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

The structure of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6P) and Catalytic Zinc Ion, PDB code: 6eed 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)	35.80 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.149, 109.230, 117.920, 90.00, 90.00, 90.00
R / Rfree (%)	15.4 / 18

The structure of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6P) 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 (6P) and Catalytic Zinc Ion (pdb code 6eed). 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 (6P) and Catalytic Zinc Ion, PDB code: 6eed:
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 (6P) 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 (6P) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1103 b:20.2 occ:0.80 O A:HOH2037 1.9 23.0 1.0 O A:GLY250 2.0 17.1 1.0 O A:HOH1818 2.1 20.1 1.0 O A:HOH1870 2.1 25.8 1.0 O A:HOH1954 2.1 28.4 1.0 O A:HOH1964 2.3 21.3 1.0 C A:GLY250 3.1 15.7 1.0 CA A:GLY250 3.7 16.1 1.0 O A:HOH1747 4.1 17.3 1.0 O A:HOH2174 4.2 27.6 1.0 N A:LEU251 4.2 16.8 1.0 ND1 A:HIS297 4.3 17.7 1.0 O A:HOH1370 4.3 29.9 1.0 O A:HOH2366 4.3 25.7 1.0 O A:HOH2258 4.4 25.4 1.0 CA A:LEU251 4.5 15.7 1.0 O A:ILE295 4.7 16.4 1.0 C A:LEU251 4.8 17.0 1.0 O A:HOH2180 4.8 18.3 1.0 N A:LYS252 4.9 16.0 1.0 CA A:ILE296 5.0 14.7 1.0 CE1 A:HIS297 5.0 17.2 1.0

Magnesium binding site 2 out of 4 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6P) 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 (6P) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1104 b:27.4 occ:1.00 O A:HOH1787 2.1 21.6 1.0 O A:HOH1377 2.1 21.1 1.0 O A:HOH2504 2.1 27.7 1.0 O A:HOH1396 2.1 22.4 1.0 O A:HOH2532 2.2 24.3 1.0 O A:HOH2304 2.2 27.1 1.0 OE2 A:GLU957 3.7 18.4 1.0 O A:HOH1898 4.1 25.8 1.0 O A:HOH2528 4.1 25.8 1.0 O A:HOH1719 4.1 23.7 1.0 O A:HOH2627 4.2 47.1 1.0 ND2 A:ASN992 4.2 16.7 1.0 O A:HOH2262 4.3 34.3 1.0 OD2 A:ASP995 4.3 14.2 1.0 O A:HOH2188 4.3 36.7 1.0 CD A:GLU957 4.5 16.7 1.0 O A:HOH1673 4.6 18.6 1.0 O A:HOH1530 4.6 20.9 1.0 CG A:GLU957 4.7 20.5 1.0

Magnesium binding site 3 out of 4 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6P) 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 (6P) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1105 b:31.1 occ:1.00 O A:HOH1689 2.0 21.2 1.0 O A:HOH2447 2.0 30.7 1.0 O A:HOH2285 2.1 32.8 1.0 O A:HOH2620 2.3 35.6 1.0 O A:HOH1424 2.3 33.7 1.0 O A:HOH1937 2.3 31.0 1.0 OD1 A:ASP438 3.9 24.8 1.0 O A:HOH1634 3.9 23.1 1.0 O A:HOH2596 4.1 44.9 1.0 OD2 A:ASP438 4.2 24.4 1.0 O A:HOH2491 4.3 47.8 1.0 O A:HOH2527 4.3 50.5 1.0 OE1 A:GLU437 4.3 22.0 1.0 CB A:ALA434 4.5 16.4 1.0 CG A:ASP438 4.5 23.5 1.0 OH A:TYR399 4.5 19.0 1.0 CD A:LYS402 4.6 25.2 1.0 O A:HOH2186 4.8 34.6 1.0 CG A:LYS402 4.9 24.8 1.0 CE A:LYS402 4.9 26.1 1.0

Magnesium binding site 4 out of 4 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6P) 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 (6P) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1106 b:29.0 occ:0.80 OD1 A:ASN1083 2.0 23.8 1.0 O A:HOH1653 2.0 34.1 1.0 O A:HOH2156 2.0 33.6 1.0 O A:HOH1803 2.2 28.6 1.0 O A:HOH2479 2.3 45.4 1.0 O A:HOH1455 2.4 28.4 1.0 CG A:ASN1083 3.1 22.3 1.0 CA A:ASN1083 3.8 22.3 1.0 CB A:ASN1083 3.9 23.0 1.0 O A:HOH2126 4.1 29.8 1.0 CG A:GLU679 4.1 34.4 1.0 ND2 A:ASN1083 4.1 24.1 1.0 O A:ARG1080 4.3 16.5 1.0 CD A:GLU679 4.5 40.1 1.0 O A:PRO558 4.5 14.3 1.0 CB A:PRO558 4.6 12.2 1.0 O A:HOH2362 4.6 50.5 1.0 C A:ASN1083 4.7 26.2 1.0 N A:ASN1083 4.7 18.8 1.0 OE2 A:GLU679 4.8 41.5 1.0 CB A:GLU679 4.9 30.5 1.0 OE1 A:GLU679 5.0 41.9 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