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Magnesium in PDB 5sia: Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2, 3-Dimethylquinoxalin-6-Yl)-3-(3-Methoxyphenyl)Urea

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2, 3-Dimethylquinoxalin-6-Yl)-3-(3-Methoxyphenyl)Urea

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2, 3-Dimethylquinoxalin-6-Yl)-3-(3-Methoxyphenyl)Urea:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2, 3-Dimethylquinoxalin-6-Yl)-3-(3-Methoxyphenyl)Urea, PDB code: 5sia was solved by C.Joseph, J.Benz, A.Flohr, M.Brunner, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.50 / 2.27
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.242, 135.242, 235.107, 90, 90, 120
R / Rfree (%) 18.8 / 24

Other elements in 5sia:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2, 3-Dimethylquinoxalin-6-Yl)-3-(3-Methoxyphenyl)Urea 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 1-(2, 3-Dimethylquinoxalin-6-Yl)-3-(3-Methoxyphenyl)Urea (pdb code 5sia). 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 1-(2, 3-Dimethylquinoxalin-6-Yl)-3-(3-Methoxyphenyl)Urea, PDB code: 5sia:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sia

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2, 3-Dimethylquinoxalin-6-Yl)-3-(3-Methoxyphenyl)Urea


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 1-(2, 3-Dimethylquinoxalin-6-Yl)-3-(3-Methoxyphenyl)Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:34.0
occ:1.00
 O A:HOH925 1.9 26.9 1.0
O A:HOH932 2.0 28.4 1.0
O A:HOH964 2.0 25.9 1.0
OD1 A:ASP564 2.0 31.2 1.0
O A:HOH951 2.1 29.0 1.0
O A:HOH915 2.1 33.0 1.0
CG A:ASP564 3.0 32.8 1.0
OD2 A:ASP564 3.3 31.6 1.0
ZN A:ZN801 3.8 39.7 1.0
OE2 A:GLU592 3.8 42.8 1.0
O A:HOH957 3.9 53.4 1.0
O A:HOH948 3.9 39.7 1.0
NE2 A:HIS595 4.0 39.7 1.0
OG1 A:THR633 4.2 34.5 1.0
CD2 A:HIS563 4.2 31.6 1.0
CD2 A:HIS595 4.2 34.4 1.0
CD2 A:HIS567 4.3 39.4 1.0
O A:HIS563 4.3 32.0 1.0
O A:HOH944 4.3 39.6 1.0
CB A:ASP564 4.3 29.5 1.0
OD2 A:ASP674 4.4 43.5 1.0
O A:THR633 4.4 38.3 1.0
NE2 A:HIS567 4.5 39.2 1.0
NE2 A:HIS563 4.6 30.2 1.0
CD2 A:HIS525 4.7 38.5 1.0
CB A:THR633 4.7 33.5 1.0
CA A:ASP564 4.7 31.4 1.0
NE2 A:HIS525 4.7 35.0 1.0
CD A:GLU592 4.7 40.7 1.0
CG A:GLU592 4.8 39.2 1.0

Magnesium binding site 2 out of 4 in 5sia

Go back to Magnesium Binding Sites List in 5sia
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2, 3-Dimethylquinoxalin-6-Yl)-3-(3-Methoxyphenyl)Urea


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 1-(2, 3-Dimethylquinoxalin-6-Yl)-3-(3-Methoxyphenyl)Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:31.9
occ:1.00
 O B:HOH922 1.9 24.3 1.0
O B:HOH929 1.9 34.3 1.0
O B:HOH938 2.0 27.7 1.0
OD1 B:ASP564 2.0 28.7 1.0
O B:HOH967 2.1 28.1 1.0
O B:HOH909 2.1 23.8 1.0
CG B:ASP564 3.1 32.3 1.0
OD2 B:ASP564 3.5 31.1 1.0
ZN B:ZN801 3.9 37.8 1.0
OE2 B:GLU592 3.9 35.7 1.0
O B:HOH961 4.0 42.5 1.0
NE2 B:HIS595 4.1 35.0 1.0
CD2 B:HIS563 4.2 28.7 1.0
O B:HIS563 4.2 34.4 1.0
OG1 B:THR633 4.2 34.2 1.0
CD2 B:HIS567 4.2 29.0 1.0
CD2 B:HIS595 4.3 39.2 1.0
NE2 B:HIS567 4.4 28.9 1.0
OD2 B:ASP674 4.4 39.1 1.0
O B:HOH950 4.4 42.5 1.0
CB B:ASP564 4.4 29.8 1.0
O B:THR633 4.5 33.5 1.0
CB B:THR633 4.6 34.9 1.0
NE2 B:HIS563 4.6 28.6 1.0
CG B:GLU592 4.6 37.9 1.0
CD2 B:HIS525 4.7 34.0 1.0
CD B:GLU592 4.7 37.1 1.0
NE2 B:HIS525 4.7 35.2 1.0
CA B:ASP564 4.7 30.6 1.0

