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Magnesium in PDB 5sh0: Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(1, 3-Dimethyl-2-Oxobenzimidazol-5-Yl)-2-[Methylsulfonyl(Naphthalen-1- Yl)Amino]Acetamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(1, 3-Dimethyl-2-Oxobenzimidazol-5-Yl)-2-[Methylsulfonyl(Naphthalen-1- Yl)Amino]Acetamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(1, 3-Dimethyl-2-Oxobenzimidazol-5-Yl)-2-[Methylsulfonyl(Naphthalen-1- Yl)Amino]Acetamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(1, 3-Dimethyl-2-Oxobenzimidazol-5-Yl)-2-[Methylsulfonyl(Naphthalen-1- Yl)Amino]Acetamide, PDB code: 5sh0 was solved by C.Joseph, J.Benz, A.Flohr, M.Brunner, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.58 / 2.29
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.07, 135.07, 234.801, 90, 90, 120
R / Rfree (%) 17.9 / 22.3

Other elements in 5sh0:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(1, 3-Dimethyl-2-Oxobenzimidazol-5-Yl)-2-[Methylsulfonyl(Naphthalen-1- Yl)Amino]Acetamide 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 N-(1, 3-Dimethyl-2-Oxobenzimidazol-5-Yl)-2-[Methylsulfonyl(Naphthalen-1- Yl)Amino]Acetamide (pdb code 5sh0). 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 N-(1, 3-Dimethyl-2-Oxobenzimidazol-5-Yl)-2-[Methylsulfonyl(Naphthalen-1- Yl)Amino]Acetamide, PDB code: 5sh0:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sh0

Go back to Magnesium Binding Sites List in 5sh0
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(1, 3-Dimethyl-2-Oxobenzimidazol-5-Yl)-2-[Methylsulfonyl(Naphthalen-1- Yl)Amino]Acetamide


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 N-(1, 3-Dimethyl-2-Oxobenzimidazol-5-Yl)-2-[Methylsulfonyl(Naphthalen-1- Yl)Amino]Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:31.8
occ:1.00
 O A:HOH976 1.9 33.0 1.0
O A:HOH939 2.0 33.5 1.0
OD1 A:ASP564 2.0 31.4 1.0
O A:HOH906 2.0 27.9 1.0
O A:HOH949 2.1 32.0 1.0
O A:HOH936 2.2 27.5 1.0
CG A:ASP564 3.0 33.0 1.0
OD2 A:ASP564 3.2 33.0 1.0
ZN A:ZN801 3.7 41.6 1.0
O A:HOH925 3.9 44.8 1.0
NE2 A:HIS595 4.0 34.5 1.0
O A:HOH941 4.0 44.9 1.0
OE2 A:GLU592 4.2 39.5 1.0
CD2 A:HIS563 4.2 31.4 1.0
CD2 A:HIS567 4.3 36.6 1.0
CD2 A:HIS595 4.3 36.8 1.0
O A:HIS563 4.4 35.8 1.0
CB A:ASP564 4.4 30.4 1.0
OG1 A:THR633 4.4 39.6 1.0
NE2 A:HIS567 4.5 36.2 1.0
OD2 A:ASP674 4.5 44.3 1.0
NE2 A:HIS563 4.5 30.0 1.0
CD2 A:HIS525 4.6 36.4 1.0
O A:THR633 4.6 38.5 1.0
NE2 A:HIS525 4.6 37.1 1.0
CB A:THR633 4.7 35.8 1.0
CA A:ASP564 4.8 33.5 1.0
CG A:GLU592 4.9 33.3 1.0
CD A:GLU592 5.0 34.9 1.0

Magnesium binding site 2 out of 4 in 5sh0

Go back to Magnesium Binding Sites List in 5sh0
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(1, 3-Dimethyl-2-Oxobenzimidazol-5-Yl)-2-[Methylsulfonyl(Naphthalen-1- Yl)Amino]Acetamide


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 N-(1, 3-Dimethyl-2-Oxobenzimidazol-5-Yl)-2-[Methylsulfonyl(Naphthalen-1- Yl)Amino]Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:29.8
occ:1.00
 O B:HOH944 1.9 32.0 1.0
O B:HOH959 1.9 24.8 1.0
O B:HOH919 2.1 20.4 1.0
OD1 B:ASP564 2.1 33.9 1.0
O B:HOH954 2.1 24.6 1.0
O B:HOH973 2.1 23.9 1.0
CG B:ASP564 3.1 33.2 1.0
OD2 B:ASP564 3.4 36.5 1.0
ZN B:ZN801 3.7 37.3 1.0
O B:HOH916 3.9 43.3 1.0
OE2 B:GLU592 4.1 31.2 1.0
NE2 B:HIS595 4.1 36.1 1.0
O B:HOH956 4.2 37.1 1.0
CD2 B:HIS563 4.2 32.9 1.0
OG1 B:THR633 4.2 29.7 1.0
CD2 B:HIS567 4.3 29.2 1.0
O B:HIS563 4.3 35.0 1.0
CD2 B:HIS595 4.3 35.6 1.0
NE2 B:HIS567 4.4 33.6 1.0
CB B:ASP564 4.4 31.9 1.0
OD2 B:ASP674 4.5 38.7 1.0
NE2 B:HIS563 4.5 32.3 1.0
O B:THR633 4.6 29.9 1.0
CD2 B:HIS525 4.6 35.7 1.0
CB B:THR633 4.6 30.9 1.0
CA B:ASP564 4.7 35.0 1.0
NE2 B:HIS525 4.8 33.5 1.0
CG B:GLU592 4.8 34.9 1.0
CD B:GLU592 4.9 33.6 1.0

