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Magnesium in PDB 5sh4: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Methoxy-3,4,6-Trimethylpyridin-2-Yl)Methylsulfanyl]-5H-[1, 3]Dioxolo[4,5-F]Benzimidazole

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Methoxy-3,4,6-Trimethylpyridin-2-Yl)Methylsulfanyl]-5H-[1, 3]Dioxolo[4,5-F]Benzimidazole

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Methoxy-3,4,6-Trimethylpyridin-2-Yl)Methylsulfanyl]-5H-[1, 3]Dioxolo[4,5-F]Benzimidazole:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Methoxy-3,4,6-Trimethylpyridin-2-Yl)Methylsulfanyl]-5H-[1, 3]Dioxolo[4,5-F]Benzimidazole, PDB code: 5sh4 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) 43.57 / 2.22
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.463, 135.463, 235.433, 90, 90, 120
R / Rfree (%) 19.5 / 24.5

Other elements in 5sh4:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Methoxy-3,4,6-Trimethylpyridin-2-Yl)Methylsulfanyl]-5H-[1, 3]Dioxolo[4,5-F]Benzimidazole 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 6-[(5- Methoxy-3,4,6-Trimethylpyridin-2-Yl)Methylsulfanyl]-5H-[1, 3]Dioxolo[4,5-F]Benzimidazole (pdb code 5sh4). 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 6-[(5- Methoxy-3,4,6-Trimethylpyridin-2-Yl)Methylsulfanyl]-5H-[1, 3]Dioxolo[4,5-F]Benzimidazole, PDB code: 5sh4:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sh4

Go back to Magnesium Binding Sites List in 5sh4
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Methoxy-3,4,6-Trimethylpyridin-2-Yl)Methylsulfanyl]-5H-[1, 3]Dioxolo[4,5-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 6-[(5- Methoxy-3,4,6-Trimethylpyridin-2-Yl)Methylsulfanyl]-5H-[1, 3]Dioxolo[4,5-F]Benzimidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:20.1
occ:1.00
 OD1 A:ASP564 1.9 22.2 1.0
O A:HOH946 2.0 23.3 1.0
O A:HOH982 2.0 29.0 1.0
O A:HOH995 2.0 18.4 1.0
O A:HOH960 2.0 19.6 1.0
O A:HOH964 2.1 13.9 1.0
CG A:ASP564 2.9 22.3 1.0
OD2 A:ASP564 3.3 24.7 1.0
ZN A:ZN801 3.8 27.2 1.0
NE2 A:HIS595 4.0 25.2 1.0
OE2 A:GLU592 4.0 32.6 1.0
O A:HOH973 4.1 34.2 1.0
CD2 A:HIS563 4.2 19.9 1.0
CD2 A:HIS595 4.2 24.1 1.0
OG1 A:THR633 4.2 23.6 1.0
O A:HIS563 4.3 20.7 1.0
CB A:ASP564 4.3 20.6 1.0
CD2 A:HIS567 4.3 27.9 1.0
O A:HOH998 4.4 33.9 1.0
OD2 A:ASP674 4.5 31.1 1.0
NE2 A:HIS563 4.6 20.9 1.0
CD2 A:HIS525 4.6 27.8 1.0
NE2 A:HIS567 4.6 28.1 1.0
O A:THR633 4.6 26.8 1.0
CA A:ASP564 4.6 21.6 1.0
NE2 A:HIS525 4.7 26.1 1.0
CB A:THR633 4.8 22.4 1.0
CG A:GLU592 4.8 28.8 1.0
CD A:GLU592 4.8 30.8 1.0

Magnesium binding site 2 out of 4 in 5sh4

Go back to Magnesium Binding Sites List in 5sh4
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Methoxy-3,4,6-Trimethylpyridin-2-Yl)Methylsulfanyl]-5H-[1, 3]Dioxolo[4,5-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 6-[(5- Methoxy-3,4,6-Trimethylpyridin-2-Yl)Methylsulfanyl]-5H-[1, 3]Dioxolo[4,5-F]Benzimidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:19.0
occ:1.00
 O B:HOH929 1.9 16.0 1.0
O B:HOH954 1.9 20.3 1.0
O B:HOH920 2.0 16.5 1.0
OD1 B:ASP564 2.0 19.8 1.0
O B:HOH1004 2.0 19.8 1.0
O B:HOH961 2.1 13.9 1.0
CG B:ASP564 3.1 18.9 1.0
OD2 B:ASP564 3.4 20.0 1.0
O B:HOH1029 3.8 48.2 1.0
ZN B:ZN801 3.8 26.1 1.0
O B:HOH987 3.9 27.6 1.0
NE2 B:HIS595 4.1 23.1 1.0
OE2 B:GLU592 4.1 26.1 1.0
CD2 B:HIS563 4.2 19.5 1.0
CD2 B:HIS567 4.3 23.6 1.0
O B:HIS563 4.3 22.6 1.0
OG1 B:THR633 4.3 20.1 1.0
CD2 B:HIS595 4.3 23.8 1.0
OD2 B:ASP674 4.3 28.5 1.0
O B:HOH978 4.3 28.5 1.0
CB B:ASP564 4.4 19.6 1.0
NE2 B:HIS567 4.5 23.5 1.0
O B:THR633 4.6 23.4 1.0
CD2 B:HIS525 4.6 25.4 1.0
NE2 B:HIS563 4.6 19.1 1.0
NE2 B:HIS525 4.7 25.5 1.0
CB B:THR633 4.7 23.0 1.0
CA B:ASP564 4.7 20.9 1.0
CG B:GLU592 4.8 26.7 1.0
CD B:GLU592 4.8 26.9 1.0