Magnesium binding site 3 out of 4 in 5sia

Go back to Magnesium Binding Sites List in 5sia
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2, 3-Dimethylquinoxalin-6-Yl)-3-(3-Methoxyphenyl)Urea


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 1-(2, 3-Dimethylquinoxalin-6-Yl)-3-(3-Methoxyphenyl)Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:33.0
occ:1.00
 O C:HOH939 2.0 32.7 1.0
O C:HOH926 2.1 30.1 1.0
O C:HOH924 2.1 38.7 1.0
O C:HOH965 2.2 42.7 1.0
OD1 C:ASP564 2.2 34.2 1.0
O C:HOH905 2.3 31.4 1.0
CG C:ASP564 3.1 35.6 1.0
OD2 C:ASP564 3.4 34.6 1.0
O C:HOH951 3.7 33.5 1.0
ZN C:ZN801 3.7 43.4 1.0
OE2 C:GLU592 4.2 44.9 1.0
CD2 C:HIS563 4.2 33.5 1.0
OG1 C:THR633 4.2 39.4 1.0
O C:THR633 4.3 35.1 1.0
NE2 C:HIS595 4.3 40.3 1.0
OD2 C:ASP674 4.3 40.8 1.0
CD2 C:HIS567 4.3 37.9 1.0
NE2 C:HIS567 4.4 35.6 1.0
O C:HOH949 4.4 38.7 1.0
CB C:ASP564 4.5 33.8 1.0
CD2 C:HIS595 4.5 36.9 1.0
CB C:THR633 4.5 37.3 1.0
NE2 C:HIS563 4.5 35.8 1.0
O C:HIS563 4.5 34.1 1.0
CD2 C:HIS525 4.7 44.0 1.0
NE2 C:HIS525 4.8 42.5 1.0
CA C:ASP564 4.9 34.3 1.0
CG C:GLU592 4.9 37.6 1.0
OD1 C:ASP674 5.0 35.1 1.0

Magnesium binding site 4 out of 4 in 5sia

Go back to Magnesium Binding Sites List in 5sia
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(2, 3-Dimethylquinoxalin-6-Yl)-3-(3-Methoxyphenyl)Urea


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 1-(2, 3-Dimethylquinoxalin-6-Yl)-3-(3-Methoxyphenyl)Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:45.7
occ:1.00
 O D:HOH928 2.0 38.8 1.0
OD1 D:ASP564 2.0 46.2 1.0
O D:HOH931 2.1 35.9 1.0
O D:HOH919 2.1 37.9 1.0
O D:HOH941 2.1 42.6 1.0
O D:HOH913 2.1 35.5 1.0
CG D:ASP564 3.0 39.7 1.0
OD2 D:ASP564 3.3 45.7 1.0
ZN D:ZN801 3.7 46.6 1.0
O D:HOH937 3.8 40.8 1.0
O D:HOH936 4.0 42.3 1.0
OE2 D:GLU592 4.1 49.3 1.0
NE2 D:HIS595 4.1 49.7 1.0
CD2 D:HIS563 4.2 37.7 1.0
OG1 D:THR633 4.3 39.4 1.0
CD2 D:HIS567 4.3 46.3 1.0
CB D:ASP564 4.3 39.6 1.0
O D:HIS563 4.3 39.1 1.0
O D:THR633 4.3 53.2 1.0
CD2 D:HIS595 4.4 46.8 1.0
NE2 D:HIS567 4.5 50.3 1.0
OD2 D:ASP674 4.6 43.7 1.0
CD2 D:HIS525 4.6 52.6 1.0
NE2 D:HIS563 4.6 35.9 1.0
CA D:ASP564 4.7 37.4 1.0
CB D:THR633 4.8 42.2 1.0
NE2 D:HIS525 4.8 52.6 1.0
CG D:GLU592 4.9 45.3 1.0
CD D:GLU592 4.9 47.2 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 04:08:05 2024

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