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Magnesium in PDB 4xy2: Crystal Structure of PDE10A in Complex with ASP9436

Enzymatic activity of Crystal Structure of PDE10A in Complex with ASP9436

All present enzymatic activity of Crystal Structure of PDE10A in Complex with ASP9436:
3.1.4.17; 3.1.4.35;

Protein crystallography data

The structure of Crystal Structure of PDE10A in Complex with ASP9436, PDB code: 4xy2 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) 79.57 / 2.03
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.447, 82.114, 159.150, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 26

Other elements in 4xy2:

The structure of Crystal Structure of PDE10A in Complex with ASP9436 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 ASP9436 (pdb code 4xy2). 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 ASP9436, PDB code: 4xy2:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4xy2

Go back to Magnesium Binding Sites List in 4xy2
Magnesium binding site 1 out of 2 in the Crystal Structure of PDE10A in Complex with ASP9436


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 ASP9436 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:25.0
occ:1.00
O A:HOH923 2.0 33.7 1.0
O A:HOH928 2.1 19.7 1.0
O A:HOH926 2.2 22.0 1.0
OD1 A:ASP564 2.3 29.2 1.0
O A:HOH960 2.3 24.1 1.0
O A:HOH924 2.4 20.6 1.0
CG A:ASP564 3.2 25.5 1.0
OD2 A:ASP564 3.5 26.9 1.0
O A:HOH922 3.6 24.9 1.0
O A:HOH925 3.6 27.3 1.0
ZN A:ZN801 3.7 31.7 1.0
OG1 A:THR633 4.0 30.9 1.0
NE2 A:HIS595 4.1 30.2 1.0
OE2 A:GLU592 4.1 36.0 1.0
O A:HOH927 4.1 36.8 1.0
CD2 A:HIS563 4.2 23.4 1.0
O A:HIS563 4.2 28.2 1.0
O A:THR633 4.3 24.9 1.0
CD2 A:HIS595 4.3 29.6 1.0
CB A:THR633 4.5 28.4 1.0
CB A:ASP564 4.6 23.4 1.0
NE2 A:HIS563 4.6 24.3 1.0
CD2 A:HIS567 4.6 29.0 1.0
OD2 A:ASP674 4.7 27.3 1.0
O A:HOH921 4.7 23.7 1.0
CG A:GLU592 4.8 35.1 1.0
O A:HOH963 4.9 32.1 1.0
CD A:GLU592 4.9 39.2 1.0
CA A:ASP564 4.9 27.8 1.0
C A:THR633 4.9 27.1 1.0
CD2 A:HIS525 5.0 31.2 1.0

Magnesium binding site 2 out of 2 in 4xy2

Go back to Magnesium Binding Sites List in 4xy2
Magnesium binding site 2 out of 2 in the Crystal Structure of PDE10A in Complex with ASP9436


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 ASP9436 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:24.0
occ:1.00
O B:HOH922 2.0 32.4 1.0
OD1 B:ASP564 2.0 26.7 1.0
O B:HOH920 2.1 20.8 1.0
O B:HOH923 2.2 22.0 1.0
O B:HOH921 2.2 22.0 1.0
O B:HOH918 2.4 29.9 1.0
CG B:ASP564 3.1 24.4 1.0
O B:HOH917 3.5 30.9 1.0
OD2 B:ASP564 3.5 19.1 1.0
ZN B:ZN801 3.6 26.0 1.0
O B:HOH924 3.9 32.8 1.0
NE2 B:HIS595 4.0 24.1 1.0
OG1 B:THR633 4.1 23.6 1.0
CD2 B:HIS563 4.1 20.2 1.0
OE2 B:GLU592 4.2 25.0 1.0
CD2 B:HIS595 4.2 24.8 1.0
O B:HOH958 4.3 23.1 1.0
O B:THR633 4.3 24.5 1.0
NE2 B:HIS563 4.4 21.2 1.0
O B:HIS563 4.4 23.0 1.0
CB B:ASP564 4.4 23.0 1.0
CD2 B:HIS567 4.5 29.6 1.0
OD2 B:ASP674 4.5 24.5 1.0
CB B:THR633 4.6 20.9 1.0
CA B:ASP564 4.8 22.9 1.0
CD2 B:HIS525 4.8 24.2 1.0
NE2 B:HIS567 4.8 36.1 1.0
CG B:GLU592 4.8 23.7 1.0
CD B:GLU592 5.0 27.3 1.0

Reference:

W.Hamaguchi, N.Masuda, S.Miyamoto, S.Kikuchi, F.Narazaki, Y.Shiina, R.Seo, Y.Amano, T.Mihara, H.Moriguchi, K.Hattori. Addressing Phototoxicity Observed in A Novel Series of Biaryl Derivatives: Discovery of Potent, Selective and Orally Active Phosphodiesterase 10A Inhibitor ASP9436 Bioorg.Med.Chem. V. 23 3351 2015.
ISSN: ESSN 1464-3391
PubMed: 25960322
DOI: 10.1016/J.BMC.2015.04.052
Page generated: Mon Dec 14 19:48:45 2020

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