Magnesium in PDB 5y1q: Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-2-(3-(3-Chlorobenzyl)Ureido)-N-Hydroxy-4-Methylpentanamide

The structure of Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-2-(3-(3-Chlorobenzyl)Ureido)-N-Hydroxy-4-Methylpentanamide, PDB code: 5y1q 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)	24.81 / 2.14
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.128, 109.609, 113.138, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 21.9

The structure of Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-2-(3-(3-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-(3-Chlorobenzyl)Ureido)-N-Hydroxy-4-Methylpentanamide (pdb code 5y1q). 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-Chlorobenzyl)Ureido)-N-Hydroxy-4-Methylpentanamide, PDB code: 5y1q:
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-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-(3-Chlorobenzyl)Ureido)-N-Hydroxy-4-Methylpentanamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1102 b:35.4 occ:1.00 O A:HOH1431 2.1 8.4 0.3 O A:HOH1319 2.2 28.2 1.0 O A:GLY250 2.2 22.8 1.0 O A:HOH1452 2.5 35.9 1.0 C A:GLY250 3.4 23.9 1.0 CA A:GLY250 4.0 24.6 1.0 O A:HOH1311 4.4 27.8 1.0 N A:LEU251 4.5 23.6 1.0 CD2 A:HIS297 4.6 31.5 1.0 O A:ILE295 4.7 22.4 1.0 CA A:LEU251 4.8 26.1 1.0 CA A:ILE296 4.8 23.8 1.0 C A:LEU251 5.0 25.8 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-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-(3-Chlorobenzyl)Ureido)-N-Hydroxy-4-Methylpentanamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1103 b:43.5 occ:1.00 O A:HOH1494 2.1 9.7 0.3 O A:HOH1372 2.2 34.5 1.0 O A:HOH1493 2.2 6.3 0.2 O A:HOH1299 2.3 36.3 1.0 O A:HOH1486 2.3 6.5 0.2 O A:HOH1266 2.3 6.5 0.3 OE2 A:GLU957 4.0 38.9 1.0 OD2 A:ASP995 4.1 34.8 1.0 ND2 A:ASN992 4.2 32.5 1.0 O A:HOH1395 4.6 27.0 1.0 O A:HOH1297 4.6 24.8 1.0 CD A:GLU957 4.8 38.5 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-2-(3-(3-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-(3-Chlorobenzyl)Ureido)-N-Hydroxy-4-Methylpentanamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1104 b:40.9 occ:1.00 O A:HOH1492 1.9 10.3 0.3 O A:HOH1445 2.1 33.3 1.0 O A:HOH1461 2.1 32.4 1.0 O A:HOH1378 2.2 28.7 1.0 O A:HOH1380 2.3 32.9 1.0 OE2 A:GLU526 2.4 42.9 1.0 CD A:GLU526 3.4 33.8 1.0 OE1 A:GLU526 3.7 26.7 1.0 OG1 A:THR492 4.2 31.2 1.0 O A:HOH1249 4.2 25.5 1.0 O A:HOH1484 4.3 40.7 1.0 CB A:THR492 4.4 25.7 1.0 OD1 A:ASN527 4.6 26.8 1.0 CG A:GLU526 4.7 29.0 1.0 CG2 A:THR492 4.9 26.1 1.0 O A:HOH1485 5.0 29.2 1.0

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