Magnesium in PDB 5y1s: Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-2-(3-(3,4-Dimethylbenzyl)Ureido)-N-Hydroxy-4- Methylpentanamide

The structure of Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-2-(3-(3,4-Dimethylbenzyl)Ureido)-N-Hydroxy-4- Methylpentanamide, PDB code: 5y1s 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)	19.68 / 1.66
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.699, 109.405, 112.991, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 20.1

The structure of Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-2-(3-(3,4-Dimethylbenzyl)Ureido)-N-Hydroxy-4- Methylpentanamide 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)-2-(3-(3,4-Dimethylbenzyl)Ureido)-N-Hydroxy-4- Methylpentanamide (pdb code 5y1s). 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)-2-(3-(3,4-Dimethylbenzyl)Ureido)-N-Hydroxy-4- Methylpentanamide, PDB code: 5y1s:
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)-2-(3-(3,4-Dimethylbenzyl)Ureido)-N-Hydroxy-4- Methylpentanamide


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)-2-(3-(3,4-Dimethylbenzyl)Ureido)-N-Hydroxy-4- Methylpentanamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1102 b:36.6 occ:1.00 O A:HOH1677 2.1 33.7 1.0 O A:GLY250 2.1 24.4 1.0 O A:HOH1403 2.1 27.5 1.0 O A:HOH1693 2.2 31.4 1.0 C A:GLY250 3.3 25.8 1.0 CA A:GLY250 3.9 26.4 1.0 O A:HOH1427 4.0 27.2 1.0 N A:LEU251 4.4 22.2 1.0 O A:ILE295 4.6 22.8 1.0 CA A:LEU251 4.7 23.4 1.0 O A:HOH1703 4.7 28.4 1.0 CD2 A:HIS297 4.8 26.7 1.0 CA A:ILE296 4.9 21.4 1.0 O A:HOH1453 4.9 29.9 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-2-(3-(3,4-Dimethylbenzyl)Ureido)-N-Hydroxy-4- Methylpentanamide


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)-2-(3-(3,4-Dimethylbenzyl)Ureido)-N-Hydroxy-4- Methylpentanamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1103 b:31.1 occ:0.70 O A:HOH1656 1.9 12.0 0.2 O A:HOH1458 2.0 30.7 1.0 O A:HOH1744 2.0 38.2 1.0 OE2 A:GLU526 2.1 24.4 0.6 O A:HOH1673 2.2 37.6 1.0 O A:HOH1459 2.4 36.9 1.0 CD A:GLU526 3.1 25.8 0.6 OE1 A:GLU526 3.4 15.5 0.6 O A:HOH1201 3.5 33.9 0.5 OE1 A:GLU526 3.6 19.0 0.4 C1 A:GOL1110 4.1 36.2 0.5 O A:HOH1660 4.1 39.1 1.0 O A:HOH1231 4.2 30.0 1.0 CB A:THR492 4.2 25.1 1.0 O A:HOH1203 4.2 27.4 0.5 OG1 A:THR492 4.2 32.9 1.0 CD A:GLU526 4.3 19.6 0.4 C11 A:E8F1105 4.4 16.1 0.5 CG A:GLU526 4.4 24.9 0.6 O A:HOH1717 4.5 36.7 1.0 CG2 A:THR492 4.5 23.2 1.0 OE2 A:GLU526 4.7 20.9 0.4 ND2 A:ASN527 4.8 26.2 1.0 C3 A:GOL1110 4.9 27.7 0.5

Magnesium binding site 3 out of 3 in the Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-2-(3-(3,4-Dimethylbenzyl)Ureido)-N-Hydroxy-4- Methylpentanamide


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)-2-(3-(3,4-Dimethylbenzyl)Ureido)-N-Hydroxy-4- Methylpentanamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1104 b:32.9 occ:1.00 O A:HOH1727 1.9 35.0 1.0 O A:HOH1762 2.0 32.3 1.0 O A:HOH1575 2.0 29.2 1.0 O A:HOH1771 2.2 22.7 0.5 O A:HOH1354 2.2 31.4 1.0 O A:HOH1567 2.2 31.8 1.0 OE2 A:GLU957 3.8 26.1 1.0 O A:HOH1283 4.1 32.3 1.0 O A:HOH1646 4.1 39.1 1.0 ND2 A:ASN992 4.1 31.3 1.0 O A:HOH1775 4.3 28.0 1.0 OD2 A:ASP995 4.3 29.6 1.0 O A:HOH1778 4.3 46.5 1.0 O A:HOH1304 4.5 30.7 1.0 O A:HOH1473 4.7 28.5 1.0 CD A:GLU957 4.7 26.9 1.0 CE A:LYS311 5.0 28.0 1.0

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