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Magnesium in PDB 5shp: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- H]Quinoline

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- H]Quinoline

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- H]Quinoline:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- H]Quinoline, PDB code: 5shp was solved by C.Joseph, J.Benz, A.Flohr, A.Krasso, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.94 / 2.18
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 136.144, 136.144, 236.749, 90, 90, 120
R / Rfree (%) 18.7 / 23.1

Other elements in 5shp:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- H]Quinoline 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-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- H]Quinoline (pdb code 5shp). 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-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- H]Quinoline, PDB code: 5shp:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5shp

Go back to Magnesium Binding Sites List in 5shp
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- H]Quinoline


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-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- H]Quinoline within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:25.8
occ:1.00
 O A:HOH1022 2.0 22.2 1.0
OD1 A:ASP564 2.0 25.5 1.0
O A:HOH954 2.0 24.8 1.0
O A:HOH938 2.0 20.1 1.0
O A:HOH961 2.1 22.4 1.0
O A:HOH958 2.1 29.4 1.0
CG A:ASP564 3.0 26.2 1.0
OD2 A:ASP564 3.4 28.9 1.0
ZN A:ZN801 3.8 31.1 1.0
O A:HOH1005 4.0 32.9 1.0
O A:HOH1041 4.0 45.0 1.0
OE2 A:GLU592 4.0 33.9 1.0
NE2 A:HIS595 4.1 27.1 1.0
OG1 A:THR633 4.2 25.4 1.0
CD2 A:HIS563 4.3 24.0 1.0
CD2 A:HIS567 4.3 28.5 1.0
CB A:ASP564 4.4 26.7 1.0
O A:HOH1014 4.4 32.1 1.0
CD2 A:HIS595 4.4 26.6 1.0
OD2 A:ASP674 4.4 32.9 1.0
O A:HIS563 4.5 27.5 1.0
O A:THR633 4.5 28.8 1.0
NE2 A:HIS567 4.6 29.4 1.0
NE2 A:HIS563 4.7 23.5 1.0
CD2 A:HIS525 4.7 28.8 1.0
NE2 A:HIS525 4.7 27.7 1.0
CA A:ASP564 4.8 25.9 1.0
CB A:THR633 4.8 26.6 1.0
CG A:GLU592 4.9 30.9 1.0
CD A:GLU592 4.9 32.5 1.0

Magnesium binding site 2 out of 4 in 5shp

Go back to Magnesium Binding Sites List in 5shp
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- H]Quinoline


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-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- H]Quinoline within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:18.1
occ:1.00
 O B:HOH925 1.9 20.1 1.0
O B:HOH1009 2.0 21.7 1.0
O B:HOH910 2.0 18.8 1.0
O B:HOH970 2.0 18.4 1.0
OD1 B:ASP564 2.1 24.9 1.0
O B:HOH916 2.1 16.6 1.0
CG B:ASP564 3.1 23.7 1.0
OD2 B:ASP564 3.5 26.0 1.0
ZN B:ZN801 3.8 29.2 1.0
O B:HOH992 3.9 34.7 1.0
OE2 B:GLU592 4.0 27.5 1.0
NE2 B:HIS595 4.1 25.8 1.0
O B:HOH976 4.2 29.1 1.0
CD2 B:HIS563 4.3 23.7 1.0
CD2 B:HIS567 4.3 25.7 1.0
OD2 B:ASP674 4.3 28.1 1.0
CD2 B:HIS595 4.3 28.0 1.0
OG1 B:THR633 4.3 24.7 1.0
CB B:ASP564 4.4 23.8 1.0
O B:HIS563 4.4 26.6 1.0
NE2 B:HIS567 4.5 24.0 1.0
CD2 B:HIS525 4.6 28.2 1.0
NE2 B:HIS563 4.6 22.3 1.0
O B:THR633 4.6 24.8 1.0
NE2 B:HIS525 4.7 28.8 1.0
CB B:THR633 4.7 24.1 1.0
CG B:GLU592 4.7 27.6 1.0
CD B:GLU592 4.8 28.1 1.0
CA B:ASP564 4.8 24.4 1.0

