Zinc in PDB 5lhd: Structure of Glycosylated Human Aminopeptidase N

All present enzymatic activity of Structure of Glycosylated Human Aminopeptidase N:
3.4.11.2;

The structure of Structure of Glycosylated Human Aminopeptidase N, PDB code: 5lhd was solved by R.Recacha, G.Mudgal, C.Santiago, J.M.Casasnovas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.97 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	127.093, 168.856, 244.249, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 21.4

The binding sites of Zinc atom in the Structure of Glycosylated Human Aminopeptidase N (pdb code 5lhd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Glycosylated Human Aminopeptidase N, PDB code: 5lhd:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Glycosylated Human Aminopeptidase N


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Glycosylated Human Aminopeptidase N within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1023 b:43.5 occ:1.00 OE1 A:GLU411 2.0 38.6 1.0 NE2 A:HIS388 2.0 34.0 1.0 O A:HOH1137 2.1 35.9 1.0 NE2 A:HIS392 2.1 42.6 1.0 CD2 A:HIS392 2.9 41.5 1.0 CD2 A:HIS388 3.0 36.8 1.0 CD A:GLU411 3.0 45.1 1.0 CE1 A:HIS388 3.1 34.0 1.0 CE1 A:HIS392 3.2 40.1 1.0 OE2 A:GLU411 3.3 50.3 1.0 OE1 A:GLU355 4.1 53.1 1.0 CG A:HIS392 4.1 42.1 1.0 CB A:ALA414 4.1 34.2 1.0 CG A:HIS388 4.1 36.7 1.0 ND1 A:HIS388 4.1 34.4 1.0 ND1 A:HIS392 4.2 42.6 1.0 CG A:GLU411 4.3 42.3 1.0 CA A:GLU411 4.4 38.8 1.0 CE1 A:TYR477 4.5 36.2 1.0 OE2 A:GLU389 4.5 49.2 1.0 OE1 A:GLU389 4.5 46.7 1.0 CB A:GLU411 4.6 39.4 1.0 CD A:GLU355 4.6 50.3 1.0 OE2 A:GLU355 4.8 53.0 1.0 CD A:GLU389 4.9 47.0 1.0 O A:GLU411 4.9 41.6 1.0 OH A:TYR477 4.9 41.9 1.0

Zinc binding site 2 out of 4 in the Structure of Glycosylated Human Aminopeptidase N


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Glycosylated Human Aminopeptidase N within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1022 b:42.1 occ:1.00 OE1 B:GLU411 2.0 35.6 1.0 NE2 B:HIS388 2.0 34.5 1.0 NE2 B:HIS392 2.1 37.5 1.0 O B:HOH1179 2.1 40.7 1.0 CD B:GLU411 2.9 37.4 1.0 CD2 B:HIS392 2.9 36.3 1.0 CD2 B:HIS388 3.0 34.4 1.0 CE1 B:HIS388 3.0 35.5 1.0 OE2 B:GLU411 3.1 40.0 1.0 CE1 B:HIS392 3.1 36.8 1.0 O B:HOH1264 4.0 49.6 1.0 CG B:HIS392 4.1 38.3 1.0 ND1 B:HIS388 4.1 34.4 1.0 OE1 B:GLU355 4.1 46.6 1.0 CG B:HIS388 4.1 35.7 1.0 ND1 B:HIS392 4.2 38.3 1.0 CB B:ALA414 4.2 37.0 1.0 CG B:GLU411 4.2 36.0 1.0 OE1 B:GLU389 4.3 45.3 1.0 CE2 B:TYR477 4.4 34.3 1.0 CD B:GLU355 4.5 46.9 1.0 CA B:GLU411 4.5 39.8 1.0 OE2 B:GLU389 4.5 47.2 1.0 CB B:GLU411 4.6 36.2 1.0 OE2 B:GLU355 4.6 46.1 1.0 CD B:GLU389 4.8 44.3 1.0 OH B:TYR477 4.9 39.9 1.0

