Magnesium in PDB 6ee6: X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6O) and Catalytic Zinc Ion

The structure of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6O) and Catalytic Zinc Ion, PDB code: 6ee6 was solved by N.Drinkwater, S.Mcgowan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.78 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.550, 108.610, 117.790, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 18.8

The structure of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6O) and Catalytic Zinc Ion also contains other interesting chemical elements:

Fluorine	(F)	3 atoms
Zinc	(Zn)	1 atom

The binding sites of Magnesium atom in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6O) and Catalytic Zinc Ion (pdb code 6ee6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6O) and Catalytic Zinc Ion, PDB code: 6ee6:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6O) and Catalytic Zinc Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6O) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1108 b:20.6 occ:0.80 O A:HOH2037 2.0 25.8 1.0 O A:GLY250 2.0 17.1 1.0 O A:HOH1831 2.1 23.3 1.0 O A:HOH1608 2.2 20.2 1.0 O A:HOH2034 2.2 26.3 1.0 O A:HOH1956 2.3 21.0 1.0 C A:GLY250 3.1 14.9 1.0 CA A:GLY250 3.7 15.7 1.0 O A:HOH2396 3.9 27.9 1.0 O A:HOH1714 4.1 14.2 1.0 N A:LEU251 4.2 16.8 1.0 O A:HOH2406 4.2 30.5 1.0 O A:HOH2203 4.2 30.2 1.0 O A:HOH1312 4.3 24.8 1.0 ND1 A:HIS297 4.3 17.7 1.0 CA A:LEU251 4.5 14.9 1.0 O A:HOH2216 4.6 25.5 1.0 O A:ILE295 4.6 17.4 1.0 O A:HOH2183 4.7 18.5 1.0 C A:LEU251 4.8 17.4 1.0 N A:LYS252 4.9 15.6 1.0 CA A:ILE296 4.9 15.0 1.0 CE1 A:HIS297 5.0 16.9 1.0

Magnesium binding site 2 out of 3 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6O) and Catalytic Zinc Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6O) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1109 b:22.5 occ:0.80 O A:HOH1444 2.0 19.4 1.0 O A:HOH2504 2.1 29.0 1.0 O A:HOH1553 2.1 23.1 1.0 O A:HOH1738 2.1 19.1 1.0 O A:HOH2455 2.2 30.8 1.0 O A:HOH2311 2.2 29.8 1.0 OE2 A:GLU957 3.7 16.9 1.0 O A:HOH2569 4.0 47.2 1.0 O A:HOH1750 4.0 26.6 1.0 O A:HOH1727 4.1 26.0 1.0 O A:HOH2234 4.1 34.4 1.0 ND2 A:ASN992 4.1 19.4 1.0 O A:HOH2493 4.2 21.9 1.0 O A:HOH2197 4.2 35.1 1.0 OD2 A:ASP995 4.3 14.2 1.0 CD A:GLU957 4.5 17.2 1.0 O A:HOH1852 4.5 18.8 1.0 O A:HOH1432 4.6 22.6 1.0 CG A:GLU957 4.7 23.8 1.0 O A:HOH2372 4.9 34.1 1.0

Magnesium binding site 3 out of 3 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6O) and Catalytic Zinc Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6O) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1110 b:30.2 occ:1.00 O A:HOH2460 2.0 30.0 1.0 O A:HOH1723 2.1 21.2 1.0 O A:HOH1930 2.2 31.1 1.0 O A:HOH2249 2.2 39.4 1.0 O A:HOH2567 2.3 36.2 1.0 O A:HOH1422 2.5 34.3 1.0 O A:HOH1747 3.8 20.0 1.0 OD1 A:ASP438 4.0 23.5 1.0 OD2 A:ASP438 4.4 22.2 1.0 OE1 A:GLU437 4.4 19.9 1.0 O A:HOH2215 4.5 42.1 1.0 CB A:ALA434 4.5 15.8 1.0 OH A:TYR399 4.5 19.7 1.0 CG A:ASP438 4.6 21.2 1.0 O A:HOH2410 4.7 55.6 1.0 CD A:LYS402 4.7 20.8 1.0 CG A:LYS402 5.0 23.5 1.0

N.B.Vinh, N.Drinkwater, T.R.Malcolm, M.Kassiou, L.Lucantoni, P.M.Grin, G.S.Butler, S.Duffy, C.M.Overall, V.M.Avery, P.J.Scammells, S.Mcgowan. Hydroxamic Acid Inhibitors Provide Cross-Species Inhibition of Plasmodium M1 and M17 Aminopeptidases. J. Med. Chem. V. 62 622 2019.
ISSN: ISSN 1520-4804
PubMed: 30537832
DOI: 10.1021/ACS.JMEDCHEM.8B01310