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Magnesium in PDB 5sg8: Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- Butoxy-4-Ethoxypyrimidin-2-Amine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- Butoxy-4-Ethoxypyrimidin-2-Amine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- Butoxy-4-Ethoxypyrimidin-2-Amine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- Butoxy-4-Ethoxypyrimidin-2-Amine, PDB code: 5sg8 was solved by C.Joseph, J.Benz, A.Flohr, A.Gruessner, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.65 / 2.16
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.073, 135.073, 235.251, 90, 90, 120
R / Rfree (%) 21.7 / 27.1

Other elements in 5sg8:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- Butoxy-4-Ethoxypyrimidin-2-Amine 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- Butoxy-4-Ethoxypyrimidin-2-Amine (pdb code 5sg8). 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- Butoxy-4-Ethoxypyrimidin-2-Amine, PDB code: 5sg8:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sg8

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- Butoxy-4-Ethoxypyrimidin-2-Amine


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- Butoxy-4-Ethoxypyrimidin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:27.9
occ:1.00
 O A:HOH927 1.9 22.7 1.0
O A:HOH917 2.0 24.8 1.0
O A:HOH983 2.0 33.7 1.0
OD1 A:ASP564 2.1 28.0 1.0
O A:HOH959 2.2 27.6 1.0
O A:HOH919 2.2 25.1 1.0
CG A:ASP564 3.1 29.6 1.0
OD2 A:ASP564 3.5 32.4 1.0
ZN A:ZN801 3.8 33.6 1.0
OE2 A:GLU592 3.9 32.0 1.0
NE2 A:HIS595 4.0 28.6 1.0
O A:HOH974 4.0 40.1 1.0
CD2 A:HIS595 4.2 27.0 1.0
OG1 A:THR633 4.2 28.9 1.0
CD2 A:HIS567 4.3 36.5 1.0
CD2 A:HIS563 4.3 28.9 1.0
O A:HOH973 4.3 38.0 1.0
O A:HIS563 4.3 27.6 1.0
OD2 A:ASP674 4.4 37.4 1.0
CB A:ASP564 4.4 28.4 1.0
NE2 A:HIS567 4.5 35.7 1.0
CD2 A:HIS525 4.6 29.3 1.0
NE2 A:HIS563 4.7 28.8 1.0
CB A:THR633 4.7 29.1 1.0
O A:THR633 4.7 28.1 1.0
NE2 A:HIS525 4.7 29.2 1.0
CA A:ASP564 4.7 32.6 1.0
CD A:GLU592 4.8 33.5 1.0
CG A:GLU592 4.8 31.2 1.0

Magnesium binding site 2 out of 4 in 5sg8

Go back to Magnesium Binding Sites List in 5sg8
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- Butoxy-4-Ethoxypyrimidin-2-Amine


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- Butoxy-4-Ethoxypyrimidin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:29.1
occ:1.00
 O B:HOH918 1.9 18.7 1.0
O B:HOH931 1.9 17.5 1.0
OD1 B:ASP564 2.0 27.3 1.0
O B:HOH949 2.0 27.2 1.0
O B:HOH977 2.1 27.0 1.0
O B:HOH976 2.2 25.3 1.0
CG B:ASP564 3.1 25.9 1.0
OD2 B:ASP564 3.6 27.8 1.0
ZN B:ZN801 3.9 34.4 1.0
NE2 B:HIS595 4.0 28.0 1.0
OE2 B:GLU592 4.0 30.5 1.0
CD2 B:HIS567 4.1 26.6 1.0
O B:HOH1000 4.1 59.1 1.0
O B:HOH953 4.1 42.5 1.0
O B:HOH968 4.2 29.4 1.0
O B:HIS563 4.2 25.6 1.0
NE2 B:HIS567 4.2 27.9 1.0
CD2 B:HIS595 4.2 28.2 1.0
OG1 B:THR633 4.2 28.3 1.0
CD2 B:HIS563 4.3 26.8 1.0
OD2 B:ASP674 4.3 31.4 1.0
CB B:ASP564 4.4 26.2 1.0
CD2 B:HIS525 4.6 29.6 1.0
NE2 B:HIS563 4.6 24.5 1.0
NE2 B:HIS525 4.6 31.7 1.0
CA B:ASP564 4.7 25.5 1.0
O B:THR633 4.7 28.2 1.0
CG B:GLU592 4.7 32.7 1.0
CB B:THR633 4.7 28.1 1.0
CD B:GLU592 4.8 31.8 1.0

