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Magnesium in PDB 5sgg: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Chloro-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-6,7-Dihydro-3H- Furo[3,2-F]Benzimidazole

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Chloro-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-6,7-Dihydro-3H- Furo[3,2-F]Benzimidazole

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Chloro-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-6,7-Dihydro-3H- Furo[3,2-F]Benzimidazole:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Chloro-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-6,7-Dihydro-3H- Furo[3,2-F]Benzimidazole, PDB code: 5sgg 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) 43.66 / 2.09
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.219, 135.219, 235.292, 90, 90, 120
R / Rfree (%) 18.8 / 23.1

Other elements in 5sgg:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Chloro-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-6,7-Dihydro-3H- Furo[3,2-F]Benzimidazole also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Chloro-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-6,7-Dihydro-3H- Furo[3,2-F]Benzimidazole (pdb code 5sgg). 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- Chloro-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-6,7-Dihydro-3H- Furo[3,2-F]Benzimidazole, PDB code: 5sgg:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sgg

Go back to Magnesium Binding Sites List in 5sgg
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Chloro-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-6,7-Dihydro-3H- Furo[3,2-F]Benzimidazole


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- Chloro-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-6,7-Dihydro-3H- Furo[3,2-F]Benzimidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:19.1
occ:1.00
 O A:HOH1025 1.9 18.2 1.0
O A:HOH975 2.0 23.1 1.0
OD1 A:ASP564 2.0 20.9 1.0
O A:HOH929 2.0 19.0 1.0
O A:HOH969 2.1 19.3 1.0
O A:HOH937 2.2 21.5 1.0
CG A:ASP564 3.0 21.9 1.0
OD2 A:ASP564 3.3 23.0 1.0
ZN A:ZN801 3.8 26.6 1.0
O A:HOH1000 4.0 31.6 1.0
NE2 A:HIS595 4.0 24.9 1.0
OE2 A:GLU592 4.0 29.5 1.0
O A:HOH1012 4.2 28.1 1.0
OG1 A:THR633 4.2 22.6 1.0
CD2 A:HIS563 4.3 21.0 1.0
CD2 A:HIS595 4.3 23.7 1.0
CD2 A:HIS567 4.3 24.4 1.0
CB A:ASP564 4.4 21.8 1.0
O A:HIS563 4.4 22.8 1.0
OD2 A:ASP674 4.5 27.6 1.0
O A:THR633 4.5 26.3 1.0
NE2 A:HIS567 4.6 24.6 1.0
CD2 A:HIS525 4.6 25.9 1.0
NE2 A:HIS563 4.6 21.8 1.0
NE2 A:HIS525 4.7 25.9 1.0
CB A:THR633 4.7 23.2 1.0
CA A:ASP564 4.8 21.4 1.0
CG A:GLU592 4.8 26.7 1.0
CD A:GLU592 4.8 27.0 1.0

Magnesium binding site 2 out of 4 in 5sgg

Go back to Magnesium Binding Sites List in 5sgg
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Chloro-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-6,7-Dihydro-3H- Furo[3,2-F]Benzimidazole


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- Chloro-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-6,7-Dihydro-3H- Furo[3,2-F]Benzimidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:19.5
occ:1.00
 O B:HOH928 1.9 20.4 1.0
O B:HOH1023 1.9 20.1 1.0
O B:HOH923 2.0 15.9 1.0
OD1 B:ASP564 2.0 22.1 1.0
O B:HOH930 2.0 17.2 1.0
O B:HOH996 2.1 16.7 1.0
CG B:ASP564 3.0 20.4 1.0
OD2 B:ASP564 3.4 22.0 1.0
ZN B:ZN801 3.7 25.7 1.0
O B:HOH980 3.8 29.1 1.0
OE2 B:GLU592 4.1 26.0 1.0
CD2 B:HIS563 4.1 20.9 1.0
NE2 B:HIS595 4.1 22.6 1.0
O B:HOH999 4.2 28.3 1.0
OG1 B:THR633 4.2 21.5 1.0
OD2 B:ASP674 4.3 24.6 1.0
CD2 B:HIS595 4.3 23.1 1.0
CD2 B:HIS567 4.3 23.0 1.0
CB B:ASP564 4.4 20.3 1.0
O B:HIS563 4.4 23.6 1.0
NE2 B:HIS563 4.4 20.2 1.0
NE2 B:HIS567 4.4 21.6 1.0
O B:THR633 4.6 22.3 1.0
CD2 B:HIS525 4.6 24.9 1.0
CB B:THR633 4.7 22.1 1.0
NE2 B:HIS525 4.7 25.3 1.0
CA B:ASP564 4.7 21.0 1.0
CG B:GLU592 4.8 23.9 1.0
CD B:GLU592 4.9 24.7 1.0

