Atomistry » Magnesium » PDB 3wo1-3wzy » 3ws8
Atomistry »
  Magnesium »
    PDB 3wo1-3wzy »
      3ws8 »

Magnesium in PDB 3ws8: Crystal Structure of PDE10A in Complex with A Benzimidazole Inhibitor

Enzymatic activity of Crystal Structure of PDE10A in Complex with A Benzimidazole Inhibitor

All present enzymatic activity of Crystal Structure of PDE10A in Complex with A Benzimidazole Inhibitor:
3.1.4.17; 3.1.4.35;

Protein crystallography data

The structure of Crystal Structure of PDE10A in Complex with A Benzimidazole Inhibitor, PDB code: 3ws8 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) 19.96 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.310, 81.107, 160.470, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 31.4

Other elements in 3ws8:

The structure of Crystal Structure of PDE10A in Complex with A Benzimidazole Inhibitor also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of PDE10A in Complex with A Benzimidazole Inhibitor (pdb code 3ws8). 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 A Benzimidazole Inhibitor, PDB code: 3ws8:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3ws8

Go back to Magnesium Binding Sites List in 3ws8
Magnesium binding site 1 out of 2 in the Crystal Structure of PDE10A in Complex with A Benzimidazole Inhibitor


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 A Benzimidazole Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:26.4
occ:1.00
OD1 A:ASP564 2.0 34.3 1.0
O A:HOH902 2.0 32.7 1.0
O A:HOH903 2.1 32.9 1.0
O A:HOH905 2.1 15.3 1.0
O A:HOH904 2.2 30.1 1.0
O A:HOH901 2.8 29.4 1.0
CG A:ASP564 2.9 37.9 1.0
OD2 A:ASP564 3.2 34.9 1.0
ZN A:ZN801 3.6 41.6 1.0
NE2 A:HIS595 3.9 39.7 1.0
O A:HOH906 3.9 10.6 1.0
CD2 A:HIS567 4.1 42.3 1.0
CD2 A:HIS595 4.2 39.4 1.0
CB A:ASP564 4.3 35.1 1.0
O A:THR633 4.3 34.6 1.0
OE2 A:GLU592 4.3 45.6 1.0
NE2 A:HIS567 4.3 43.2 1.0
OG1 A:THR633 4.4 37.9 1.0
CD2 A:HIS563 4.4 37.8 1.0
NE2 A:HIS563 4.6 36.6 1.0
CD2 A:HIS525 4.6 46.0 1.0
O A:HIS563 4.6 33.6 1.0
CA A:ASP564 4.8 37.1 1.0
CB A:THR633 4.8 35.1 1.0
OD2 A:ASP674 4.8 45.6 1.0
CG A:GLU592 4.9 46.0 1.0
NE2 A:HIS525 5.0 45.4 1.0

Magnesium binding site 2 out of 2 in 3ws8

Go back to Magnesium Binding Sites List in 3ws8
Magnesium binding site 2 out of 2 in the Crystal Structure of PDE10A in Complex with A Benzimidazole Inhibitor


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 A Benzimidazole Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:25.7
occ:1.00
OD1 B:ASP564 2.1 34.8 1.0
O B:HOH901 2.1 21.1 1.0
O B:HOH902 2.1 26.8 1.0
O B:HOH906 2.4 23.3 1.0
O B:HOH903 2.7 63.0 1.0
ZN B:ZN801 3.0 43.2 1.0
CG B:ASP564 3.1 34.3 1.0
OD2 B:ASP564 3.4 35.2 1.0
CD2 B:HIS563 3.6 46.8 1.0
OG1 B:THR633 3.7 28.7 1.0
OD2 B:ASP674 3.9 36.5 1.0
O B:HOH904 3.9 36.7 1.0
NE2 B:HIS563 4.0 48.1 1.0
O B:HIS563 4.0 47.2 1.0
CB B:THR633 4.2 34.4 1.0
CD2 B:HIS525 4.2 42.0 1.0
NE2 B:HIS525 4.2 41.6 1.0
NE2 B:HIS595 4.3 38.7 1.0
CB B:ASP564 4.4 38.4 1.0
OE2 B:GLU592 4.4 64.8 1.0
CD2 B:HIS595 4.5 38.6 1.0
O B:THR633 4.5 39.0 1.0
O B:HOH905 4.6 25.2 1.0
CD2 B:HIS567 4.7 39.7 1.0
CG B:ASP674 4.8 37.5 1.0
CA B:ASP564 4.8 39.3 1.0
OD1 B:ASP674 4.8 37.0 1.0
CG B:HIS563 4.8 44.6 1.0
C B:HIS563 4.8 43.0 1.0
C B:THR633 4.9 38.3 1.0

Reference:

A.Chino, N.Masuda, Y.Amano, K.Honbou, T.Mihara, M.Yamazaki, M.Tomishima. Novel Benzimidazole Derivatives As Phosphodiesterase 10A (PDE10A) Inhibitors with Improved Metabolic Stability. Bioorg.Med.Chem. 2014.
ISSN: ESSN 1464-3391
PubMed: 24837154
DOI: 10.1016/J.BMC.2014.04.023
Page generated: Mon Dec 14 09:01:48 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy