Magnesium in PDB 4k5n: Phosphonic Arginine Mimetics As Inhibitors of the M1 Aminopeptidases From Plasmodium Falciparum

The structure of Phosphonic Arginine Mimetics As Inhibitors of the M1 Aminopeptidases From Plasmodium Falciparum, PDB code: 4k5n was solved by S.Mcgowan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	80.45 / 1.91
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.762, 109.451, 118.638, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 21

The structure of Phosphonic Arginine Mimetics As Inhibitors of the M1 Aminopeptidases From Plasmodium Falciparum also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Magnesium atom in the Phosphonic Arginine Mimetics As Inhibitors of the M1 Aminopeptidases From Plasmodium Falciparum (pdb code 4k5n). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Phosphonic Arginine Mimetics As Inhibitors of the M1 Aminopeptidases From Plasmodium Falciparum, PDB code: 4k5n:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Phosphonic Arginine Mimetics As Inhibitors of the M1 Aminopeptidases From Plasmodium Falciparum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Phosphonic Arginine Mimetics As Inhibitors of the M1 Aminopeptidases From Plasmodium Falciparum within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1102 b:31.4 occ:1.00 O A:HOH2185 2.0 25.4 1.0 O A:GLY250 2.1 19.0 1.0 O A:HOH2184 2.1 22.3 1.0 O A:HOH2128 2.2 25.0 1.0 O A:HOH2129 2.3 25.7 1.0 O A:HOH2130 2.3 16.1 1.0 C A:GLY250 3.2 18.2 1.0 CA A:GLY250 3.8 18.3 1.0 O A:HOH1350 4.2 13.1 1.0 N A:LEU251 4.3 18.2 1.0 O A:HOH1888 4.4 27.4 1.0 ND1 A:HIS297 4.4 21.1 1.0 CA A:LEU251 4.6 18.6 1.0 O A:ILE295 4.7 17.6 1.0 O A:HOH2131 4.7 11.6 1.0 C A:LEU251 4.9 19.5 1.0 CA A:ILE296 4.9 16.7 1.0

Magnesium binding site 2 out of 3 in the Phosphonic Arginine Mimetics As Inhibitors of the M1 Aminopeptidases From Plasmodium Falciparum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Phosphonic Arginine Mimetics As Inhibitors of the M1 Aminopeptidases From Plasmodium Falciparum within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1103 b:28.0 occ:1.00 O A:HOH2177 2.0 17.0 1.0 O A:HOH2180 2.0 24.9 1.0 O A:HOH2181 2.1 25.7 1.0 O A:HOH2178 2.1 17.6 1.0 O A:HOH2179 2.3 18.3 1.0 OE2 A:GLU957 3.6 19.7 1.0 ND2 A:ASN992 4.1 17.2 1.0 O A:HOH1800 4.1 23.4 1.0 O A:HOH1583 4.1 23.7 1.0 O A:HOH2132 4.2 16.8 1.0 OD2 A:ASP995 4.3 14.1 1.0 CD A:GLU957 4.4 21.8 1.0 O A:HOH1311 4.5 16.1 1.0 O A:HOH1209 4.6 11.7 1.0 CG A:GLU957 4.7 22.4 1.0 CE A:LYS311 4.8 19.2 1.0

Magnesium binding site 3 out of 3 in the Phosphonic Arginine Mimetics As Inhibitors of the M1 Aminopeptidases From Plasmodium Falciparum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Phosphonic Arginine Mimetics As Inhibitors of the M1 Aminopeptidases From Plasmodium Falciparum within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1107 b:41.4 occ:1.00 O A:HOH2222 2.2 30.4 1.0 O A:HOH2183 2.3 30.6 1.0 O A:HOH2182 2.3 28.0 1.0 O A:HOH1689 2.4 24.6 1.0 O A:HOH1508 3.9 20.9 1.0 OD1 A:ASP438 4.1 23.8 1.0 CB A:ALA434 4.3 17.5 1.0 OD2 A:ASP438 4.3 25.0 1.0 OE1 A:GLU437 4.4 21.3 1.0 OH A:TYR399 4.4 21.2 1.0 CG A:ASP438 4.7 25.0 1.0 O A:HOH1996 4.7 36.3 1.0 CA A:ALA434 4.9 17.2 1.0

K.Kannan Sivaraman, A.Paiardini, M.Sienczyk, C.Ruggeri, C.A.Oellig, J.P.Dalton, P.J.Scammells, M.Drag, S.Mcgowan. Synthesis and Structure-Activity Relationships of Phosphonic Arginine Mimetics As Inhibitors of the M1 and M17 Aminopeptidases From Plasmodium Falciparum. J.Med.Chem. V. 56 5213 2013.
ISSN: ISSN 0022-2623
PubMed: 23713488
DOI: 10.1021/JM4005972