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Magnesium in PDB 5si7: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Benzyl-6,6-Dimethyl-1H-Imidazo[4,5-H]Isoquinoline-7,9-Dione

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Benzyl-6,6-Dimethyl-1H-Imidazo[4,5-H]Isoquinoline-7,9-Dione

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Benzyl-6,6-Dimethyl-1H-Imidazo[4,5-H]Isoquinoline-7,9-Dione:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Benzyl-6,6-Dimethyl-1H-Imidazo[4,5-H]Isoquinoline-7,9-Dione, PDB code: 5si7 was solved by C.Joseph, J.Benz, A.Flohr, M.Boehringer, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.50 / 2.10
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.21, 135.21, 235.625, 90, 90, 120
R / Rfree (%) 19.1 / 23.3

Other elements in 5si7:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Benzyl-6,6-Dimethyl-1H-Imidazo[4,5-H]Isoquinoline-7,9-Dione 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 2- Benzyl-6,6-Dimethyl-1H-Imidazo[4,5-H]Isoquinoline-7,9-Dione (pdb code 5si7). 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 2- Benzyl-6,6-Dimethyl-1H-Imidazo[4,5-H]Isoquinoline-7,9-Dione, PDB code: 5si7:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5si7

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Benzyl-6,6-Dimethyl-1H-Imidazo[4,5-H]Isoquinoline-7,9-Dione


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 2- Benzyl-6,6-Dimethyl-1H-Imidazo[4,5-H]Isoquinoline-7,9-Dione within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:24.5
occ:1.00
 O A:HOH984 1.9 27.0 1.0
O A:HOH957 2.0 19.0 1.0
O A:HOH1007 2.0 20.5 1.0
OD1 A:ASP564 2.1 23.5 1.0
O A:HOH946 2.1 21.4 1.0
O A:HOH917 2.1 24.1 1.0
CG A:ASP564 3.1 24.5 1.0
OD2 A:ASP564 3.4 25.3 1.0
ZN A:ZN801 3.8 30.1 1.0
O A:HOH992 3.8 39.8 1.0
OE2 A:GLU592 4.0 27.8 1.0
NE2 A:HIS595 4.1 23.4 1.0
O A:HOH1020 4.2 44.1 1.0
CD2 A:HIS567 4.2 28.2 1.0
OG1 A:THR633 4.2 26.9 1.0
O A:HOH972 4.3 31.7 1.0
CD2 A:HIS595 4.4 24.0 1.0
CD2 A:HIS563 4.4 23.5 1.0
O A:HIS563 4.4 27.9 1.0
CB A:ASP564 4.4 25.7 1.0
NE2 A:HIS567 4.4 27.2 1.0
O A:THR633 4.5 27.9 1.0
OD2 A:ASP674 4.5 32.1 1.0
CD2 A:HIS525 4.5 27.3 1.0
NE2 A:HIS525 4.6 26.0 1.0
NE2 A:HIS563 4.7 24.5 1.0
CB A:THR633 4.7 26.9 1.0
CA A:ASP564 4.8 25.3 1.0
CD A:GLU592 4.8 28.8 1.0
CG A:GLU592 4.8 26.5 1.0

Magnesium binding site 2 out of 4 in 5si7

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Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Benzyl-6,6-Dimethyl-1H-Imidazo[4,5-H]Isoquinoline-7,9-Dione


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 2- Benzyl-6,6-Dimethyl-1H-Imidazo[4,5-H]Isoquinoline-7,9-Dione within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:20.8
occ:1.00
 O B:HOH959 1.9 21.2 1.0
O B:HOH968 1.9 19.5 1.0
O B:HOH990 2.0 19.5 1.0
O B:HOH931 2.1 19.9 1.0
OD1 B:ASP564 2.1 23.6 1.0
O B:HOH1007 2.2 19.9 1.0
CG B:ASP564 3.2 24.2 1.0
OD2 B:ASP564 3.6 25.3 1.0
ZN B:ZN801 3.8 28.7 1.0
OE2 B:GLU592 4.0 27.6 1.0
O B:HOH987 4.0 33.6 1.0
NE2 B:HIS595 4.1 25.7 1.0
CD2 B:HIS563 4.2 22.1 1.0
OG1 B:THR633 4.2 24.0 1.0
O B:HIS563 4.3 26.7 1.0
CD2 B:HIS595 4.3 25.8 1.0
CD2 B:HIS567 4.3 26.7 1.0
OD2 B:ASP674 4.4 25.1 1.0
O B:HOH969 4.4 24.8 1.0
O B:THR633 4.5 23.8 1.0
CB B:ASP564 4.5 24.5 1.0
NE2 B:HIS567 4.5 25.8 1.0
NE2 B:HIS563 4.6 21.6 1.0
CB B:THR633 4.6 24.7 1.0
CD2 B:HIS525 4.7 22.7 1.0
CG B:GLU592 4.7 26.0 1.0
CD B:GLU592 4.7 25.4 1.0
CA B:ASP564 4.8 24.5 1.0
NE2 B:HIS525 4.8 22.9 1.0

