Magnesium in PDB 5ohj: Human Phosphodiesterase 4B Catalytic Domain in Complex with A Pyrrolidinyl Inhibitor.

All present enzymatic activity of Human Phosphodiesterase 4B Catalytic Domain in Complex with A Pyrrolidinyl Inhibitor.:
3.1.4.53;

The structure of Human Phosphodiesterase 4B Catalytic Domain in Complex with A Pyrrolidinyl Inhibitor., PDB code: 5ohj was solved by A.Rizzi, L.Carzaniga, E.Armani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.61 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.270, 55.730, 225.560, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 21.2

The structure of Human Phosphodiesterase 4B Catalytic Domain in Complex with A Pyrrolidinyl Inhibitor. also contains other interesting chemical elements:

Fluorine	(F)	4 atoms
Zinc	(Zn)	2 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Magnesium atom in the Human Phosphodiesterase 4B Catalytic Domain in Complex with A Pyrrolidinyl Inhibitor. (pdb code 5ohj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human Phosphodiesterase 4B Catalytic Domain in Complex with A Pyrrolidinyl Inhibitor., PDB code: 5ohj:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Phosphodiesterase 4B Catalytic Domain in Complex with A Pyrrolidinyl Inhibitor.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Phosphodiesterase 4B Catalytic Domain in Complex with A Pyrrolidinyl Inhibitor. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg700 b:7.0 occ:1.00 OD1 A:ASP447 2.2 10.0 1.0 O A:HOH746 2.2 15.2 1.0 O A:HOH745 2.2 15.6 1.0 O A:HOH748 2.2 14.2 1.0 O A:HOH749 2.3 12.8 1.0 O A:HOH747 2.3 11.4 1.0 CG A:ASP447 3.2 10.6 1.0 OD2 A:ASP447 3.5 10.7 1.0 ZN A:ZN699 4.0 13.3 1.0 O A:HOH714 4.1 16.3 1.0 NE2 A:HIS479 4.2 10.2 1.0 OE2 A:GLU476 4.3 15.1 1.0 CD2 A:HIS446 4.3 10.9 1.0 O A:HIS446 4.4 11.0 1.0 OG1 A:THR517 4.4 13.2 1.0 O A:HOH750 4.4 15.9 1.0 C28 A:9VE801 4.5 17.5 1.0 CB A:ASP447 4.5 9.9 1.0 CD2 A:HIS479 4.5 10.6 1.0 O A:HOH761 4.6 21.6 1.0 N2 A:9VE801 4.6 17.6 1.0 OD2 A:ASP564 4.6 13.0 1.0 CD2 A:HIS450 4.6 9.7 1.0 NE2 A:HIS406 4.7 12.2 1.0 NE2 A:HIS446 4.7 9.7 1.0 CD2 A:HIS406 4.7 11.3 1.0 O7 A:9VE801 4.8 35.5 1.0 O A:THR517 4.8 13.4 1.0 CB A:THR517 4.9 13.2 1.0 NE2 A:HIS450 4.9 10.6 1.0 CA A:ASP447 4.9 10.1 1.0 CG A:GLU476 5.0 12.8 1.0

Magnesium binding site 2 out of 2 in the Human Phosphodiesterase 4B Catalytic Domain in Complex with A Pyrrolidinyl Inhibitor.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Phosphodiesterase 4B Catalytic Domain in Complex with A Pyrrolidinyl Inhibitor. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg700 b:10.4 occ:1.00 OD1 B:ASP447 2.2 13.8 1.0 O B:HOH748 2.2 18.0 1.0 O B:HOH744 2.2 17.3 1.0 O B:HOH752 2.3 17.8 1.0 O B:HOH741 2.3 16.5 1.0 O B:HOH747 2.3 13.6 1.0 CG B:ASP447 3.2 14.8 1.0 OD2 B:ASP447 3.5 13.9 1.0 ZN B:ZN699 4.0 15.0 1.0 O B:HOH702 4.1 20.9 1.0 NE2 B:HIS479 4.2 14.0 1.0 OE2 B:GLU476 4.2 19.1 1.0 O B:HOH749 4.3 17.7 1.0 OG1 B:THR517 4.3 17.5 1.0 O B:HIS446 4.3 15.7 1.0 CD2 B:HIS446 4.4 14.5 1.0 C28 B:9VE801 4.5 20.2 1.0 CD2 B:HIS479 4.5 14.4 1.0 OD2 B:ASP564 4.5 14.0 1.0 N2 B:9VE801 4.6 20.4 1.0 CB B:ASP447 4.6 14.4 1.0 O B:HOH756 4.6 28.0 1.0 CD2 B:HIS450 4.6 14.4 1.0 NE2 B:HIS406 4.6 14.3 1.0 NE2 B:HIS446 4.7 13.8 1.0 CD2 B:HIS406 4.7 13.8 1.0 O B:THR517 4.8 15.8 1.0 NE2 B:HIS450 4.8 15.1 1.0 O7 B:9VE801 4.8 25.1 1.0 CB B:THR517 4.8 15.7 1.0 CG B:GLU476 4.9 16.0 1.0 CA B:ASP447 5.0 14.1 1.0

L.Carzaniga, G.Amari, A.Rizzi, C.Capaldi, R.De Fanti, E.Ghidini, G.Villetti, C.Carnini, N.Moretto, F.Facchinetti, P.Caruso, G.Marchini, L.Battipaglia, R.Patacchini, V.Cenacchi, R.Volta, F.Amadei, A.Pappani, S.Capacchi, V.Bagnacani, M.Delcanale, P.Puccini, S.Catinella, M.Civelli, E.Armani. Discovery and Optimization of Thiazolidinyl and Pyrrolidinyl Derivatives As Inhaled PDE4 Inhibitors For Respiratory Diseases. J. Med. Chem. V. 60 10026 2017.
ISSN: ISSN 1520-4804
PubMed: 29200281
DOI: 10.1021/ACS.JMEDCHEM.7B01044