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Magnesium in PDB 5shu: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3,5,6,7- Tetrahydropyrrolo[3,2-F]Benzimidazole

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

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3,5,6,7- Tetrahydropyrrolo[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- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3,5,6,7- Tetrahydropyrrolo[3,2-F]Benzimidazole, PDB code: 5shu 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) 43.64 / 1.98
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.672, 135.672, 235.693, 90, 90, 120
R / Rfree (%) 18.8 / 22.1

Other elements in 5shu:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3,5,6,7- Tetrahydropyrrolo[3,2-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 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3,5,6,7- Tetrahydropyrrolo[3,2-F]Benzimidazole (pdb code 5shu). 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]-3,5,6,7- Tetrahydropyrrolo[3,2-F]Benzimidazole, PDB code: 5shu:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5shu

Go back to Magnesium Binding Sites List in 5shu
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]-3,5,6,7- Tetrahydropyrrolo[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- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3,5,6,7- Tetrahydropyrrolo[3,2-F]Benzimidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:20.9
occ:1.00
 O A:HOH945 2.0 20.5 1.0
O A:HOH930 2.0 19.7 1.0
O A:HOH1031 2.0 19.4 1.0
OD1 A:ASP564 2.0 21.7 1.0
O A:HOH977 2.1 21.1 1.0
O A:HOH942 2.1 22.9 1.0
CG A:ASP564 3.1 22.0 1.0
OD2 A:ASP564 3.4 21.3 1.0
ZN A:ZN801 3.7 25.8 1.0
O A:HOH1006 4.0 32.4 1.0
O A:HOH1052 4.0 40.8 1.0
OE2 A:GLU592 4.1 27.2 1.0
NE2 A:HIS595 4.1 23.1 1.0
OG1 A:THR633 4.2 24.4 1.0
CD2 A:HIS563 4.2 21.0 1.0
O A:HOH991 4.3 29.8 1.0
CD2 A:HIS567 4.4 25.1 1.0
CD2 A:HIS595 4.4 23.2 1.0
OD2 A:ASP674 4.4 28.8 1.0
O A:HIS563 4.4 21.8 1.0
CB A:ASP564 4.4 21.2 1.0
O A:THR633 4.5 24.6 1.0
NE2 A:HIS563 4.6 21.4 1.0
NE2 A:HIS567 4.6 25.2 1.0
CD2 A:HIS525 4.6 25.4 1.0
CB A:THR633 4.7 24.3 1.0
NE2 A:HIS525 4.7 26.3 1.0
CA A:ASP564 4.8 21.6 1.0
CG A:GLU592 4.9 24.7 1.0
CD A:GLU592 4.9 25.5 1.0

Magnesium binding site 2 out of 4 in 5shu

Go back to Magnesium Binding Sites List in 5shu
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]-3,5,6,7- Tetrahydropyrrolo[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- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3,5,6,7- Tetrahydropyrrolo[3,2-F]Benzimidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:19.4
occ:1.00
 O B:HOH941 1.9 17.6 1.0
OD1 B:ASP564 2.0 20.6 1.0
O B:HOH1031 2.0 20.6 1.0
O B:HOH926 2.1 20.6 1.0
O B:HOH993 2.1 17.9 1.0
O B:HOH945 2.1 20.7 1.0
CG B:ASP564 3.0 19.9 1.0
OD2 B:ASP564 3.4 20.2 1.0
ZN B:ZN801 3.8 24.7 1.0
O B:HOH1003 4.0 26.9 1.0
O B:HOH1067 4.0 45.0 1.0
NE2 B:HIS595 4.1 20.2 1.0
OE2 B:GLU592 4.1 24.2 1.0
CD2 B:HIS563 4.2 18.9 1.0
OG1 B:THR633 4.2 19.3 1.0
CD2 B:HIS567 4.3 21.5 1.0
CD2 B:HIS595 4.3 19.8 1.0
O B:HOH1012 4.3 23.9 1.0
CB B:ASP564 4.4 18.8 1.0
OD2 B:ASP674 4.4 23.0 1.0
O B:HIS563 4.4 21.1 1.0
NE2 B:HIS563 4.5 16.8 1.0
NE2 B:HIS567 4.5 21.6 1.0
O B:THR633 4.5 20.0 1.0
CD2 B:HIS525 4.6 24.9 1.0
CB B:THR633 4.7 20.4 1.0
CA B:ASP564 4.7 18.8 1.0
NE2 B:HIS525 4.7 25.1 1.0
CG B:GLU592 4.8 20.9 1.0
CD B:GLU592 4.9 22.7 1.0

