Magnesium in PDB 5y1k: Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-2-(3-(2-Chlorobenzyl)Ureido)-N-Hydroxy-4-Methylpentanamide

The structure of Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-2-(3-(2-Chlorobenzyl)Ureido)-N-Hydroxy-4-Methylpentanamide, PDB code: 5y1k 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)	23.71 / 1.81
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.275, 109.254, 111.884, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 21.3

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

Chlorine	(Cl)	1 atom
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-(2-Chlorobenzyl)Ureido)-N-Hydroxy-4-Methylpentanamide (pdb code 5y1k). 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-(2-Chlorobenzyl)Ureido)-N-Hydroxy-4-Methylpentanamide, PDB code: 5y1k:
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-(2-Chlorobenzyl)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-(2-Chlorobenzyl)Ureido)-N-Hydroxy-4-Methylpentanamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1102 b:38.1 occ:1.00 O A:HOH1652 2.1 32.0 1.0 O A:HOH1584 2.1 30.5 1.0 O A:HOH1278 2.1 23.4 1.0 O A:GLY250 2.1 22.2 1.0 O A:HOH1588 2.3 35.2 1.0 C A:GLY250 3.3 26.0 1.0 CA A:GLY250 4.0 26.6 1.0 O A:HOH1386 4.0 25.8 1.0 N A:LEU251 4.4 23.4 1.0 O A:ILE295 4.5 23.3 1.0 CD2 A:HIS297 4.6 28.9 1.0 O A:HOH1611 4.6 24.6 1.0 CA A:LEU251 4.7 24.2 1.0 CA A:ILE296 4.7 21.0 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-2-(3-(2-Chlorobenzyl)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-(2-Chlorobenzyl)Ureido)-N-Hydroxy-4-Methylpentanamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1103 b:31.4 occ:1.00 OE2 A:GLU526 2.0 24.9 1.0 O A:HOH1585 2.1 30.9 1.0 O A:HOH1623 2.1 32.1 1.0 O A:HOH1410 2.2 33.5 1.0 O A:HOH1207 2.2 15.1 0.3 O A:HOH1238 2.2 26.4 1.0 CD A:GLU526 3.1 27.7 1.0 O3 A:GOL1107 3.3 49.4 1.0 O A:HOH1233 3.4 90.3 1.0 OE1 A:GLU526 3.4 21.8 1.0 OG1 A:THR492 4.1 26.7 1.0 C3 A:GOL1107 4.2 33.7 1.0 O A:HOH1503 4.2 28.1 1.0 CB A:THR492 4.3 23.7 1.0 CG A:GLU526 4.4 22.4 1.0 OD1 A:ASN527 4.4 25.1 1.0 O A:HOH1474 4.5 42.5 1.0 C2 A:GOL1107 4.7 24.1 1.0 CG2 A:THR492 4.8 26.8 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-2-(3-(2-Chlorobenzyl)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-(2-Chlorobenzyl)Ureido)-N-Hydroxy-4-Methylpentanamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1104 b:43.2 occ:1.00 O A:HOH1655 2.1 19.8 0.4 O A:HOH1442 2.1 33.7 1.0 O A:HOH1638 2.2 42.7 1.0 O A:HOH1658 2.2 18.1 0.3 O A:HOH1406 2.2 34.5 1.0 O A:HOH1300 2.3 32.2 1.0 OE2 A:GLU957 3.8 27.8 1.0 O A:HOH1656 4.1 32.0 1.0 O A:HOH1462 4.2 35.5 1.0 OD2 A:ASP995 4.2 30.6 1.0 O A:HOH1627 4.3 40.2 1.0 ND2 A:ASN992 4.3 28.6 1.0 O A:HOH1481 4.5 29.2 1.0 CD A:GLU957 4.6 31.5 1.0 O A:HOH1275 4.7 34.3 1.0 CG A:GLU957 4.8 34.0 1.0

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