
OD2 A:ASP674 4.6 29.6 1.0
CD2 A:HIS525 4.6 31.0 1.0
NE2 A:HIS567 4.6 26.7 1.0
NE2 A:HIS525 4.7 33.1 1.0
CB A:THR633 4.7 29.2 1.0
NE2 A:HIS563 4.8 28.1 1.0
CA A:ASP564 4.8 28.4 1.0
CG A:GLU592 4.8 33.1 1.0
CD A:GLU592 4.9 31.7 1.0

Magnesium binding site 2 out of 4 in 5sg6

Go back to Magnesium Binding Sites List in 5sg6
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-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-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-A]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:25.8
occ:1.00
 O B:HOH951 2.0 23.6 1.0
O B:HOH936 2.0 27.4 1.0
O B:HOH918 2.1 26.5 1.0
O B:HOH992 2.1 25.3 1.0
O B:HOH974 2.1 25.0 1.0
OD1 B:ASP564 2.1 29.0 1.0
CG B:ASP564 3.1 26.5 1.0
OD2 B:ASP564 3.5 27.1 1.0
ZN B:ZN801 3.8 31.9 1.0
O B:HOH913 3.9 42.2 1.0
OE2 B:GLU592 4.0 31.3 1.0
NE2 B:HIS595 4.1 27.4 1.0
O B:HOH1045 4.1 47.6 1.0
OG1 B:THR633 4.2 28.2 1.0
O B:HOH963 4.2 27.0 1.0
CD2 B:HIS563 4.2 25.9 1.0
CD2 B:HIS567 4.3 32.2 1.0
CD2 B:HIS595 4.4 26.1 1.0
O B:HIS563 4.4 27.4 1.0
OD2 B:ASP674 4.4 30.0 1.0
CB B:ASP564 4.5 26.3 1.0
CD2 B:HIS525 4.5 27.4 1.0
NE2 B:HIS563 4.5 24.5 1.0
O B:THR633 4.6 26.2 1.0
NE2 B:HIS567 4.6 28.8 1.0
NE2 B:HIS525 4.6 31.9 1.0
CB B:THR633 4.6 31.4 1.0
CA B:ASP564 4.8 27.4 1.0
CG B:GLU592 4.8 28.9 1.0
CD B:GLU592 4.8 26.4 1.0

Magnesium binding site 3 out of 4 in 5sg6

Go back to Magnesium Binding Sites List in 5sg6
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-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-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-A]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:28.5
occ:1.00
 O C:HOH937 2.0 27.2 1.0
O C:HOH971 2.0 28.1 1.0
OD1 C:ASP564 2.0 26.4 1.0
O C:HOH930 2.0 24.1 1.0
O C:HOH1007 2.1 26.4 1.0
O C:HOH940 2.2 25.9 1.0
CG C:ASP564 3.1 28.3 1.0
OD2 C:ASP564 3.4 27.4 1.0
ZN C:ZN801 3.7 33.7 1.0
O C:HOH975 3.9 40.5 1.0
NE2 C:HIS595 4.1 30.1 1.0
OE2 C:GLU592 4.1 34.3 1.0
OG1 C:THR633 4.2 29.9 1.0
O C:HOH988 4.3 27.9 1.0
CD2 C:HIS563 4.3 25.8 1.0
CD2 C:HIS567 4.3 29.7 1.0
O C:HIS563 4.4 29.3 1.0
OD2 C:ASP674 4.4 33.9 1.0
CB C:ASP564 4.4 24.6 1.0
CD2 C:HIS595 4.5 27.3 1.0
CD2 C:HIS525 4.5 29.2 1.0
O C:THR633 4.5 28.2 1.0
NE2 C:HIS567 4.6 27.4 1.0
CB C:THR633 4.6 29.6 1.0
NE2 C:HIS525 4.6 33.7 1.0
NE2 C:HIS563 4.7 27.8 1.0
CA C:ASP564 4.8 26.4 1.0
CG C:GLU592 4.9 27.4 1.0
CD C:GLU592 4.9 29.4 1.0

Magnesium binding site 4 out of 4 in 5sg6

Go back to Magnesium Binding Sites List in 5sg6
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-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-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-A]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:38.5
occ:1.00
 O D:HOH922 2.1 37.6 1.0
O D:HOH935 2.1 30.6 1.0
O D:HOH959 2.1 33.7 1.0
O D:HOH957 2.1 33.8 1.0
O D:HOH910 2.2 40.6 1.0
OD1 D:ASP564 2.2 37.7 1.0
CG D:ASP564 3.2 34.8 1.0
OD2 D:ASP564 3.5 40.7 1.0
O D:HOH945 3.7 40.6 1.0
ZN D:ZN801 3.7 40.8 1.0
OE2 D:GLU592 4.0 44.8 1.0
O D:HOH956 4.1 41.5 1.0
OG1 D:THR633 4.2 37.8 1.0
NE2 D:HIS595 4.2 38.8 1.0
CD2 D:HIS563 4.3 35.6 1.0
OD2 D:ASP674 4.4 39.8 1.0
CD2 D:HIS567 4.4 42.1 1.0
O D:THR633 4.4 40.7 1.0
O D:HIS563 4.5 38.0 1.0
CD2 D:HIS595 4.5 39.1 1.0
CB D:ASP564 4.5 34.7 1.0
CD2 D:HIS525 4.6 39.5 1.0
NE2 D:HIS525 4.6 47.1 1.0
NE2 D:HIS563 4.7 29.9 1.0
CB D:THR633 4.7 38.8 1.0
NE2 D:HIS567 4.8 43.4 1.0
CA D:ASP564 4.9 32.5 1.0
CD D:GLU592 5.0 43.1 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 03:43:43 2024

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