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

The structure of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6J) and Catalytic Zinc Ion, PDB code: 6eab 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)	35.36 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.030, 109.101, 118.240, 90.00, 90.00, 90.00
R / Rfree (%)	14.8 / 19.1

The structure of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6J) 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 (6J) and Catalytic Zinc Ion (pdb code 6eab). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6J) and Catalytic Zinc Ion, PDB code: 6eab:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6J) 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 (6J) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1105 b:38.1 occ:1.00 O A:GLY250 2.0 15.5 1.0 O A:HOH1892 2.1 28.4 1.0 O A:HOH1724 2.1 28.3 1.0 O A:HOH1774 2.2 32.7 1.0 O A:HOH1472 2.3 16.4 1.0 O A:HOH1887 2.4 18.5 1.0 C A:GLY250 3.1 16.9 1.0 CA A:GLY250 3.7 18.1 1.0 O A:HOH2024 4.1 28.2 1.0 N A:LEU251 4.2 17.1 1.0 O A:HOH1398 4.2 14.1 1.0 ND1 A:HIS297 4.4 17.9 1.0 O A:HOH1221 4.4 31.8 1.0 O A:HOH2042 4.5 43.7 1.0 CA A:LEU251 4.6 16.4 1.0 O A:HOH1992 4.6 15.6 1.0 O A:ILE295 4.7 16.7 1.0 C A:LEU251 4.8 18.2 1.0 N A:LYS252 4.9 17.4 1.0 CA A:ILE296 5.0 15.8 1.0

Magnesium binding site 2 out of 4 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6J) 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 (6J) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1106 b:41.6 occ:1.00 O A:HOH1421 2.1 19.8 1.0 O A:HOH1399 2.1 26.7 1.0 O A:HOH1545 2.2 23.5 1.0 O A:HOH2096 2.2 27.9 1.0 O A:HOH2263 2.3 27.7 1.0 O A:HOH2224 2.4 32.9 1.0 OE2 A:GLU957 3.7 21.5 1.0 O A:HOH2060 4.0 39.1 1.0 O A:HOH1710 4.0 28.9 1.0 ND2 A:ASN992 4.1 17.3 1.0 O A:HOH1466 4.1 35.2 1.0 OD2 A:ASP995 4.2 15.5 1.0 O A:HOH2237 4.2 25.0 1.0 O A:HOH2014 4.3 35.2 1.0 CD A:GLU957 4.4 20.8 1.0 O A:HOH1683 4.4 16.8 1.0 CG A:GLU957 4.5 22.9 1.0 O A:HOH1522 4.6 21.6 1.0 CE A:LYS311 4.9 23.3 1.0 CB A:ASN992 5.0 15.8 1.0

Magnesium binding site 3 out of 4 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6J) 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 (6J) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1107 b:48.4 occ:1.00 O A:HOH2246 2.1 35.1 1.0 O A:HOH1331 2.2 27.6 1.0 O A:HOH1956 2.5 38.5 1.0 O A:HOH2312 2.5 44.4 1.0 O A:HOH1427 2.6 35.5 1.0 OD1 A:ASP438 3.8 26.9 1.0 O A:HOH1446 3.9 22.5 1.0 OE1 A:GLU437 4.3 22.4 1.0 OD2 A:ASP438 4.4 26.7 1.0 CD A:LYS402 4.5 28.8 1.0 OH A:TYR399 4.5 19.4 1.0 CG A:ASP438 4.5 24.9 1.0 CB A:ALA434 4.6 19.6 1.0 CG A:LYS402 4.8 29.0 1.0 O A:HOH2059 4.8 43.0 1.0 CB A:LYS402 4.9 24.6 1.0 CE A:LYS402 4.9 30.5 1.0

Magnesium binding site 4 out of 4 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6J) and Catalytic Zinc Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6J) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1108 b:15.1 occ:1.00 O A:HOH1919 2.0 18.9 1.0 O A:HOH1760 2.1 21.1 1.0 OE2 A:GLU526 2.1 13.9 1.0 O A:HOH2203 2.1 24.4 1.0 O A:HOH1784 2.1 15.7 1.0 O A:HOH1474 2.1 16.8 1.0 CD A:GLU526 3.1 18.1 1.0 OE1 A:GLU526 3.5 10.0 1.0 O A:HOH1477 3.9 23.9 1.0 O A:HOH2129 4.0 41.6 1.0 O A:HOH1860 4.0 26.5 1.0 O A:HOH1494 4.2 13.7 1.0 OG1 A:THR492 4.2 15.5 1.0 O A:HOH1269 4.2 28.8 1.0 OAS A:J2D1102 4.3 24.6 1.0 CB A:THR492 4.3 17.4 1.0 O A:HOH2230 4.4 33.6 1.0 CG A:GLU526 4.5 13.7 1.0 OD1 A:ASN527 4.5 14.8 1.0 CG2 A:THR492 5.0 16.0 1.0 CAN A:J2D1102 5.0 22.9 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