Magnesium in PDB 5y1t: Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-2-(3-(2,3-Dimethylbenzyl)Ureido)-N-Hydroxy-4- Methylpentanamide

The structure of Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-2-(3-(2,3-Dimethylbenzyl)Ureido)-N-Hydroxy-4- Methylpentanamide, PDB code: 5y1t 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)	25.00 / 2.14
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.450, 109.285, 112.275, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 22.3

The structure of Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-2-(3-(2,3-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-(2,3-Dimethylbenzyl)Ureido)-N-Hydroxy-4- Methylpentanamide (pdb code 5y1t). 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-(2,3-Dimethylbenzyl)Ureido)-N-Hydroxy-4- Methylpentanamide, PDB code: 5y1t:
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-(2,3-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-(2,3-Dimethylbenzyl)Ureido)-N-Hydroxy-4- Methylpentanamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1102 b:38.8 occ:1.00 O A:HOH1273 2.1 3.5 0.4 O A:HOH1518 2.2 5.1 0.3 O A:GLY250 2.2 21.3 1.0 O A:HOH1469 2.3 27.2 1.0 C A:GLY250 3.4 21.8 1.0 O A:HOH1375 4.0 23.8 1.0 CA A:GLY250 4.1 24.9 1.0 O A:ILE295 4.4 21.5 1.0 N A:LEU251 4.5 22.4 1.0 CA A:ILE296 4.6 21.0 1.0 CD2 A:HIS297 4.6 29.5 1.0 O A:HOH1533 4.6 21.0 1.0 CA A:LEU251 4.7 22.9 1.0 O A:HOH1301 4.9 24.9 1.0 N A:HIS297 4.9 22.6 1.0 CG2 A:ILE296 5.0 21.9 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-2-(3-(2,3-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-(2,3-Dimethylbenzyl)Ureido)-N-Hydroxy-4- Methylpentanamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1103 b:43.8 occ:1.00 OE2 A:GLU526 2.2 28.5 1.0 O A:HOH1207 2.2 7.6 0.3 O A:HOH1520 2.3 2.0 0.2 O A:HOH1406 2.4 12.2 0.4 O A:HOH1549 2.5 47.1 1.0 O A:HOH1272 2.5 26.5 1.0 CD A:GLU526 3.3 24.0 1.0 O A:HOH1495 3.5 48.5 1.0 O2 A:GOL1107 3.7 55.3 1.0 OE1 A:GLU526 3.7 22.1 1.0 O A:HOH1323 4.0 24.7 1.0 OG1 A:THR492 4.2 22.2 1.0 O A:HOH1546 4.3 47.2 1.0 ND2 A:ASN527 4.4 26.7 1.0 CB A:THR492 4.5 22.0 1.0 CG A:GLU526 4.5 23.1 1.0 C2 A:GOL1107 4.8 43.2 1.0 C1 A:GOL1107 5.0 40.8 1.0 CG2 A:THR492 5.0 23.0 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-2-(3-(2,3-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-(2,3-Dimethylbenzyl)Ureido)-N-Hydroxy-4- Methylpentanamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1104 b:44.8 occ:1.00 O A:HOH1309 2.1 9.7 0.4 O A:HOH1377 2.1 6.8 0.4 O A:HOH1558 2.1 42.2 1.0 O A:HOH1545 2.1 8.0 0.3 O A:HOH1559 2.2 8.6 0.4 O A:HOH1302 2.5 5.7 0.3 OE2 A:GLU957 3.9 25.6 1.0 OD2 A:ASP995 4.0 28.0 1.0 ND2 A:ASN992 4.0 23.8 1.0 O A:HOH1472 4.3 27.9 1.0 O A:HOH1304 4.4 31.7 1.0 O A:HOH1560 4.4 26.0 1.0 O A:HOH1265 4.6 32.2 1.0 CD A:GLU957 4.7 28.0 1.0 CB A:ASN992 4.8 23.9 1.0 CG A:GLU957 4.8 31.0 1.0 CG A:ASN992 4.9 25.0 1.0 CG A:ASP995 4.9 27.0 1.0 O A:HOH1551 4.9 30.3 1.0 OD1 A:ASP995 5.0 30.7 1.0

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