Magnesium binding site 3 out of 4 in 5sgg

Go back to Magnesium Binding Sites List in 5sgg
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Chloro-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-6,7-Dihydro-3H- Furo[3,2-F]Benzimidazole


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- Chloro-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-6,7-Dihydro-3H- Furo[3,2-F]Benzimidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:23.2
occ:1.00
 O C:HOH923 2.0 27.8 1.0
O C:HOH996 2.0 19.9 1.0
O C:HOH1016 2.0 22.3 1.0
OD1 C:ASP564 2.1 21.6 1.0
O C:HOH962 2.1 20.8 1.0
O C:HOH953 2.2 22.1 1.0
CG C:ASP564 3.1 22.7 1.0
OD2 C:ASP564 3.4 22.2 1.0
ZN C:ZN801 3.8 28.9 1.0
O C:HOH1011 3.9 31.0 1.0
O C:HOH1043 3.9 55.5 1.0
OE2 C:GLU592 4.1 31.9 1.0
NE2 C:HIS595 4.1 25.9 1.0
O C:HOH999 4.1 31.6 1.0
CD2 C:HIS567 4.2 27.9 1.0
CD2 C:HIS563 4.3 20.2 1.0
OG1 C:THR633 4.3 26.7 1.0
OD2 C:ASP674 4.4 29.2 1.0
NE2 C:HIS567 4.4 27.0 1.0
O C:HIS563 4.4 23.0 1.0
CD2 C:HIS595 4.4 25.1 1.0
CB C:ASP564 4.4 22.3 1.0
O C:THR633 4.5 24.8 1.0
CD2 C:HIS525 4.6 29.4 1.0
NE2 C:HIS563 4.6 20.6 1.0
NE2 C:HIS525 4.7 30.3 1.0
CA C:ASP564 4.8 22.1 1.0
CB C:THR633 4.8 24.8 1.0
CG C:GLU592 4.9 27.7 1.0
CD C:GLU592 4.9 29.3 1.0

Magnesium binding site 4 out of 4 in 5sgg

Go back to Magnesium Binding Sites List in 5sgg
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Chloro-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-6,7-Dihydro-3H- Furo[3,2-F]Benzimidazole


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- Chloro-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-6,7-Dihydro-3H- Furo[3,2-F]Benzimidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:30.1
occ:1.00
 O D:HOH975 2.0 30.0 1.0
O D:HOH979 2.1 32.6 1.0
O D:HOH922 2.1 29.3 1.0
OD1 D:ASP564 2.1 28.7 1.0
O D:HOH925 2.1 25.0 1.0
O D:HOH937 2.2 31.2 1.0
CG D:ASP564 3.2 30.1 1.0
OD2 D:ASP564 3.5 37.0 1.0
ZN D:ZN801 3.9 37.0 1.0
NE2 D:HIS595 4.0 36.1 1.0
OE2 D:GLU592 4.0 37.8 1.0
O D:HOH961 4.1 37.0 1.0
O D:HOH971 4.1 33.3 1.0
OG1 D:THR633 4.2 36.9 1.0
CD2 D:HIS595 4.2 34.3 1.0
CD2 D:HIS563 4.3 27.4 1.0
CD2 D:HIS567 4.3 41.2 1.0
O D:HIS563 4.3 29.2 1.0
OD2 D:ASP674 4.5 34.5 1.0
CB D:ASP564 4.5 29.9 1.0
O D:THR633 4.5 35.9 1.0
NE2 D:HIS567 4.6 40.9 1.0
NE2 D:HIS563 4.7 26.5 1.0
CD2 D:HIS525 4.7 35.5 1.0
CB D:THR633 4.7 36.3 1.0
CG D:GLU592 4.7 37.9 1.0
NE2 D:HIS525 4.8 37.4 1.0
CA D:ASP564 4.8 29.4 1.0
CD D:GLU592 4.8 38.3 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 03:46:38 2024

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