Magnesium binding site 3 out of 4 in 5si7

Go back to Magnesium Binding Sites List in 5si7
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Benzyl-6,6-Dimethyl-1H-Imidazo[4,5-H]Isoquinoline-7,9-Dione


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 2- Benzyl-6,6-Dimethyl-1H-Imidazo[4,5-H]Isoquinoline-7,9-Dione within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:27.1
occ:1.00
 O C:HOH936 2.0 24.1 1.0
O C:HOH950 2.0 23.1 1.0
O C:HOH982 2.1 17.9 1.0
OD1 C:ASP564 2.1 24.7 1.0
O C:HOH1012 2.1 23.4 1.0
O C:HOH926 2.2 21.3 1.0
CG C:ASP564 3.1 24.7 1.0
OD2 C:ASP564 3.4 26.1 1.0
O C:HOH961 3.7 43.1 1.0
ZN C:ZN801 3.8 30.8 1.0
OE2 C:GLU592 4.0 28.7 1.0
NE2 C:HIS595 4.1 26.9 1.0
OG1 C:THR633 4.2 26.3 1.0
CD2 C:HIS567 4.2 24.3 1.0
CD2 C:HIS563 4.2 25.5 1.0
O C:HIS563 4.3 23.0 1.0
CD2 C:HIS595 4.3 26.4 1.0
OD2 C:ASP674 4.4 29.5 1.0
O C:HOH951 4.4 27.5 1.0
CB C:ASP564 4.4 24.3 1.0
O C:THR633 4.4 26.5 1.0
NE2 C:HIS567 4.5 24.4 1.0
CD2 C:HIS525 4.6 28.0 1.0
CB C:THR633 4.7 26.5 1.0
NE2 C:HIS525 4.7 28.4 1.0
NE2 C:HIS563 4.7 26.3 1.0
O C:HOH1005 4.8 44.7 1.0
CA C:ASP564 4.8 24.6 1.0
CG C:GLU592 4.8 27.3 1.0
CD C:GLU592 4.9 29.2 1.0

Magnesium binding site 4 out of 4 in 5si7

Go back to Magnesium Binding Sites List in 5si7
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Benzyl-6,6-Dimethyl-1H-Imidazo[4,5-H]Isoquinoline-7,9-Dione


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 2- Benzyl-6,6-Dimethyl-1H-Imidazo[4,5-H]Isoquinoline-7,9-Dione within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:35.6
occ:1.00
 O D:HOH924 2.0 26.4 1.0
O D:HOH967 2.1 26.6 1.0
O D:HOH959 2.1 35.2 1.0
OD1 D:ASP564 2.1 33.1 1.0
O D:HOH922 2.2 27.9 1.0
O D:HOH926 2.2 25.5 1.0
CG D:ASP564 3.2 32.2 1.0
OD2 D:ASP564 3.6 34.8 1.0
O D:HOH974 3.8 36.0 1.0
ZN D:ZN801 3.9 36.2 1.0
OE2 D:GLU592 4.0 32.3 1.0
NE2 D:HIS595 4.1 36.4 1.0
O D:HOH956 4.1 32.2 1.0
CD2 D:HIS567 4.3 35.9 1.0
OG1 D:THR633 4.3 32.2 1.0
CD2 D:HIS595 4.3 33.5 1.0
OD2 D:ASP674 4.4 31.9 1.0
CD2 D:HIS563 4.4 27.1 1.0
O D:HIS563 4.5 28.6 1.0
NE2 D:HIS567 4.5 33.6 1.0
CB D:ASP564 4.5 31.0 1.0
CD2 D:HIS525 4.6 33.0 1.0
O D:THR633 4.6 33.0 1.0
NE2 D:HIS525 4.7 35.7 1.0
CB D:THR633 4.7 33.6 1.0
CD D:GLU592 4.8 34.8 1.0
NE2 D:HIS563 4.8 25.3 1.0
CG D:GLU592 4.8 34.3 1.0
CA D:ASP564 4.8 30.8 1.0
O D:HOH981 4.9 36.8 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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