Magnesium in PDB 5y1h: Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-2-(3-(2,4-Difluorobenzyl)Ureido)-N-Hydroxy-4- Methylpentanamide

The structure of Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-2-(3-(2,4-Difluorobenzyl)Ureido)-N-Hydroxy-4- Methylpentanamide, PDB code: 5y1h 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)	24.66 / 1.73
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.564, 109.241, 112.518, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 20.1

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

Fluorine	(F)	2 atoms
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-(2,4-Difluorobenzyl)Ureido)-N-Hydroxy-4- Methylpentanamide (pdb code 5y1h). 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-(2,4-Difluorobenzyl)Ureido)-N-Hydroxy-4- Methylpentanamide, PDB code: 5y1h:
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-(2,4-Difluorobenzyl)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-(2,4-Difluorobenzyl)Ureido)-N-Hydroxy-4- Methylpentanamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1101 b:30.2 occ:1.00 O A:HOH1653 2.1 28.0 1.0 O A:HOH1699 2.1 23.6 1.0 O A:GLY250 2.2 17.2 1.0 O A:HOH1354 2.2 21.1 1.0 C A:GLY250 3.3 20.1 1.0 CA A:GLY250 3.9 19.4 1.0 O A:HOH1384 4.0 20.8 1.0 N A:LEU251 4.4 16.4 1.0 O A:ILE295 4.6 17.1 1.0 CA A:LEU251 4.7 16.5 1.0 CD2 A:HIS297 4.7 20.4 1.0 O A:HOH1705 4.7 8.3 0.5 CA A:ILE296 4.8 14.9 1.0 O A:HOH1577 4.8 21.7 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-2-(3-(2,4-Difluorobenzyl)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-(2,4-Difluorobenzyl)Ureido)-N-Hydroxy-4- Methylpentanamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1102 b:22.8 occ:1.00 OE2 A:GLU526 2.0 20.3 1.0 O A:HOH1729 2.0 24.5 1.0 O A:HOH1571 2.0 27.3 1.0 O A:HOH1304 2.1 20.5 1.0 O A:HOH1655 2.1 24.4 1.0 O A:HOH1428 2.3 27.8 1.0 CD A:GLU526 3.1 20.2 1.0 OE1 A:GLU526 3.4 15.0 1.0 O1 A:GOL1106 3.7 44.2 1.0 O A:HOH1537 4.1 25.6 1.0 OG1 A:THR492 4.1 18.8 1.0 C1 A:GOL1106 4.2 27.9 1.0 O A:HOH1504 4.2 23.1 1.0 CB A:THR492 4.3 16.8 1.0 O A:HOH1739 4.4 27.4 1.0 CG A:GLU526 4.4 18.6 1.0 OD1 A:ASN527 4.5 18.4 1.0 C2 A:GOL1106 4.6 18.2 1.0 CG2 A:THR492 4.7 17.6 1.0 O2 A:GOL1106 5.0 32.8 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-2-(3-(2,4-Difluorobenzyl)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-(2,4-Difluorobenzyl)Ureido)-N-Hydroxy-4- Methylpentanamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1103 b:27.2 occ:1.00 O A:HOH1723 2.0 31.7 1.0 O A:HOH1597 2.0 24.1 1.0 O A:HOH1751 2.0 24.4 1.0 O A:HOH1757 2.1 29.0 1.0 O A:HOH1586 2.2 25.2 1.0 O A:HOH1397 2.2 25.9 1.0 OE2 A:GLU957 3.8 20.6 1.0 O A:HOH1367 4.1 24.6 1.0 ND2 A:ASN992 4.1 20.9 1.0 O A:HOH1758 4.2 23.0 1.0 OD2 A:ASP995 4.3 22.0 1.0 O A:HOH1550 4.5 20.7 1.0 O A:HOH1271 4.6 21.4 1.0 CD A:GLU957 4.6 22.6 1.0 CE A:LYS311 4.9 22.8 1.0 CG A:GLU957 5.0 26.9 1.0

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