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Zinc in PDB 3ws9: Crystal Structure of PDE10A in Complex with A Benzimdazole Inhibitor

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

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

Protein crystallography data

The structure of Crystal Structure of PDE10A in Complex with A Benzimdazole Inhibitor, PDB code: 3ws9 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) 29.50 / 2.99
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.421, 81.542, 161.255, 90.00, 90.00, 90.00
R / Rfree (%) 22.3 / 34.6

Other elements in 3ws9:

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

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of PDE10A in Complex with A Benzimdazole Inhibitor (pdb code 3ws9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of PDE10A in Complex with A Benzimdazole Inhibitor, PDB code: 3ws9:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3ws9

Go back to Zinc Binding Sites List in 3ws9
Zinc binding site 1 out of 2 in the Crystal Structure of PDE10A in Complex with A Benzimdazole Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of PDE10A in Complex with A Benzimdazole Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:37.0
occ:1.00
OD2 A:ASP564 1.9 39.0 1.0
NE2 A:HIS529 2.2 31.9 1.0
NE2 A:HIS563 2.3 41.0 1.0
OD1 A:ASP674 2.4 31.6 1.0
OD2 A:ASP674 2.9 37.2 1.0
CG A:ASP564 2.9 35.5 1.0
CD2 A:HIS563 3.0 40.2 1.0
CG A:ASP674 3.0 32.3 1.0
O A:HOH902 3.1 7.7 1.0
CE1 A:HIS529 3.1 33.5 1.0
CD2 A:HIS529 3.2 33.3 1.0
OD1 A:ASP564 3.3 36.6 1.0
CE1 A:HIS563 3.5 39.5 1.0
MG A:MG802 3.5 19.7 1.0
CD2 A:HIS525 3.7 41.1 1.0
NE2 A:HIS525 3.9 42.1 1.0
CB A:ASP564 4.1 33.2 1.0
CG A:HIS563 4.2 36.1 1.0
ND1 A:HIS529 4.2 33.1 1.0
O A:HOH901 4.3 44.5 1.0
CG A:HIS529 4.3 32.0 1.0
ND1 A:HIS563 4.4 37.3 1.0
CB A:ASP674 4.4 30.1 1.0
O A:ASP674 4.8 32.3 1.0

Zinc binding site 2 out of 2 in 3ws9

Go back to Zinc Binding Sites List in 3ws9
Zinc binding site 2 out of 2 in the Crystal Structure of PDE10A in Complex with A Benzimdazole Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of PDE10A in Complex with A Benzimdazole Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:34.6
occ:1.00
OD2 B:ASP564 1.8 34.0 1.0
NE2 B:HIS563 2.0 32.9 1.0
NE2 B:HIS529 2.1 30.6 1.0
OD1 B:ASP674 2.3 24.0 1.0
OD2 B:ASP674 2.7 22.7 1.0
CG B:ASP674 2.9 23.2 1.0
CD2 B:HIS563 2.9 32.2 1.0
O B:HOH903 3.0 22.9 1.0
CG B:ASP564 3.0 33.2 1.0
CD2 B:HIS529 3.0 31.9 1.0
CE1 B:HIS563 3.0 32.3 1.0
MG B:MG802 3.1 14.2 1.0
CE1 B:HIS529 3.2 31.9 1.0
OD1 B:ASP564 3.7 35.5 1.0
CD2 B:HIS525 3.8 42.0 1.0
CB B:ASP564 3.9 31.8 1.0
CG B:HIS563 4.1 31.3 1.0
ND1 B:HIS563 4.1 30.3 1.0
CG B:HIS529 4.2 32.7 1.0
NE2 B:HIS525 4.2 41.8 1.0
ND1 B:HIS529 4.3 32.5 1.0
CB B:ASP674 4.3 23.4 1.0
O B:HOH901 4.7 19.4 1.0
O B:HOH902 4.8 17.6 1.0
CA B:ASP674 4.9 24.2 1.0
O B:ASP674 5.0 23.4 1.0
CG B:HIS525 5.0 39.0 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: Sat Oct 26 18:16:01 2024

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