Magnesium binding site 3 out of 4 in 5sh4

Go back to Magnesium Binding Sites List in 5sh4
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Methoxy-3,4,6-Trimethylpyridin-2-Yl)Methylsulfanyl]-5H-[1, 3]Dioxolo[4,5-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 6-[(5- Methoxy-3,4,6-Trimethylpyridin-2-Yl)Methylsulfanyl]-5H-[1, 3]Dioxolo[4,5-F]Benzimidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:22.9
occ:1.00
 O C:HOH986 2.0 18.6 1.0
O C:HOH941 2.0 16.9 1.0
O C:HOH977 2.1 19.3 1.0
OD1 C:ASP564 2.1 22.6 1.0
O C:HOH930 2.1 23.1 1.0
O C:HOH1023 2.1 17.3 1.0
CG C:ASP564 3.1 23.2 1.0
OD2 C:ASP564 3.4 22.0 1.0
ZN C:ZN801 3.9 28.9 1.0
NE2 C:HIS595 4.0 29.1 1.0
O C:HOH1013 4.0 26.1 1.0
OE2 C:GLU592 4.1 32.0 1.0
CD2 C:HIS567 4.1 28.9 1.0
O C:HOH980 4.2 33.6 1.0
NE2 C:HIS567 4.2 28.5 1.0
CD2 C:HIS595 4.3 27.4 1.0
CD2 C:HIS563 4.3 21.0 1.0
OG1 C:THR633 4.3 24.0 1.0
OD2 C:ASP674 4.4 28.5 1.0
O C:HIS563 4.4 24.6 1.0
CB C:ASP564 4.4 22.7 1.0
O C:THR633 4.5 26.3 1.0
CD2 C:HIS525 4.7 30.7 1.0
NE2 C:HIS563 4.7 22.0 1.0
CA C:ASP564 4.8 22.2 1.0
NE2 C:HIS525 4.8 30.6 1.0
CG C:GLU592 4.8 25.9 1.0
CB C:THR633 4.8 23.3 1.0
CD C:GLU592 4.9 28.1 1.0

Magnesium binding site 4 out of 4 in 5sh4

Go back to Magnesium Binding Sites List in 5sh4
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Methoxy-3,4,6-Trimethylpyridin-2-Yl)Methylsulfanyl]-5H-[1, 3]Dioxolo[4,5-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 6-[(5- Methoxy-3,4,6-Trimethylpyridin-2-Yl)Methylsulfanyl]-5H-[1, 3]Dioxolo[4,5-F]Benzimidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:29.9
occ:1.00
 OD1 D:ASP564 2.0 28.9 1.0
O D:HOH927 2.0 27.1 1.0
O D:HOH981 2.0 32.1 1.0
O D:HOH960 2.2 28.0 1.0
O D:HOH930 2.2 31.0 1.0
O D:HOH945 2.2 20.1 1.0
CG D:ASP564 3.0 31.2 1.0
OD2 D:ASP564 3.4 43.5 1.0
O D:HOH983 3.8 29.5 1.0
ZN D:ZN801 3.9 36.8 1.0
O D:HOH970 4.0 32.1 1.0
NE2 D:HIS595 4.0 32.0 1.0
OE2 D:GLU592 4.2 33.2 1.0
CD2 D:HIS595 4.3 32.2 1.0
CD2 D:HIS567 4.3 44.9 1.0
OG1 D:THR633 4.3 35.3 1.0
CD2 D:HIS563 4.4 29.1 1.0
CB D:ASP564 4.4 30.2 1.0
O D:HIS563 4.5 26.7 1.0
O D:THR633 4.5 42.2 1.0
NE2 D:HIS567 4.6 44.5 1.0
OD2 D:ASP674 4.6 35.4 1.0
CD2 D:HIS525 4.6 35.0 1.0
NE2 D:HIS563 4.6 27.5 1.0
CA D:ASP564 4.7 29.6 1.0
NE2 D:HIS525 4.8 34.3 1.0
CG D:GLU592 4.8 36.8 1.0
CB D:THR633 4.8 35.4 1.0
CD D:GLU592 4.9 38.0 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 03:54:37 2024

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