Zinc binding site 3 out of 4 in the Structure of Glycosylated Human Aminopeptidase N


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Glycosylated Human Aminopeptidase N within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1134 b:41.5 occ:1.00 OE1 C:GLU411 2.0 44.3 1.0 NE2 C:HIS388 2.0 36.4 1.0 NE2 C:HIS392 2.1 39.0 1.0 O C:HOH1243 2.2 42.6 1.0 CD2 C:HIS392 2.9 39.6 1.0 CD C:GLU411 2.9 48.7 1.0 CE1 C:HIS388 3.0 38.9 1.0 CD2 C:HIS388 3.0 36.7 1.0 CE1 C:HIS392 3.2 37.4 1.0 OE2 C:GLU411 3.2 53.1 1.0 CB C:ALA414 4.1 32.5 1.0 ND1 C:HIS388 4.1 38.8 1.0 CG C:HIS392 4.1 41.2 1.0 CG C:HIS388 4.1 37.5 1.0 OE1 C:GLU355 4.1 48.8 1.0 ND1 C:HIS392 4.2 41.4 1.0 OE2 C:GLU389 4.3 53.0 1.0 CG C:GLU411 4.3 46.6 1.0 CE2 C:TYR477 4.4 36.1 1.0 CA C:GLU411 4.5 39.8 1.0 CD C:GLU355 4.6 43.5 1.0 OE1 C:GLU389 4.6 51.5 1.0 CB C:GLU411 4.7 41.8 1.0 OE2 C:GLU355 4.7 42.1 1.0 OH C:TYR477 4.7 44.0 1.0 CD C:GLU389 4.8 49.4 1.0 CZ C:TYR477 5.0 40.1 1.0

Zinc binding site 4 out of 4 in the Structure of Glycosylated Human Aminopeptidase N


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Glycosylated Human Aminopeptidase N within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1026 b:43.5 occ:1.00 O D:HOH1167 1.9 22.1 1.0 OE1 D:GLU411 2.0 48.7 1.0 NE2 D:HIS388 2.1 33.0 1.0 NE2 D:HIS392 2.1 44.8 1.0 CD D:GLU411 2.9 49.1 1.0 CD2 D:HIS392 3.0 41.3 1.0 CD2 D:HIS388 3.0 31.4 1.0 CE1 D:HIS388 3.0 31.0 1.0 OE2 D:GLU411 3.1 52.0 1.0 CE1 D:HIS392 3.2 44.0 1.0 CB D:ALA414 4.0 34.7 1.0 ND1 D:HIS388 4.1 29.6 1.0 CG D:HIS388 4.1 30.8 1.0 CG D:HIS392 4.2 41.0 1.0 ND1 D:HIS392 4.2 43.4 1.0 OE1 D:GLU355 4.2 49.6 1.0 CG D:GLU411 4.3 44.8 1.0 CA D:GLU411 4.4 41.3 1.0 CE2 D:TYR477 4.5 37.9 1.0 OE2 D:GLU389 4.5 50.9 1.0 OE1 D:GLU389 4.5 51.7 1.0 CB D:GLU411 4.6 40.9 1.0 CD D:GLU355 4.7 46.1 1.0 OH D:TYR477 4.8 43.4 1.0 OE2 D:GLU355 4.8 45.9 1.0 CD D:GLU389 4.9 50.0 1.0 O D:GLU411 5.0 41.0 1.0

C.Santiago, G.Mudgal, J.Reguera, R.Recacha, S.Albrecht, L.Enjuanes, J.M.Casasnovas. Allosteric Inhibition of Aminopeptidase N Functions Related to Tumor Growth and Virus Infection. Sci Rep V. 7 46045 2017.
ISSN: ESSN 2045-2322
PubMed: 28393915
DOI: 10.1038/SREP46045