Magnesium binding site 3 out of 4 in 5sg8

Go back to Magnesium Binding Sites List in 5sg8
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- Butoxy-4-Ethoxypyrimidin-2-Amine


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- Butoxy-4-Ethoxypyrimidin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:30.2
occ:1.00
 O C:HOH966 1.9 30.1 1.0
O C:HOH960 2.0 30.2 1.0
O C:HOH994 2.0 26.4 1.0
O C:HOH940 2.1 35.3 1.0
OD1 C:ASP564 2.1 28.0 1.0
O C:HOH930 2.3 32.0 1.0
CG C:ASP564 3.2 29.6 1.0
OD2 C:ASP564 3.6 30.9 1.0
NE2 C:HIS595 4.0 40.8 1.0
ZN C:ZN801 4.0 39.4 1.0
CD2 C:HIS567 4.0 35.7 1.0
OE2 C:GLU592 4.1 41.3 1.0
O C:HOH988 4.1 37.7 1.0
NE2 C:HIS567 4.1 32.8 1.0
O C:HOH975 4.2 29.5 1.0
CD2 C:HIS595 4.2 38.8 1.0
CD2 C:HIS563 4.3 32.8 1.0
O C:HIS563 4.4 33.3 1.0
OG1 C:THR633 4.4 30.5 1.0
CB C:ASP564 4.5 28.1 1.0
O C:THR633 4.5 29.1 1.0
OD2 C:ASP674 4.5 39.6 1.0
CD2 C:HIS525 4.6 37.5 1.0
NE2 C:HIS563 4.6 28.7 1.0
NE2 C:HIS525 4.7 35.7 1.0
CA C:ASP564 4.7 28.8 1.0
CG C:GLU592 4.7 32.3 1.0
CB C:THR633 4.8 30.7 1.0
CD C:GLU592 4.8 39.0 1.0

Magnesium binding site 4 out of 4 in 5sg8

Go back to Magnesium Binding Sites List in 5sg8
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- Butoxy-4-Ethoxypyrimidin-2-Amine


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- Butoxy-4-Ethoxypyrimidin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:42.9
occ:1.00
 O D:HOH955 2.0 33.4 1.0
O D:HOH929 2.0 41.6 1.0
O D:HOH910 2.2 31.7 1.0
O D:HOH951 2.2 35.5 1.0
O D:HOH943 2.3 31.7 1.0
OD1 D:ASP564 2.3 34.4 1.0
CG D:ASP564 3.4 35.7 1.0
OD2 D:ASP564 3.8 43.0 1.0
OE2 D:GLU592 3.8 38.7 1.0
ZN D:ZN801 3.9 42.5 1.0
O D:HOH975 4.0 38.2 1.0
O D:HOH938 4.0 39.1 1.0
NE2 D:HIS595 4.1 39.6 1.0
OG1 D:THR633 4.1 33.2 1.0
CD2 D:HIS567 4.3 49.3 1.0
CD2 D:HIS595 4.4 38.4 1.0
NE2 D:HIS567 4.4 48.1 1.0
CD2 D:HIS563 4.4 36.8 1.0
O D:HIS563 4.5 34.2 1.0
CD2 D:HIS525 4.5 39.8 1.0
O D:THR633 4.5 50.1 1.0
OD2 D:ASP674 4.6 40.7 1.0
NE2 D:HIS525 4.6 38.1 1.0
CB D:ASP564 4.7 37.1 1.0
CB D:THR633 4.7 40.3 1.0
CD D:GLU592 4.7 40.1 1.0
CG D:GLU592 4.8 41.6 1.0
NE2 D:HIS563 4.8 32.6 1.0
CA D:ASP564 4.9 34.3 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 03:43:44 2024

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