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Magnesium in PDB 4oex: 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: 4oex was solved by T.T.Chen, J.Ren, Y.C.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.27 / 2.14
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 74.030, 74.030, 131.950, 90.00, 90.00, 120.00
R / Rfree (%) 19.1 / 24

Other elements in 4oex:

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

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 4oex). 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: 4oex:

Magnesium binding site 1 out of 1 in 4oex

Go back to Magnesium Binding Sites List in 4oex
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:40.0
occ:1.00
 O A:HOH1115 2.0 32.1 1.0
OD1 A:ASP654 2.1 28.4 1.0
O A:HOH1093 2.1 28.6 1.0
O A:HOH1002 2.2 28.1 1.0
O A:HOH1004 2.2 31.2 1.0
O A:HOH1086 2.3 36.9 1.0
CG A:ASP654 3.0 29.2 1.0
OD2 A:ASP654 3.3 25.7 1.0
ZN A:ZN902 3.8 36.4 1.0
O A:HOH1003 4.1 27.7 1.0
OE2 A:GLU682 4.1 36.0 1.0
CD2 A:HIS657 4.1 31.5 1.0
O A:HOH1125 4.2 43.4 1.0
NE2 A:HIS685 4.2 29.4 1.0
CD2 A:HIS653 4.3 21.2 1.0
OG1 A:THR723 4.3 25.7 1.0
NE2 A:HIS657 4.3 31.4 1.0
O A:HIS653 4.3 26.7 1.0
CB A:ASP654 4.4 27.5 1.0
CD2 A:HIS685 4.4 30.3 1.0
O A:THR723 4.6 34.3 1.0
NE2 A:HIS653 4.7 26.8 1.0
CD2 A:HIS613 4.7 29.9 1.0
NE2 A:HIS613 4.7 33.2 1.0
CA A:ASP654 4.8 23.0 1.0
CB A:THR723 4.9 28.0 1.0
OD2 A:ASP764 4.9 31.8 1.0
CD A:GLU682 5.0 37.6 1.0

Reference:

J.Ren, Y.He, W.Chen, T.Chen, G.Wang, Z.Wang, Z.Xu, X.Luo, W.Zhu, H.Jiang, J.Shen, Y.Xu. Thermodynamic and Structural Characterization of Halogen Bonding in Protein-Ligand Interactions: A Case Study of PDE5 and Its Inhibitors. J.Med.Chem. V. 57 3588 2014.
ISSN: ISSN 0022-2623
PubMed: 24702184
DOI: 10.1021/JM5002315
Page generated: Mon Dec 14 19:17:30 2020

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