Magnesium in PDB 8ex3: Plasmodium Falciparum M1 in Complex with Inhibitor 9AA

The structure of Plasmodium Falciparum M1 in Complex with Inhibitor 9AA, PDB code: 8ex3 was solved by P.P.S.Calic, S.Mcgowan, C.T.Webb, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.05 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.44, 108.95, 118.166, 90, 90, 90
R / Rfree (%)	16.8 / 19.6

The structure of Plasmodium Falciparum M1 in Complex with Inhibitor 9AA also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Plasmodium Falciparum M1 in Complex with Inhibitor 9AA (pdb code 8ex3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Plasmodium Falciparum M1 in Complex with Inhibitor 9AA, PDB code: 8ex3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Plasmodium Falciparum M1 in Complex with Inhibitor 9AA


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Plasmodium Falciparum M1 in Complex with Inhibitor 9AA within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1103 b:21.4 occ:0.49 O A:HOH2302 2.0 32.4 1.0 O A:HOH1301 2.1 24.2 1.0 O A:HOH1751 2.1 25.0 1.0 O A:HOH1455 2.2 28.6 1.0 O A:HOH2332 2.2 28.7 1.0 O A:HOH2177 2.3 30.2 1.0 OE1 A:GLU957 3.7 19.1 1.0 O A:HOH1522 3.9 30.1 1.0 O A:HOH1786 4.1 23.4 0.7 ND2 A:ASN992 4.2 20.7 1.0 O A:HOH2109 4.2 35.3 1.0 OD2 A:ASP995 4.2 17.4 1.0 O A:HOH2337 4.3 23.4 1.0 O A:HOH2044 4.3 33.4 1.0 O A:HOH2407 4.4 45.9 1.0 CD A:GLU957 4.5 21.0 1.0 O A:HOH1685 4.5 19.8 1.0 O A:HOH1430 4.7 25.1 1.0 CG A:GLU957 4.7 22.8 1.0 CD A:LYS311 4.8 23.9 0.4 NZ A:LYS311 5.0 21.3 0.6 CE A:LYS311 5.0 23.3 0.6

Magnesium binding site 2 out of 5 in the Plasmodium Falciparum M1 in Complex with Inhibitor 9AA


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Plasmodium Falciparum M1 in Complex with Inhibitor 9AA within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1104 b:17.7 occ:0.48 O A:HOH2253 2.0 31.6 1.0 OE2 A:GLU526 2.0 17.2 0.8 O A:HOH1330 2.1 27.2 1.0 O A:HOH2032 2.1 32.8 1.0 O A:HOH1373 2.3 29.2 1.0 O A:HOH1718 2.3 29.2 1.0 CD A:GLU526 3.1 17.0 0.6 OE1 A:GLU526 3.4 15.0 1.0 O A:HOH1870 3.8 31.5 1.0 OG1 A:THR492 4.1 20.5 1.0 O A:HOH2257 4.1 30.5 1.0 O A:HOH1362 4.2 30.8 1.0 O A:HOH1489 4.2 31.6 1.0 CB A:THR492 4.2 20.3 1.0 O A:HOH1291 4.2 24.6 1.0 CG A:GLU526 4.4 17.7 0.9 O A:HOH2310 4.4 36.9 1.0 O A:HOH1980 4.6 35.0 1.0 O A:HOH1938 4.6 32.7 1.0 OD1 A:ASN527 4.7 22.0 1.0 CG2 A:THR492 4.9 18.5 1.0 O A:HOH2011 4.9 30.6 1.0

Magnesium binding site 3 out of 5 in the Plasmodium Falciparum M1 in Complex with Inhibitor 9AA


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Plasmodium Falciparum M1 in Complex with Inhibitor 9AA within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1105 b:21.6 occ:0.56 O A:HOH1935 2.0 28.6 1.0 O A:GLY250 2.0 18.1 1.0 O A:HOH1687 2.2 29.4 1.0 O A:HOH1453 2.2 22.3 1.0 O A:HOH1957 2.3 32.4 1.0 O A:HOH2034 2.4 23.6 1.0 C A:GLY250 3.1 19.6 1.0 CA A:GLY250 3.7 21.1 1.0 O A:HOH1601 4.1 19.5 1.0 N A:LEU251 4.2 20.8 1.0 O A:HOH2113 4.2 34.2 1.0 ND1 A:HIS297 4.3 19.9 1.0 O A:HOH1265 4.3 30.7 1.0 CA A:LEU251 4.5 19.1 1.0 O A:ILE295 4.6 20.5 1.0 O A:HOH2078 4.7 20.7 1.0 C A:LEU251 4.8 22.0 1.0 N A:LYS252 4.9 19.5 1.0 CA A:ILE296 4.9 16.9 1.0 CE1 A:HIS297 5.0 21.7 1.0

Magnesium binding site 4 out of 5 in the Plasmodium Falciparum M1 in Complex with Inhibitor 9AA


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Plasmodium Falciparum M1 in Complex with Inhibitor 9AA within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1106 b:40.1 occ:1.00 O A:HOH2296 2.1 37.1 1.0 O A:HOH1637 2.2 23.8 1.0 O A:HOH2404 2.2 40.3 1.0 O A:HOH2136 2.3 38.0 1.0 O A:HOH1931 2.3 35.8 1.0 O A:HOH1401 2.5 35.2 1.0 O A:HOH1630 3.9 23.9 1.0 OD1 A:ASP438 4.0 27.2 1.0 OD2 A:ASP438 4.3 22.7 1.0 CB A:ALA434 4.4 23.4 1.0 OE1 A:GLU437 4.5 23.4 1.0 O A:HOH2341 4.5 48.6 1.0 OH A:TYR399 4.6 24.1 1.0 CG A:ASP438 4.6 23.9 1.0 O A:HOH2108 4.7 36.0 1.0 CD A:LYS402 4.9 31.0 1.0

Magnesium binding site 5 out of 5 in the Plasmodium Falciparum M1 in Complex with Inhibitor 9AA


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Plasmodium Falciparum M1 in Complex with Inhibitor 9AA within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1107 b:38.8 occ:1.00 OD1 A:ASN1083 2.1 27.5 1.0 O A:HOH1912 2.1 37.6 1.0 O A:HOH2140 2.2 40.6 1.0 O A:HOH1878 2.4 29.7 1.0 O A:HOH1317 2.5 31.0 1.0 O A:HOH2342 2.6 48.9 1.0 CG A:ASN1083 3.2 29.1 1.0 CA A:ASN1083 3.7 29.9 1.0 CB A:ASN1083 3.8 29.6 1.0 O A:ARG1080 4.3 21.0 1.0 ND2 A:ASN1083 4.3 32.7 1.0 CG A:GLU679 4.3 33.8 1.0 O A:HOH2046 4.4 29.1 1.0 C A:ASN1083 4.6 37.7 1.0 N A:ASN1083 4.6 21.1 1.0 CD A:GLU679 4.6 37.4 0.6 O A:PRO558 4.6 19.1 1.0 O A:HOH2199 4.7 39.5 1.0 CB A:PRO558 4.7 13.9 1.0 O A:HOH2008 4.7 46.0 1.0 OE2 A:GLU679 4.8 39.1 0.8

P.P.S.Calic, N.B.Vinh, C.T.Webb, T.R.Malcolm, A.Ngo, K.Lowes, N.Drinkwater, S.Mcgowan, P.J.Scammells. Structure-Based Development of Potent Plasmodium Falciparum M1 and M17 Aminopeptidase Selective and Dual Inhibitors Via S1'-Region Optimisation Eur.J.Med.Chem. 2023.
ISSN: ISSN 0223-5234