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Magnesium in PDB 5k32: PDE4D Crystal Structure in Complex with Small Molecule Inhibitor

Enzymatic activity of PDE4D Crystal Structure in Complex with Small Molecule Inhibitor

All present enzymatic activity of PDE4D Crystal Structure in Complex with Small Molecule Inhibitor:
3.1.4.53;

Protein crystallography data

The structure of PDE4D Crystal Structure in Complex with Small Molecule Inhibitor, PDB code: 5k32 was solved by V.Segarra, B.Hernandez, R.Roberts, J.Gracia, M.Soler, I.Bonin, J.Aymami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.99
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.967, 79.739, 163.845, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 28.1

Other elements in 5k32:

The structure of PDE4D Crystal Structure in Complex with Small Molecule Inhibitor also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the PDE4D Crystal Structure in Complex with Small Molecule Inhibitor (pdb code 5k32). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the PDE4D Crystal Structure in Complex with Small Molecule Inhibitor, PDB code: 5k32:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5k32

Go back to Magnesium Binding Sites List in 5k32
Magnesium binding site 1 out of 2 in the PDE4D Crystal Structure in Complex with Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of PDE4D Crystal Structure in Complex with Small Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:18.4
occ:1.00
O A:HOH1214 1.9 21.6 1.0
OD1 A:ASP201 2.1 20.3 1.0
O A:HOH1218 2.1 17.6 1.0
O A:HOH1141 2.1 14.7 1.0
O A:HOH1169 2.3 18.9 1.0
O A:HOH1200 2.4 15.7 1.0
CG A:ASP201 3.1 20.0 1.0
OD2 A:ASP201 3.3 15.0 1.0
ZN A:ZN1001 3.6 26.9 1.0
O A:HOH1154 4.0 22.1 1.0
O A:HIS200 4.0 18.5 1.0
NE2 A:HIS233 4.0 18.9 1.0
OE2 A:GLU230 4.1 22.9 1.0
OG1 A:THR271 4.2 23.8 1.0
CD2 A:HIS200 4.2 17.2 1.0
O A:HOH1126 4.3 18.8 1.0
CD2 A:HIS233 4.3 14.7 1.0
CB A:ASP201 4.4 17.1 1.0
O A:HOH1143 4.5 31.3 1.0
CD2 A:HIS204 4.5 19.4 1.0
C26 A:6Q21003 4.6 27.3 1.0
NE2 A:HIS200 4.6 14.9 1.0
OD2 A:ASP318 4.6 19.9 1.0
O A:HOH1186 4.7 24.1 1.0
CD2 A:HIS160 4.7 16.9 1.0
NE2 A:HIS160 4.7 18.6 1.0
CA A:ASP201 4.7 18.4 1.0
CB A:THR271 4.8 24.5 1.0
NE2 A:HIS204 4.8 15.2 1.0
C A:HIS200 4.8 18.1 1.0
O25 A:6Q21003 4.8 26.4 1.0
O A:THR271 4.9 25.1 1.0
CG A:GLU230 5.0 20.4 1.0

Magnesium binding site 2 out of 2 in 5k32

Go back to Magnesium Binding Sites List in 5k32
Magnesium binding site 2 out of 2 in the PDE4D Crystal Structure in Complex with Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of PDE4D Crystal Structure in Complex with Small Molecule Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1002

b:17.0
occ:1.00
OD1 B:ASP201 2.0 16.1 1.0
O B:HOH1150 2.0 17.6 1.0
O B:HOH1162 2.1 21.2 1.0
O B:HOH1238 2.1 17.5 1.0
O B:HOH1178 2.2 17.0 1.0
O B:HOH1147 2.3 22.6 1.0
CG B:ASP201 3.0 17.0 1.0
OD2 B:ASP201 3.3 15.3 1.0
ZN B:ZN1001 3.6 24.7 1.0
OE2 B:GLU230 4.0 27.2 1.0
O B:HOH1186 4.0 14.2 1.0
CD2 B:HIS200 4.1 9.8 1.0
OG1 B:THR271 4.2 25.9 1.0
O B:HIS200 4.3 16.3 1.0
NE2 B:HIS233 4.3 16.4 1.0
O B:HOH1124 4.4 16.1 1.0
CB B:ASP201 4.4 17.6 1.0
OD2 B:ASP318 4.5 21.1 1.0
CD2 B:HIS233 4.5 17.2 1.0
O25 B:6Q21003 4.5 23.9 1.0
CD2 B:HIS204 4.5 14.7 1.0
NE2 B:HIS200 4.5 19.4 1.0
C26 B:6Q21003 4.6 21.4 1.0
O B:THR271 4.7 25.2 1.0
NE2 B:HIS160 4.7 22.2 1.0
O B:HOH1180 4.7 39.1 1.0
CD2 B:HIS160 4.7 23.6 1.0
NE2 B:HIS204 4.7 15.1 1.0
CB B:THR271 4.8 23.9 1.0
CA B:ASP201 4.8 17.9 1.0
CD B:GLU230 4.9 20.6 1.0
CG B:GLU230 4.9 23.1 1.0
OD1 B:ASP318 5.0 15.6 1.0
C B:HIS200 5.0 16.9 1.0

Reference:

R.S.Roberts, S.Sevilla, M.Ferrer, J.Taltavull, B.Hernandez, V.Segarra, J.Gracia, M.D.Lehner, A.Gavalda, M.Andres, J.Cabedo, D.Vilella, P.Eichhorn, E.Calama, C.Carcasona, M.Miralpeix. 4-Amino-7,8-Dihydro-1,6-Naphthyridin-5(6 H)-Ones As Inhaled Phosphodiesterase Type 4 (PDE4) Inhibitors: Structural Biology and Structure-Activity Relationships. J. Med. Chem. V. 61 2472 2018.
ISSN: ISSN 1520-4804
PubMed: 29502405
DOI: 10.1021/ACS.JMEDCHEM.7B01751
Page generated: Mon Dec 14 20:36:48 2020

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