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

The structure of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6I) and Catalytic Zinc Ion, PDB code: 6eaa 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)	46.40 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.399, 108.850, 117.720, 90.00, 90.00, 90.00
R / Rfree (%)	15.1 / 18.3

The structure of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6I) 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 (6I) and Catalytic Zinc Ion (pdb code 6eaa). 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 (6I) and Catalytic Zinc Ion, PDB code: 6eaa:
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 (6I) 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 (6I) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1107 b:34.0 occ:1.00 O A:HOH2362 2.0 33.2 1.0 O A:HOH1692 2.0 22.5 1.0 O A:HOH2158 2.1 34.4 1.0 O A:HOH2497 2.3 35.2 1.0 O A:HOH1659 2.3 33.0 1.0 O A:HOH1508 2.4 34.3 1.0 O A:HOH1595 3.9 23.2 1.0 OD1 A:ASP438 3.9 25.6 1.0 O A:HOH2387 4.2 55.7 1.0 OE1 A:GLU437 4.3 21.1 1.0 OD2 A:ASP438 4.3 26.0 1.0 OH A:TYR399 4.4 17.2 1.0 CB A:ALA434 4.5 16.2 1.0 CD A:LYS402 4.5 27.5 1.0 CG A:ASP438 4.6 23.7 1.0 CG A:LYS402 4.9 27.3 1.0 O A:HOH2117 4.9 40.1 1.0 CE A:LYS402 5.0 29.2 1.0 CA A:ALA434 5.0 15.7 1.0

Magnesium binding site 2 out of 3 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6I) 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 (6I) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1109 b:29.0 occ:1.00 O A:HOH1932 1.9 24.8 1.0 O A:GLY250 2.0 18.3 1.0 O A:HOH1906 2.2 26.8 1.0 O A:HOH1433 2.2 19.6 1.0 O A:HOH2036 2.4 22.9 1.0 C A:GLY250 3.1 17.5 1.0 CA A:GLY250 3.8 17.8 1.0 O A:HOH1514 4.1 15.9 1.0 O A:HOH2152 4.2 32.0 1.0 N A:LEU251 4.2 18.1 1.0 O A:HOH1317 4.2 29.0 1.0 O A:HOH2314 4.3 32.4 1.0 ND1 A:HIS297 4.4 18.3 1.0 CA A:LEU251 4.5 15.6 1.0 O A:ILE295 4.6 17.1 1.0 O A:HOH2127 4.8 20.7 1.0 C A:LEU251 4.8 18.0 1.0 N A:LYS252 4.8 18.9 1.0 CA A:ILE296 5.0 14.9 1.0 CE1 A:HIS297 5.0 17.7 1.0

Magnesium binding site 3 out of 3 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6I) 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 (6I) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1110 b:37.5 occ:1.00 O A:HOH1301 2.0 23.0 1.0 O A:HOH1776 2.2 24.2 1.0 O A:HOH2226 2.2 29.7 1.0 O A:HOH2444 2.2 25.8 1.0 O A:HOH1498 2.2 27.5 1.0 O A:HOH2374 2.4 39.1 1.0 OE2 A:GLU957 3.7 19.3 1.0 O A:HOH1800 4.0 29.1 1.0 O A:HOH1416 4.0 28.1 1.0 ND2 A:ASN992 4.1 21.5 1.0 O A:HOH2179 4.1 38.3 1.0 O A:HOH2504 4.2 42.6 1.0 OD2 A:ASP995 4.2 16.2 1.0 O A:HOH2150 4.3 41.5 1.0 O A:HOH2406 4.3 25.4 1.0 CD A:GLU957 4.4 18.6 1.0 O A:HOH1579 4.6 20.4 1.0 O A:HOH1374 4.6 23.3 1.0 CG A:GLU957 4.7 22.1 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