Magnesium binding site 3 out of 4 in 5shu

Go back to Magnesium Binding Sites List in 5shu
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]-3,5,6,7- Tetrahydropyrrolo[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- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3,5,6,7- Tetrahydropyrrolo[3,2-F]Benzimidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:23.8
occ:1.00
 O C:HOH935 2.0 23.8 1.0
O C:HOH973 2.0 24.9 1.0
O C:HOH1028 2.1 21.1 1.0
O C:HOH999 2.1 20.6 1.0
OD1 C:ASP564 2.1 23.5 1.0
O C:HOH976 2.1 19.0 1.0
CG C:ASP564 3.1 23.6 1.0
OD2 C:ASP564 3.4 22.4 1.0
ZN C:ZN801 3.8 27.8 1.0
O C:HOH1065 3.8 48.9 1.0
O C:HOH1027 3.9 31.3 1.0
NE2 C:HIS595 4.0 23.7 1.0
OE2 C:GLU592 4.0 26.6 1.0
O C:HOH1010 4.2 30.5 1.0
CD2 C:HIS563 4.3 20.3 1.0
CD2 C:HIS567 4.3 24.8 1.0
OG1 C:THR633 4.3 25.2 1.0
O C:HIS563 4.3 22.8 1.0
CD2 C:HIS595 4.3 21.8 1.0
OD2 C:ASP674 4.4 27.5 1.0
CB C:ASP564 4.5 22.8 1.0
NE2 C:HIS567 4.5 24.3 1.0
O C:THR633 4.6 23.5 1.0
CD2 C:HIS525 4.6 28.3 1.0
NE2 C:HIS563 4.6 19.3 1.0
NE2 C:HIS525 4.7 29.2 1.0
CB C:THR633 4.8 25.1 1.0
CA C:ASP564 4.8 23.0 1.0
CG C:GLU592 4.8 24.9 1.0
CD C:GLU592 4.9 24.9 1.0

Magnesium binding site 4 out of 4 in 5shu

Go back to Magnesium Binding Sites List in 5shu
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]-3,5,6,7- Tetrahydropyrrolo[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- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3,5,6,7- Tetrahydropyrrolo[3,2-F]Benzimidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:29.0
occ:1.00
 O D:HOH989 2.1 28.6 1.0
OD1 D:ASP564 2.1 28.2 1.0
O D:HOH912 2.1 27.3 1.0
O D:HOH970 2.1 24.3 1.0
O D:HOH924 2.1 25.7 1.0
O D:HOH923 2.2 27.6 1.0
CG D:ASP564 3.1 28.5 1.0
OD2 D:ASP564 3.5 30.3 1.0
ZN D:ZN801 3.8 33.5 1.0
O D:HOH964 4.0 35.5 1.0
NE2 D:HIS595 4.0 30.6 1.0
OE2 D:GLU592 4.1 33.1 1.0
OG1 D:THR633 4.2 32.1 1.0
O D:HOH975 4.2 30.2 1.0
CD2 D:HIS563 4.2 27.9 1.0
CD2 D:HIS595 4.2 30.3 1.0
CD2 D:HIS567 4.3 35.2 1.0
O D:HIS563 4.3 27.1 1.0
CB D:ASP564 4.4 29.2 1.0
OD2 D:ASP674 4.5 29.4 1.0
O D:THR633 4.5 31.4 1.0
NE2 D:HIS563 4.6 26.6 1.0
NE2 D:HIS567 4.6 34.4 1.0
CD2 D:HIS525 4.6 32.2 1.0
CB D:THR633 4.7 31.1 1.0
NE2 D:HIS525 4.7 32.8 1.0
CA D:ASP564 4.8 29.0 1.0
CG D:GLU592 4.8 33.1 1.0
CD D:GLU592 4.9 32.8 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 04:03:13 2024

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