Magnesium in PDB 6ea1: X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6DA) and Catalytic Zinc Ion

The structure of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6DA) and Catalytic Zinc Ion, PDB code: 6ea1 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)	54.46 / 1.82
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.491, 108.920, 118.150, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 20.1

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

Fluorine	(F)	7 atoms
Zinc	(Zn)	1 atom

The binding sites of Magnesium atom in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6DA) and Catalytic Zinc Ion (pdb code 6ea1). 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 (6DA) and Catalytic Zinc Ion, PDB code: 6ea1:
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 (6DA) 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 (6DA) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1108 b:35.3 occ:1.00 O A:HOH1935 2.0 26.0 1.0 O A:GLY250 2.0 14.6 1.0 O A:HOH1807 2.1 21.4 1.0 O A:HOH1426 2.2 15.1 1.0 O A:HOH2011 2.5 21.0 1.0 C A:GLY250 3.1 16.4 1.0 CA A:GLY250 3.8 16.8 1.0 O A:HOH1523 4.2 12.8 1.0 N A:LEU251 4.2 17.9 1.0 O A:HOH2041 4.3 28.8 1.0 O A:HOH2132 4.3 32.6 1.0 ND1 A:HIS297 4.4 17.9 1.0 O A:HOH1290 4.4 29.0 1.0 O A:HOH2259 4.4 33.7 1.0 CA A:LEU251 4.5 13.6 1.0 O A:ILE295 4.6 15.0 1.0 C A:LEU251 4.7 14.8 1.0 O A:HOH2009 4.8 15.0 1.0 N A:LYS252 4.8 14.6 1.0 CA A:ILE296 4.9 13.7 1.0 CE1 A:HIS297 4.9 19.7 1.0

Magnesium binding site 2 out of 4 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6DA) 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 (6DA) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1109 b:37.6 occ:1.00 O A:HOH1319 2.0 17.6 1.0 O A:HOH2163 2.1 24.0 1.0 O A:HOH2281 2.2 29.0 1.0 O A:HOH2331 2.2 24.6 1.0 O A:HOH1389 2.3 19.1 1.0 O A:HOH1318 2.3 24.3 1.0 OE2 A:GLU957 3.7 17.4 1.0 O A:HOH1520 3.9 29.6 1.0 ND2 A:ASN992 4.0 14.2 1.0 O A:HOH2125 4.0 31.3 1.0 O A:HOH1406 4.1 24.5 1.0 O A:HOH2105 4.2 31.2 1.0 OD2 A:ASP995 4.3 11.5 1.0 CD A:GLU957 4.4 17.8 1.0 O A:HOH1511 4.4 21.8 1.0 O A:HOH2278 4.4 20.9 1.0 O A:HOH1639 4.6 12.6 1.0 CG A:GLU957 4.6 19.3 1.0 O A:HOH2215 4.9 32.7 1.0 CB A:ASN992 4.9 11.9 1.0 CE A:LYS311 5.0 15.5 1.0 CG A:ASN992 5.0 15.2 1.0

Magnesium binding site 3 out of 4 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6DA) 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 (6DA) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1110 b:40.7 occ:1.00 O A:HOH1552 2.0 39.6 1.0 OD1 A:ASN1083 2.1 21.8 1.0 O A:HOH2073 2.1 36.7 1.0 O A:HOH1776 2.2 26.3 1.0 O A:HOH2282 2.3 46.3 1.0 O A:HOH1287 2.5 18.0 1.0 CG A:ASN1083 3.2 22.4 1.0 CA A:ASN1083 3.9 21.3 1.0 CB A:ASN1083 3.9 21.8 1.0 CG A:GLU679 4.1 33.6 1.0 ND2 A:ASN1083 4.2 22.5 1.0 O A:ARG1080 4.3 16.1 1.0 O A:HOH2001 4.4 20.7 1.0 O A:HOH2212 4.4 34.5 1.0 O A:PRO558 4.5 12.7 1.0 CD A:GLU679 4.6 39.0 1.0 CB A:PRO558 4.7 9.1 1.0 N A:ASN1083 4.8 16.3 1.0 C A:ASN1083 4.8 27.5 1.0 OE2 A:GLU679 4.8 40.1 1.0

Magnesium binding site 4 out of 4 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6DA) 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 (6DA) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1111 b:30.0 occ:1.00 O A:HOH1436 2.2 17.8 1.0 O A:HOH1755 2.3 34.5 1.0 O A:HOH2272 2.3 33.4 1.0 O A:HOH2386 2.3 27.7 1.0 O A:HOH2067 2.3 30.4 1.0 O A:HOH1670 2.5 24.7 1.0 O A:HOH1458 4.0 15.9 1.0 OD1 A:ASP438 4.0 23.5 1.0 CB A:ALA434 4.3 13.0 1.0 OE1 A:GLU437 4.3 17.5 1.0 OD2 A:ASP438 4.3 22.4 1.0 OH A:TYR399 4.4 17.4 1.0 O A:HOH2334 4.6 53.5 1.0 CG A:ASP438 4.6 22.3 1.0 O A:HOH2049 4.7 36.1 1.0 CA A:ALA434 4.8 12.2 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