Magnesium in PDB 6ee3: X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6K) and Catalytic Zinc Ion

The structure of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6K) and Catalytic Zinc Ion, PDB code: 6ee3 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 / 1.82
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.960, 108.601, 118.160, 90.00, 90.00, 90.00
R / Rfree (%)	15.1 / 19.6

The structure of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6K) 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 (6K) and Catalytic Zinc Ion (pdb code 6ee3). 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 (6K) and Catalytic Zinc Ion, PDB code: 6ee3:
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 (6K) 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 (6K) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1106 b:16.3 occ:1.00 O A:GLY250 2.0 9.8 1.0 O A:HOH1679 2.1 12.6 1.0 O A:HOH1457 2.1 10.1 1.0 O A:HOH1777 2.1 17.4 1.0 O A:HOH1944 2.2 15.1 1.0 O A:HOH1671 2.2 10.6 1.0 C A:GLY250 3.2 9.5 1.0 CA A:GLY250 3.8 9.8 1.0 O A:HOH2294 3.9 16.1 1.0 O A:HOH1481 4.2 8.7 1.0 N A:LEU251 4.2 10.2 1.0 ND1 A:HIS297 4.2 14.0 1.0 O A:HOH2139 4.3 21.5 1.0 O A:HOH1366 4.3 22.9 1.0 O A:ILE295 4.4 10.1 1.0 O A:HOH2103 4.5 8.7 1.0 CA A:LEU251 4.5 10.3 1.0 CA A:ILE296 4.7 11.0 1.0 C A:LEU251 4.8 11.7 1.0 CE1 A:HIS297 4.8 15.6 1.0 N A:LYS252 4.9 10.4 1.0

Magnesium binding site 2 out of 4 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6K) 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 (6K) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1107 b:27.4 occ:1.00 O A:HOH2343 2.0 28.1 1.0 O A:HOH1576 2.1 12.9 1.0 O A:HOH2129 2.1 21.7 1.0 O A:HOH1922 2.2 19.9 1.0 O A:HOH2472 2.2 35.0 1.0 O A:HOH1296 2.4 22.1 1.0 OD1 A:ASP438 3.9 18.8 1.0 O A:HOH1434 4.0 15.1 1.0 O A:HOH2157 4.1 51.3 1.0 OD2 A:ASP438 4.1 19.3 1.0 OE1 A:GLU437 4.4 14.7 1.0 CG A:ASP438 4.4 18.1 1.0 OH A:TYR399 4.5 12.0 1.0 CB A:ALA434 4.5 9.8 1.0 CD A:LYS402 4.6 14.2 1.0 O A:HOH2410 4.7 41.0 1.0 CE A:LYS402 4.9 16.2 1.0 CG A:LYS402 4.9 15.3 1.0 CA A:ALA434 5.0 10.6 1.0 O A:HOH2119 5.0 30.4 1.0

Magnesium binding site 3 out of 4 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6K) 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 (6K) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1108 b:31.5 occ:1.00 O A:HOH2382 2.1 21.2 1.0 O A:HOH2341 2.2 23.6 1.0 O A:HOH1386 2.2 21.6 1.0 O A:HOH1793 2.2 14.7 1.0 O A:HOH2211 2.3 24.0 1.0 O A:HOH1279 2.3 17.1 1.0 OE2 A:GLU957 3.7 13.7 1.0 O A:HOH2188 4.0 32.8 1.0 O A:HOH1733 4.1 28.1 1.0 O A:HOH1232 4.1 21.3 1.0 ND2 A:ASN992 4.2 14.5 1.0 O A:HOH2378 4.2 22.5 1.0 OD2 A:ASP995 4.3 10.4 1.0 O A:HOH2131 4.3 24.1 1.0 CD A:GLU957 4.4 15.8 1.0 O A:HOH1749 4.5 14.1 1.0 CG A:GLU957 4.6 20.0 1.0 O A:HOH1280 4.7 19.5 1.0 CE A:LYS311 4.9 13.9 1.0 O A:HOH2305 4.9 32.6 1.0

Magnesium binding site 4 out of 4 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6K) 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 (6K) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1109 b:29.0 occ:1.00 OD1 A:ASN1083 2.0 14.3 1.0 O A:HOH1962 2.0 26.2 1.0 O A:HOH1332 2.0 25.8 1.0 O A:HOH2311 2.1 32.7 1.0 O A:HOH1740 2.3 13.8 1.0 O A:HOH1271 2.3 14.8 1.0 O A:HOH2323 3.1 25.1 1.0 CG A:ASN1083 3.2 14.1 1.0 O A:HOH2329 3.6 29.1 1.0 CA A:ASN1083 3.9 15.6 1.0 CB A:ASN1083 4.0 14.4 1.0 CG A:GLU679 4.0 39.1 1.0 ND2 A:ASN1083 4.2 16.6 1.0 O A:ARG1080 4.3 13.2 1.0 O A:PRO558 4.4 11.7 1.0 O A:HOH1940 4.5 17.2 1.0 CD A:GLU679 4.5 49.5 1.0 O A:HOH1204 4.6 45.6 1.0 CB A:PRO558 4.7 7.6 1.0 O A:HOH1876 4.8 40.3 1.0 N A:ASN1083 4.8 11.7 1.0 O A:HOH2454 4.8 37.0 1.0 C A:ASN1083 4.8 24.0 1.0 OE2 A:GLU679 4.8 50.9 1.0 CB A:GLU679 4.9 29.4 1.0 OE1 A:GLU679 5.0 55.7 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