Magnesium in PDB 7f2k: Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 17A

Enzymatic activity of Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 17A

All present enzymatic activity of Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 17A:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 17A, PDB code: 7f2k was solved by Y.-Y.Huang, X.He, H.-B.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.58 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.063, 80.697, 163.385, 90, 90, 90
R / Rfree (%) 20.8 / 25.7

Other elements in 7f2k:

The structure of Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 17A also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 17A (pdb code 7f2k). 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 PDE4D Catalytic Domain Complexed with Compound 17A, PDB code: 7f2k:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7f2k

Go back to Magnesium Binding Sites List in 7f2k
Magnesium binding site 1 out of 2 in the Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 17A


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 PDE4D Catalytic Domain Complexed with Compound 17A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:11.4
occ:1.00
O A:HOH774 1.9 11.3 1.0
O A:HOH701 2.0 11.7 1.0
OD1 A:ASP201 2.1 9.2 1.0
O A:HOH788 2.1 13.6 1.0
O A:HOH750 2.2 10.5 1.0
O A:HOH765 2.3 12.4 1.0
CG A:ASP201 3.1 13.5 1.0
O35 A:0X8603 3.2 31.7 1.0
OD2 A:ASP201 3.4 10.2 1.0
ZN A:ZN601 3.8 22.4 1.0
OE2 A:GLU230 4.1 15.6 1.0
CD2 A:HIS200 4.1 10.0 1.0
C34 A:0X8603 4.1 23.9 1.0
O A:HIS200 4.2 12.7 1.0
NE2 A:HIS233 4.2 13.3 1.0
OG1 A:THR271 4.2 14.5 1.0
O A:HOH785 4.3 13.2 1.0
CD2 A:HIS233 4.4 11.2 1.0
O36 A:0X8603 4.4 18.3 1.0
CB A:ASP201 4.4 9.3 1.0
CD2 A:HIS204 4.5 9.1 1.0
NE2 A:HIS200 4.6 11.1 1.0
OD2 A:ASP318 4.6 18.7 1.0
CA A:ASP201 4.8 9.1 1.0
O A:THR271 4.8 17.0 1.0
NE2 A:HIS204 4.9 14.1 1.0
CD2 A:HIS160 4.9 15.0 1.0
CB A:THR271 4.9 18.1 1.0
CD A:GLU230 5.0 16.9 1.0

Magnesium binding site 2 out of 2 in 7f2k

Go back to Magnesium Binding Sites List in 7f2k
Magnesium binding site 2 out of 2 in the Crystal Structure of PDE4D Catalytic Domain Complexed with Compound 17A


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 PDE4D Catalytic Domain Complexed with Compound 17A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:14.2
occ:1.00
O B:HOH701 2.0 14.3 1.0
OD1 B:ASP201 2.0 13.4 1.0
O B:HOH711 2.1 13.0 1.0
O B:HOH742 2.1 15.8 1.0
O B:HOH739 2.2 14.9 1.0
O B:HOH749 2.2 14.5 1.0
CG B:ASP201 3.1 15.1 1.0
O35 B:0X8603 3.4 31.9 1.0
OD2 B:ASP201 3.4 10.8 1.0
ZN B:ZN601 3.6 21.9 1.0
O B:HIS200 3.9 14.2 1.0
CD2 B:HIS200 4.1 16.2 1.0
OG1 B:THR271 4.1 13.6 1.0
NE2 B:HIS233 4.2 14.2 1.0
OE2 B:GLU230 4.2 16.8 1.0
C34 B:0X8603 4.2 22.7 1.0
CD2 B:HIS233 4.3 13.6 1.0
CB B:ASP201 4.4 13.5 1.0
O B:HOH751 4.5 20.0 1.0
O36 B:0X8603 4.5 16.2 1.0
O B:HOH768 4.6 28.2 1.0
NE2 B:HIS200 4.6 14.7 1.0
CD2 B:HIS204 4.6 13.8 1.0
OD2 B:ASP318 4.7 22.8 1.0
CD2 B:HIS160 4.8 14.0 1.0
CA B:ASP201 4.8 14.6 1.0
CB B:THR271 4.8 17.6 1.0
C B:HIS200 4.8 16.1 1.0
O B:THR271 4.9 21.0 1.0
CG B:GLU230 4.9 16.1 1.0
CD B:GLU230 5.0 18.0 1.0
NE2 B:HIS204 5.0 15.9 1.0
OD1 B:ASP318 5.0 16.4 1.0

Reference:

Y.Y.Huang, J.Deng, Y.J.Tian, J.Liang, X.Xie, Y.Huang, J.Zhu, Z.Zhu, Q.Zhou, X.He, H.B.Luo. Mangostanin Derivatives As Novel and Orally Active Phosphodiesterase 4 Inhibitors For the Treatment of Idiopathic Pulmonary Fibrosis with Improved Safety. J.Med.Chem. V. 64 13736 2021.
ISSN: ISSN 0022-2623
PubMed: 34520193
DOI: 10.1021/ACS.JMEDCHEM.1C01085
Page generated: Fri Nov 5 15:11:19 2021

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