Magnesium in PDB 5xuj: Crystal Structure of PDE10A in Complex with 7-(4-Chlorophenyl)-2- Methylpyrazolo[1,5-A]Pyrimidine

Enzymatic activity of Crystal Structure of PDE10A in Complex with 7-(4-Chlorophenyl)-2- Methylpyrazolo[1,5-A]Pyrimidine

All present enzymatic activity of Crystal Structure of PDE10A in Complex with 7-(4-Chlorophenyl)-2- Methylpyrazolo[1,5-A]Pyrimidine:
3.1.4.17; 3.1.4.35;

Protein crystallography data

The structure of Crystal Structure of PDE10A in Complex with 7-(4-Chlorophenyl)-2- Methylpyrazolo[1,5-A]Pyrimidine, PDB code: 5xuj was solved by Y.Amano, K.Honbou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 78.80 / 2.44
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.339, 81.299, 157.597, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 28

Other elements in 5xuj:

The structure of Crystal Structure of PDE10A in Complex with 7-(4-Chlorophenyl)-2- Methylpyrazolo[1,5-A]Pyrimidine also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of PDE10A in Complex with 7-(4-Chlorophenyl)-2- Methylpyrazolo[1,5-A]Pyrimidine (pdb code 5xuj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of PDE10A in Complex with 7-(4-Chlorophenyl)-2- Methylpyrazolo[1,5-A]Pyrimidine, PDB code: 5xuj:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5xuj

Go back to Magnesium Binding Sites List in 5xuj
Magnesium binding site 1 out of 2 in the Crystal Structure of PDE10A in Complex with 7-(4-Chlorophenyl)-2- Methylpyrazolo[1,5-A]Pyrimidine


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 PDE10A in Complex with 7-(4-Chlorophenyl)-2- Methylpyrazolo[1,5-A]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:27.6
occ:1.00
OD1 A:ASP564 1.8 48.1 1.0
O A:HOH906 2.0 33.0 1.0
O A:HOH908 2.1 42.6 1.0
O A:HOH905 2.2 32.3 1.0
O A:HOH925 2.3 25.3 1.0
CG A:ASP564 2.9 42.5 1.0
OD2 A:ASP564 3.3 46.7 1.0
O A:HOH904 3.8 37.3 1.0
CD2 A:HIS563 3.8 40.6 1.0
NE2 A:HIS595 3.8 49.0 1.0
ZN A:ZN801 3.8 43.3 1.0
OE2 A:GLU592 3.9 36.4 1.0
O A:HOH927 3.9 28.1 1.0
OG1 A:THR633 4.0 38.5 1.0
O A:HOH931 4.0 34.7 1.0
NE2 A:HIS563 4.0 45.3 1.0
O A:HIS563 4.1 39.4 1.0
CD2 A:HIS595 4.1 44.6 1.0
CB A:ASP564 4.2 42.1 1.0
O A:THR633 4.2 38.2 1.0
CD2 A:HIS567 4.4 45.0 1.0
O A:HOH902 4.4 47.7 1.0
CA A:ASP564 4.5 42.0 1.0
CB A:THR633 4.5 34.1 1.0
CG A:GLU592 4.6 38.3 1.0
CD A:GLU592 4.7 39.2 1.0
OD2 A:ASP674 4.7 33.9 1.0
NE2 A:HIS567 4.7 44.9 1.0
C A:HIS563 4.7 41.3 1.0
CE1 A:HIS595 4.8 44.9 1.0
CD2 A:HIS525 4.9 50.8 1.0
N A:ASP564 4.9 37.3 1.0
CG A:HIS563 5.0 37.0 1.0

Magnesium binding site 2 out of 2 in 5xuj

Go back to Magnesium Binding Sites List in 5xuj
Magnesium binding site 2 out of 2 in the Crystal Structure of PDE10A in Complex with 7-(4-Chlorophenyl)-2- Methylpyrazolo[1,5-A]Pyrimidine


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 PDE10A in Complex with 7-(4-Chlorophenyl)-2- Methylpyrazolo[1,5-A]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:34.3
occ:1.00
OD1 B:ASP564 1.8 26.7 1.0
O B:HOH934 2.1 34.6 1.0
O B:HOH906 2.2 26.5 1.0
O B:HOH901 2.2 32.1 1.0
O B:HOH933 2.3 23.0 1.0
O B:HOH927 2.3 32.6 1.0
CG B:ASP564 2.9 30.4 1.0
O B:HOH939 3.3 47.1 1.0
OD2 B:ASP564 3.3 28.9 1.0
ZN B:ZN801 3.6 38.5 1.0
NE2 B:HIS595 4.0 35.0 1.0
CD2 B:HIS563 4.0 32.0 1.0
O B:HOH941 4.1 20.0 1.0
O B:HIS563 4.1 36.9 1.0
CB B:ASP564 4.2 31.4 1.0
OE2 B:GLU592 4.3 49.9 1.0
CD2 B:HIS595 4.3 36.9 1.0
CD2 B:HIS567 4.3 40.2 1.0
NE2 B:HIS563 4.4 36.2 1.0
CA B:ASP564 4.6 36.1 1.0
OD2 B:ASP674 4.6 49.6 1.0
OG1 B:THR633 4.6 43.6 1.0
NE2 B:HIS567 4.6 37.2 1.0
CD2 B:HIS525 4.7 38.8 1.0
CB B:THR633 4.8 39.6 1.0
NE2 B:HIS525 4.8 41.5 1.0
O B:THR633 4.9 40.0 1.0
CG B:GLU592 4.9 43.0 1.0
CE1 B:HIS595 4.9 38.5 1.0
C B:HIS563 4.9 35.9 1.0
CD B:GLU592 5.0 43.3 1.0

Reference:

A.Chino, R.Seo, Y.Amano, I.Namatame, W.Hamaguchi, K.Honbou, T.Mihara, M.Yamazaki, M.Tomishima, N.Masuda. Fragment-Based Discovery of Pyrimido[1,2-B]Indazole PDE10A Inhibitors. Chem. Pharm. Bull. V. 66 286 2018.
ISSN: ISSN 1347-5223
PubMed: 29491261
DOI: 10.1248/CPB.C17-00836
Page generated: Mon Dec 14 22:11:38 2020

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