Magnesium binding site 3 out of 4 in 5shp

Go back to Magnesium Binding Sites List in 5shp
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- H]Quinoline


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-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- H]Quinoline within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:27.0
occ:1.00
 O C:HOH976 2.0 24.2 1.0
O C:HOH937 2.0 28.4 1.0
O C:HOH1023 2.0 26.6 1.0
OD1 C:ASP564 2.1 23.9 1.0
O C:HOH961 2.1 23.1 1.0
O C:HOH933 2.1 22.5 1.0
CG C:ASP564 3.2 24.5 1.0
OD2 C:ASP564 3.6 24.0 1.0
O C:HOH1045 3.8 53.1 1.0
ZN C:ZN801 3.9 31.9 1.0
O C:HOH1010 4.0 36.1 1.0
OE2 C:GLU592 4.0 33.8 1.0
NE2 C:HIS595 4.1 27.7 1.0
CD2 C:HIS567 4.2 29.1 1.0
O C:HOH1001 4.3 35.5 1.0
CD2 C:HIS563 4.3 25.5 1.0
OG1 C:THR633 4.4 28.3 1.0
NE2 C:HIS567 4.4 28.6 1.0
OD2 C:ASP674 4.4 30.3 1.0
O C:HIS563 4.5 25.2 1.0
CD2 C:HIS595 4.5 28.3 1.0
O C:THR633 4.5 28.5 1.0
CB C:ASP564 4.5 23.8 1.0
CD2 C:HIS525 4.6 32.4 1.0
NE2 C:HIS525 4.7 31.7 1.0
NE2 C:HIS563 4.7 25.7 1.0
CG C:GLU592 4.8 30.4 1.0
CB C:THR633 4.8 28.9 1.0
CD C:GLU592 4.8 32.9 1.0
CA C:ASP564 4.9 23.8 1.0

Magnesium binding site 4 out of 4 in 5shp

Go back to Magnesium Binding Sites List in 5shp
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- H]Quinoline


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-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- H]Quinoline within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:35.7
occ:1.00
 O D:HOH969 2.0 37.0 1.0
O D:HOH968 2.0 28.2 1.0
O D:HOH925 2.1 32.7 1.0
O D:HOH929 2.1 26.1 1.0
O D:HOH916 2.2 38.4 1.0
OD1 D:ASP564 2.2 32.5 1.0
CG D:ASP564 3.2 33.9 1.0
OD2 D:ASP564 3.6 39.8 1.0
O D:HOH964 3.9 35.8 1.0
O D:HOH938 3.9 39.6 1.0
ZN D:ZN801 3.9 39.3 1.0
OE2 D:GLU592 4.1 38.2 1.0
NE2 D:HIS595 4.1 38.0 1.0
OG1 D:THR633 4.2 36.8 1.0
CD2 D:HIS567 4.3 43.4 1.0
CD2 D:HIS595 4.4 36.6 1.0
CD2 D:HIS563 4.4 30.3 1.0
O D:HIS563 4.4 33.1 1.0
OD2 D:ASP674 4.4 37.1 1.0
O D:THR633 4.5 36.9 1.0
NE2 D:HIS567 4.5 43.9 1.0
CB D:ASP564 4.6 34.6 1.0
CB D:THR633 4.8 37.2 1.0
CD2 D:HIS525 4.8 35.5 1.0
NE2 D:HIS563 4.8 29.4 1.0
NE2 D:HIS525 4.8 36.5 1.0
CD D:GLU592 4.9 41.8 1.0
CA D:ASP564 4.9 32.8 1.0
CG D:GLU592 5.0 40.9 1.0
O D:HOH965 5.0 36.9 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: Wed Apr 5 11:27:13 2023

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