Zinc 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:

Magnesium

(Mg)

3 atoms

The binding sites of Zinc 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 Zinc atom.
In total only one binding site of Zinc was 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:

Zinc binding site 1 out of 1 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 Zinc with other atoms in the Zn 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:Zn1101 b:21.0 occ:1.00 O2 A:E8G1105 1.9 23.1 1.0 OE1 A:GLU519 2.0 17.3 1.0 NE2 A:HIS496 2.1 24.4 1.0 NE2 A:HIS500 2.1 19.1 1.0 O3 A:E8G1105 2.3 22.9 1.0 CD A:GLU519 2.7 18.4 1.0 C16 A:E8G1105 2.7 29.8 1.0 OE2 A:GLU519 2.8 16.2 1.0 N3 A:E8G1105 3.0 29.1 1.0 CD2 A:HIS496 3.0 22.5 1.0 CD2 A:HIS500 3.1 19.4 1.0 CE1 A:HIS500 3.1 21.1 1.0 CE1 A:HIS496 3.1 22.1 1.0 O A:HOH1237 3.3 33.3 1.0 O1 A:GOL1107 3.9 43.9 1.0 OH A:TYR580 4.0 19.7 1.0 CG A:HIS496 4.2 21.1 1.0 CE2 A:TYR580 4.2 19.7 1.0 ND1 A:HIS496 4.2 21.4 1.0 C11 A:E8G1105 4.2 33.8 1.0 ND1 A:HIS500 4.2 19.7 1.0 CG A:GLU519 4.2 16.3 1.0 CG A:HIS500 4.2 19.2 1.0 OE1 A:GLU463 4.2 21.6 1.0 O3 A:GOL1107 4.2 54.2 1.0 OE1 A:GLU497 4.3 21.5 1.0 CZ A:TYR580 4.5 20.3 1.0 CG2 A:THR522 4.8 20.0 1.0 CB A:GLU519 4.8 16.9 1.0 CD A:GLU463 4.8 20.7 1.0 C12 A:E8G1105 4.8 34.4 1.0 OE2 A:GLU463 4.9 20.4 1.0 OE2 A:GLU497 4.9 19.6 1.0 CA A:GLU519 4.9 17.5 1.0 NZ A:LYS518 4.9 20.8 1.0 N2 A:E8G1105 5.0 44.1 1.0 C1 A:GOL1107 5.0 40.8 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.