Zinc in PDB 7bpi: The Crystal Structue of PDE10A Complexed with 14

Enzymatic activity of The Crystal Structue of PDE10A Complexed with 14

All present enzymatic activity of The Crystal Structue of PDE10A Complexed with 14:
3.1.4.17; 3.1.4.35;

Protein crystallography data

The structure of The Crystal Structue of PDE10A Complexed with 14, PDB code: 7bpi was solved by Y.Yang, S.Zhang, Q.Zhou, Y.-Y.Huang, L.Guo, H.-B.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.26 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.941, 81.683, 162.493, 90, 90, 90
R / Rfree (%) 25.2 / 32.6

Other elements in 7bpi:

The structure of The Crystal Structue of PDE10A Complexed with 14 also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the The Crystal Structue of PDE10A Complexed with 14 (pdb code 7bpi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the The Crystal Structue of PDE10A Complexed with 14, PDB code: 7bpi:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7bpi

Go back to Zinc Binding Sites List in 7bpi
Zinc binding site 1 out of 2 in the The Crystal Structue of PDE10A Complexed with 14


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structue of PDE10A Complexed with 14 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:32.5
occ:1.00
OD2 A:ASP564 2.1 18.3 1.0
O A:HOH926 2.2 23.9 1.0
OD1 A:ASP674 2.2 11.5 1.0
NE2 A:HIS563 2.3 15.7 1.0
NE2 A:HIS529 2.3 14.4 1.0
CD2 A:HIS563 2.9 16.6 1.0
CG A:ASP674 3.0 13.3 1.0
CG A:ASP564 3.0 16.7 1.0
CD2 A:HIS529 3.2 19.5 1.0
OD2 A:ASP674 3.2 12.7 1.0
OD1 A:ASP564 3.3 19.5 1.0
CE1 A:HIS529 3.4 14.9 1.0
CE1 A:HIS563 3.5 17.6 1.0
CD2 A:HIS525 4.0 20.4 1.0
CG A:HIS563 4.2 13.8 1.0
MG A:MG802 4.2 17.2 1.0
NE2 A:HIS525 4.4 16.6 1.0
CB A:ASP564 4.4 22.6 1.0
ND1 A:HIS563 4.4 13.6 1.0
CG A:HIS529 4.4 12.3 1.0
CB A:ASP674 4.4 18.7 1.0
ND1 A:HIS529 4.5 13.9 1.0
O A:HOH918 4.5 15.1 1.0
CA A:ASP674 4.9 11.8 1.0
CG2 A:VAL533 4.9 11.0 1.0

Zinc binding site 2 out of 2 in 7bpi

Go back to Zinc Binding Sites List in 7bpi
Zinc binding site 2 out of 2 in the The Crystal Structue of PDE10A Complexed with 14


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structue of PDE10A Complexed with 14 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:37.6
occ:1.00
OD2 B:ASP674 1.8 21.9 1.0
OD2 B:ASP564 2.1 27.2 1.0
NE2 B:HIS563 2.1 26.1 1.0
NE2 B:HIS529 2.5 18.2 1.0
CG B:ASP674 2.7 17.0 1.0
CD2 B:HIS563 2.8 23.0 1.0
OD1 B:ASP674 2.9 16.2 1.0
O B:HOH914 3.1 30.3 1.0
CG B:ASP564 3.2 25.0 1.0
CE1 B:HIS563 3.3 23.8 1.0
CD2 B:HIS529 3.4 19.9 1.0
CE1 B:HIS529 3.6 18.2 1.0
OD1 B:ASP564 3.8 15.1 1.0
MG B:MG802 3.9 29.0 1.0
CD2 B:HIS525 4.0 25.0 1.0
CG B:HIS563 4.1 24.5 1.0
CB B:ASP674 4.1 15.0 1.0
NE2 B:HIS525 4.2 29.4 1.0
ND1 B:HIS563 4.2 29.7 1.0
CB B:ASP564 4.3 27.0 1.0
CG B:HIS529 4.6 22.3 1.0
ND1 B:HIS529 4.6 17.9 1.0
O B:HOH925 4.7 17.1 1.0
CA B:ASP674 4.7 9.9 1.0
O B:ASP674 4.8 11.2 1.0
CG2 B:VAL533 4.9 10.3 1.0

Reference:

Y.Yang, S.Zhang, Q.Zhou, C.Zhang, Y.Gao, H.Wang, Z.Li, D.Wu, Y.Wu, Y.Y.Huang, L.Guo, H.B.Luo. Discovery of Highly Selective and Orally Available Benzimidazole-Based Phosphodiesterase 10 Inhibitors with Improved Solubility and Pharmacokinetic Properties For Treatment of Pulmonary Arterial Hypertension. Acta Pharm Sin B V. 10 2339 2020.
ISSN: ISSN 2211-3835
PubMed: 33354505
DOI: 10.1016/J.APSB.2020.04.003
Page generated: Wed Mar 3 16:18:48 2021

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