Zinc in PDB 5y3i: Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-N-Hydroxy-4-Methyl-2-(3-(3-Methylbenzyl)Ureido)Pentanamide

The structure of Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-N-Hydroxy-4-Methyl-2-(3-(3-Methylbenzyl)Ureido)Pentanamide, PDB code: 5y3i 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 / 1.73
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.436, 109.267, 112.504, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 19.6

The structure of Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-N-Hydroxy-4-Methyl-2-(3-(3-Methylbenzyl)Ureido)Pentanamide 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)-N-Hydroxy-4-Methyl-2-(3-(3-Methylbenzyl)Ureido)Pentanamide (pdb code 5y3i). 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)-N-Hydroxy-4-Methyl-2-(3-(3-Methylbenzyl)Ureido)Pentanamide, PDB code: 5y3i:

Zinc binding site 1 out of 1 in the Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-N-Hydroxy-4-Methyl-2-(3-(3-Methylbenzyl)Ureido)Pentanamide


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)-N-Hydroxy-4-Methyl-2-(3-(3-Methylbenzyl)Ureido)Pentanamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1101 b:12.3 occ:1.00 OE1 A:GLU519 2.0 11.9 1.0 O3 A:8N31105 2.1 14.5 1.0 NE2 A:HIS500 2.1 10.4 1.0 NE2 A:HIS496 2.1 11.5 1.0 O2 A:8N31105 2.1 13.4 1.0 CD A:GLU519 2.8 11.4 1.0 OE2 A:GLU519 2.8 12.3 1.0 C14 A:8N31105 2.8 16.8 1.0 N3 A:8N31105 2.9 16.6 1.0 CD2 A:HIS496 3.0 12.0 1.0 CE1 A:HIS500 3.1 11.5 1.0 CD2 A:HIS500 3.1 10.2 1.0 CE1 A:HIS496 3.1 11.7 1.0 O A:HOH1209 3.4 17.4 1.0 O1 A:GOL1106 3.7 36.5 1.0 OE1 A:GLU463 4.1 12.5 1.0 OH A:TYR580 4.1 12.2 1.0 ND1 A:HIS500 4.2 11.4 1.0 CE2 A:TYR580 4.2 10.3 1.0 CG A:HIS496 4.2 11.0 1.0 CG A:HIS500 4.2 10.8 1.0 ND1 A:HIS496 4.2 12.0 1.0 CG A:GLU519 4.2 11.3 1.0 OE1 A:GLU497 4.3 12.7 1.0 C9 A:8N31105 4.3 17.1 1.0 CZ A:TYR580 4.5 11.8 1.0 CD A:GLU463 4.7 13.7 1.0 CG2 A:THR522 4.8 12.2 1.0 OE2 A:GLU497 4.8 13.7 1.0 N2 A:8N31105 4.8 17.8 1.0 OE2 A:GLU463 4.8 12.2 1.0 CB A:GLU519 4.8 10.3 1.0 O2 A:GOL1106 4.9 27.8 1.0 CA A:GLU519 4.9 10.9 1.0 C10 A:8N31105 4.9 15.5 1.0 CD A:GLU497 5.0 13.5 1.0

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