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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 5ohj:

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

Magnesium Binding Sites:

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 5ohj

Go back to Magnesium Binding Sites List in 5ohj
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 5ohj

Go back to Magnesium Binding Sites List in 5ohj
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

Reference:

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
Page generated: Mon Sep 30 00:59:46 2024

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