Magnesium in PDB 5y1r: Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-N-Hydroxy-4-Methyl-2-(3-( O-Tolyl)Ureido)Pentanamide

The structure of Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-N-Hydroxy-4-Methyl-2-(3-( O-Tolyl)Ureido)Pentanamide, PDB code: 5y1r was solved by A.K.Marapaka, Y.Zhang, A.Addlagatta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.68 / 1.69
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.510, 109.320, 112.695, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 19.5

The structure of Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-N-Hydroxy-4-Methyl-2-(3-( O-Tolyl)Ureido)Pentanamide also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-N-Hydroxy-4-Methyl-2-(3-( O-Tolyl)Ureido)Pentanamide (pdb code 5y1r). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-N-Hydroxy-4-Methyl-2-(3-( O-Tolyl)Ureido)Pentanamide, PDB code: 5y1r:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-N-Hydroxy-4-Methyl-2-(3-( O-Tolyl)Ureido)Pentanamide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-N-Hydroxy-4-Methyl-2-(3-( O-Tolyl)Ureido)Pentanamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1102 b:23.3 occ:1.00 O A:HOH1701 2.0 24.0 1.0 O A:HOH1720 2.1 21.9 1.0 O A:GLY250 2.1 15.3 1.0 O A:HOH1393 2.2 18.6 1.0 C A:GLY250 3.2 17.2 1.0 CA A:GLY250 3.9 17.3 1.0 O A:HOH1352 4.0 18.4 1.0 O A:HOH1770 4.3 34.3 1.0 N A:LEU251 4.3 14.1 1.0 CA A:LEU251 4.7 15.1 1.0 O A:ILE295 4.7 14.0 1.0 CD2 A:HIS297 4.8 18.1 1.0 CA A:ILE296 4.8 12.2 1.0 O A:HOH1581 4.8 20.3 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-N-Hydroxy-4-Methyl-2-(3-( O-Tolyl)Ureido)Pentanamide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-N-Hydroxy-4-Methyl-2-(3-( O-Tolyl)Ureido)Pentanamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1103 b:20.9 occ:1.00 O A:HOH1591 2.0 18.4 1.0 O A:HOH1845 2.0 24.3 1.0 O A:HOH1791 2.0 24.0 1.0 O A:HOH1840 2.0 20.8 1.0 O A:HOH1614 2.2 19.3 1.0 O A:HOH1355 2.2 21.7 1.0 OE2 A:GLU957 3.8 17.9 1.0 O A:HOH1619 4.0 28.2 1.0 ND2 A:ASN992 4.1 19.0 1.0 O A:HOH1317 4.1 20.9 1.0 O A:HOH1854 4.2 18.5 1.0 OD2 A:ASP995 4.3 20.5 1.0 O A:HOH1798 4.3 27.6 1.0 O A:HOH1573 4.5 16.9 1.0 O A:HOH1309 4.5 20.5 1.0 CD A:GLU957 4.6 20.8 1.0 O A:HOH1812 4.9 30.0 1.0 CE A:LYS311 5.0 17.6 1.0 CG A:GLU957 5.0 23.9 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-N-Hydroxy-4-Methyl-2-(3-( O-Tolyl)Ureido)Pentanamide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-N-Hydroxy-4-Methyl-2-(3-( O-Tolyl)Ureido)Pentanamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1104 b:25.2 occ:1.00 O A:HOH1637 1.9 21.1 0.4 OE1 A:GLU526 2.1 18.0 1.0 O A:HOH1649 2.1 26.7 1.0 O A:HOH1718 2.1 29.6 1.0 O A:HOH1240 2.2 23.3 1.0 O A:HOH1830 2.3 41.5 1.0 O A:HOH1781 2.4 36.6 1.0 O A:HOH1207 2.9 58.9 1.0 CD A:GLU526 3.1 17.7 1.0 OE2 A:GLU526 3.4 13.0 1.0 O A:HOH1810 4.0 32.5 1.0 O A:HOH1310 4.0 17.6 1.0 O A:HOH1544 4.0 26.4 1.0 OG1 A:THR492 4.1 16.8 1.0 O A:HOH1828 4.2 25.4 1.0 CB A:THR492 4.4 14.2 1.0 O A:HOH1857 4.4 36.1 1.0 CG A:GLU526 4.4 17.2 1.0 CG2 A:THR492 4.9 15.1 1.0 NH2 A:ARG489 4.9 29.5 1.0 OD1 A:ASN527 4.9 17.2 1.0

A.K.Marapaka, A.Addlagatta. Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-N-Hydroxy-4-Methyl-2-(3-( O-Tolyl)Ureido)Pentanamide To Be Published.