Magnesium binding site 3 out of 4 in 5sh0

Go back to Magnesium Binding Sites List in 5sh0
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(1, 3-Dimethyl-2-Oxobenzimidazol-5-Yl)-2-[Methylsulfonyl(Naphthalen-1- Yl)Amino]Acetamide


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 N-(1, 3-Dimethyl-2-Oxobenzimidazol-5-Yl)-2-[Methylsulfonyl(Naphthalen-1- Yl)Amino]Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:32.1
occ:1.00
 O C:HOH940 2.0 32.6 1.0
O C:HOH967 2.0 27.4 1.0
O C:HOH977 2.0 30.2 1.0
O C:HOH924 2.0 29.6 1.0
OD1 C:ASP564 2.1 34.6 1.0
O C:HOH915 2.2 25.8 1.0
CG C:ASP564 3.1 32.9 1.0
OD2 C:ASP564 3.4 34.3 1.0
ZN C:ZN801 3.7 40.7 1.0
O C:HOH909 3.8 52.1 1.0
OE2 C:GLU592 4.0 38.0 1.0
NE2 C:HIS595 4.1 39.8 1.0
CD2 C:HIS563 4.1 32.6 1.0
O C:HOH947 4.1 37.6 1.0
CD2 C:HIS567 4.2 34.3 1.0
OG1 C:THR633 4.2 32.8 1.0
O C:HIS563 4.3 32.6 1.0
CD2 C:HIS595 4.3 37.8 1.0
NE2 C:HIS567 4.4 34.9 1.0
OD2 C:ASP674 4.4 32.1 1.0
CB C:ASP564 4.4 30.9 1.0
O C:THR633 4.5 37.1 1.0
NE2 C:HIS563 4.5 35.4 1.0
CB C:THR633 4.7 33.0 1.0
CD2 C:HIS525 4.7 39.0 1.0
NE2 C:HIS525 4.7 39.9 1.0
CA C:ASP564 4.8 32.2 1.0
CD C:GLU592 4.9 39.3 1.0
CG C:GLU592 4.9 36.4 1.0

Magnesium binding site 4 out of 4 in 5sh0

Go back to Magnesium Binding Sites List in 5sh0
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(1, 3-Dimethyl-2-Oxobenzimidazol-5-Yl)-2-[Methylsulfonyl(Naphthalen-1- Yl)Amino]Acetamide


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 N-(1, 3-Dimethyl-2-Oxobenzimidazol-5-Yl)-2-[Methylsulfonyl(Naphthalen-1- Yl)Amino]Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:45.7
occ:1.00
 O D:HOH906 2.0 38.1 1.0
O D:HOH928 2.0 36.6 1.0
O D:HOH934 2.1 39.1 1.0
O D:HOH912 2.1 36.9 1.0
O D:HOH920 2.2 32.8 1.0
OD1 D:ASP564 2.2 40.7 1.0
CG D:ASP564 3.1 39.7 1.0
OD2 D:ASP564 3.4 46.0 1.0
O D:HOH933 3.7 45.9 1.0
ZN D:ZN801 3.8 48.7 1.0
OE2 D:GLU592 3.9 42.7 1.0
O D:HOH927 3.9 43.2 1.0
NE2 D:HIS595 4.0 44.6 1.0
CD2 D:HIS567 4.1 46.1 1.0
OG1 D:THR633 4.3 43.1 1.0
NE2 D:HIS567 4.3 45.7 1.0
CD2 D:HIS563 4.4 36.4 1.0
CD2 D:HIS595 4.4 43.4 1.0
O D:HIS563 4.4 40.3 1.0
CD2 D:HIS525 4.5 55.6 1.0
CB D:ASP564 4.5 41.1 1.0
OD2 D:ASP674 4.5 45.6 1.0
O D:THR633 4.6 43.6 1.0
NE2 D:HIS525 4.6 52.8 1.0
NE2 D:HIS563 4.7 35.1 1.0
CD D:GLU592 4.7 43.1 1.0
CG D:GLU592 4.8 43.9 1.0
CA D:ASP564 4.9 40.6 1.0
CB D:THR633 4.9 43.4 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 03:52:26 2024

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