Magnesium in PDB 6a3n: Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 2

Enzymatic activity of Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 2

All present enzymatic activity of Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 2:
3.1.4.35;

Protein crystallography data

The structure of Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 2, PDB code: 6a3n was solved by Y.N.Wu, Q.Zhou, Y.P.Chen, H.B.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.46 / 2.60
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 104.110, 104.110, 269.079, 90.00, 90.00, 90.00
R / Rfree (%) 24.8 / 28

Other elements in 6a3n:

The structure of Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 2 also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 2 (pdb code 6a3n). 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 the PDE9 Catalytic Domain in Complex with Inhibitor 2, PDB code: 6a3n:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6a3n

Go back to Magnesium Binding Sites List in 6a3n
Magnesium binding site 1 out of 2 in the Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 2


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 the PDE9 Catalytic Domain in Complex with Inhibitor 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:28.3
occ:1.00
O A:HOH707 2.2 27.0 1.0
OD1 A:ASP293 2.2 26.9 1.0
O A:HOH737 2.2 27.4 1.0
O A:HOH702 2.2 26.8 1.0
O A:HOH701 2.2 38.3 1.0
O A:HOH772 2.2 26.9 1.0
CG A:ASP293 3.1 26.0 1.0
OD2 A:ASP293 3.3 31.9 1.0
OE2 A:GLU322 3.7 16.8 1.0
O A:HOH703 3.8 51.5 1.0
ZN A:ZN601 3.9 51.9 1.0
CD2 A:HIS296 4.1 18.5 1.0
NE2 A:HIS325 4.1 16.7 1.0
NE2 A:HIS252 4.1 24.5 1.0
NE2 A:HIS296 4.3 18.3 1.0
CD2 A:HIS252 4.4 24.2 1.0
CB A:ASP293 4.5 24.1 1.0
CD2 A:HIS325 4.5 16.9 1.0
CD2 A:HIS292 4.6 31.9 1.0
OG1 A:THR363 4.7 17.6 1.0
NE2 A:HIS292 4.8 35.4 1.0
CD A:GLU322 4.8 17.5 1.0
O A:HIS292 4.8 26.1 1.0
CE1 A:HIS252 4.8 24.4 1.0
OD2 A:ASP402 4.9 28.3 1.0

Magnesium binding site 2 out of 2 in 6a3n

Go back to Magnesium Binding Sites List in 6a3n
Magnesium binding site 2 out of 2 in the Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 2


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 the PDE9 Catalytic Domain in Complex with Inhibitor 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:22.3
occ:1.00
O B:HOH702 2.2 31.1 1.0
O B:HOH701 2.2 20.8 1.0
O B:HOH738 2.2 20.1 1.0
O B:HOH733 2.2 18.5 1.0
OD1 B:ASP293 2.2 24.1 1.0
O B:HOH705 2.2 21.4 1.0
CG B:ASP293 3.1 24.3 1.0
OD2 B:ASP293 3.3 28.6 1.0
O B:HOH707 3.4 47.1 1.0
OE2 B:GLU322 3.8 16.6 1.0
ZN B:ZN601 3.9 44.1 1.0
CD2 B:HIS296 4.1 29.4 1.0
NE2 B:HIS296 4.1 28.9 1.0
NE2 B:HIS325 4.2 15.6 1.0
NE2 B:HIS252 4.3 22.3 1.0
CD2 B:HIS252 4.4 22.4 1.0
OG1 B:THR363 4.5 19.8 1.0
CD2 B:HIS292 4.5 27.2 1.0
CB B:ASP293 4.5 23.2 1.0
O B:HIS292 4.6 23.2 1.0
CD2 B:HIS325 4.6 15.9 1.0
CD B:GLU322 4.8 17.1 1.0
OD2 B:ASP402 4.8 26.7 1.0
NE2 B:HIS292 4.8 30.1 1.0
O B:HOH726 4.9 11.5 1.0
CB B:THR363 5.0 20.2 1.0

Reference:

Y.Wu, Q.Zhou, T.Zhang, Z.Li, Y.P.Chen, P.Zhang, Y.F.Yu, H.Geng, Y.J.Tian, C.Zhang, Y.Wang, J.W.Chen, Y.Chen, H.B.Luo. Discovery of Potent, Selective, and Orally Bioavailable Inhibitors Against Phosphodiesterase-9, A Novel Target For the Treatment of Vascular Dementia. J. Med. Chem. V. 62 4218 2019.
ISSN: ISSN 1520-4804
PubMed: 30916555
DOI: 10.1021/ACS.JMEDCHEM.8B01041
Page generated: Mon Dec 14 22:19:11 2020

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