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Magnesium in PDB 4i9z: Crystal Structure of the PDE5A1 Catalytic Domain in Complex with Novel Inhibitors

Enzymatic activity of Crystal Structure of the PDE5A1 Catalytic Domain in Complex with Novel Inhibitors

All present enzymatic activity of Crystal Structure of the PDE5A1 Catalytic Domain in Complex with Novel Inhibitors:
3.1.4.35;

Protein crystallography data

The structure of Crystal Structure of the PDE5A1 Catalytic Domain in Complex with Novel Inhibitors, PDB code: 4i9z was solved by J.Ren, T.Chen, Y.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.30 / 2.08
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 74.850, 74.850, 132.280, 90.00, 90.00, 120.00
R / Rfree (%) 20.1 / 23.7

Other elements in 4i9z:

The structure of Crystal Structure of the PDE5A1 Catalytic Domain in Complex with Novel Inhibitors also contains other interesting chemical elements:

Bromine (Br) 1 atom
Zinc (Zn) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the PDE5A1 Catalytic Domain in Complex with Novel Inhibitors (pdb code 4i9z). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of the PDE5A1 Catalytic Domain in Complex with Novel Inhibitors, PDB code: 4i9z:

Magnesium binding site 1 out of 1 in 4i9z

Go back to Magnesium Binding Sites List in 4i9z
Magnesium binding site 1 out of 1 in the Crystal Structure of the PDE5A1 Catalytic Domain in Complex with Novel Inhibitors


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 PDE5A1 Catalytic Domain in Complex with Novel Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg903

b:26.2
occ:1.00
 O A:HOH1137 2.0 19.9 1.0
O A:HOH1002 2.1 22.8 1.0
OD2 A:ASP654 2.1 19.6 1.0
O A:HOH1015 2.1 23.5 1.0
O A:HOH1138 2.1 19.9 1.0
O A:HOH1001 2.1 24.7 1.0
CG A:ASP654 3.1 20.4 1.0
OD1 A:ASP654 3.5 18.8 1.0
ZN A:ZN902 3.9 31.2 1.0
OE2 A:GLU682 4.1 28.2 1.0
O A:HIS653 4.2 17.8 1.0
NE2 A:HIS685 4.2 22.6 1.0
CD2 A:HIS657 4.2 19.1 1.0
CD2 A:HIS653 4.3 18.0 1.0
OG1 A:THR723 4.3 20.6 1.0
O A:HOH1004 4.3 21.2 1.0
O A:HOH1151 4.3 33.6 1.0
CD2 A:HIS685 4.4 20.7 1.0
NE2 A:HIS657 4.4 21.3 1.0
CB A:ASP654 4.5 19.3 1.0
O A:THR723 4.5 24.0 1.0
NE2 A:HIS653 4.7 16.2 1.0
CA A:ASP654 4.8 14.6 1.0
NE2 A:HIS613 4.8 22.8 1.0
CB A:THR723 4.8 18.9 1.0
CD2 A:HIS613 4.8 22.4 1.0
OD1 A:ASP764 4.9 26.8 1.0
CD A:GLU682 5.0 26.1 1.0

Reference:

X.Gong, G.Wang, J.Ren, Z.Liu, Z.Wang, T.Chen, X.Yang, X.Jiang, J.Shen, H.Jiang, H.A.Aisa, Y.Xu, J.Li. Exploration of the 5-Bromopyrimidin-4(3H)-Ones As Potent Inhibitors of PDE5. Bioorg.Med.Chem.Lett. V. 23 4944 2013.
ISSN: ISSN 0960-894X
PubMed: 23867165
DOI: 10.1016/J.BMCL.2013.06.062
Page generated: Mon Aug 11 14:06:40 2025

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