Zinc in PDB 5lds: Structure of the Porcine Aminopeptidase N Ectodomain

All present enzymatic activity of Structure of the Porcine Aminopeptidase N Ectodomain:
3.4.11.2;

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

Resolution Low / High (Å)	24.96 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	78.670, 78.770, 223.870, 99.66, 92.62, 111.33
R / Rfree (%)	16.9 / 20.7

The binding sites of Zinc atom in the Structure of the Porcine Aminopeptidase N Ectodomain (pdb code 5lds). 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 the Porcine Aminopeptidase N Ectodomain, PDB code: 5lds:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of the Porcine Aminopeptidase N Ectodomain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Porcine Aminopeptidase N Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:3.4 occ:1.00 O A:ACT1017 1.9 6.0 1.0 OE1 A:GLU406 2.0 3.0 1.0 NE2 A:HIS387 2.0 3.5 1.0 NE2 A:HIS383 2.1 3.0 1.0 C A:ACT1017 2.5 13.6 1.0 OXT A:ACT1017 2.6 11.1 1.0 CD A:GLU406 2.8 7.7 1.0 CD2 A:HIS387 3.0 2.9 1.0 CE1 A:HIS383 3.0 4.8 1.0 OE2 A:GLU406 3.0 7.8 1.0 CE1 A:HIS387 3.0 3.0 1.0 CD2 A:HIS383 3.1 6.4 1.0 O A:HOH1203 3.4 6.6 1.0 CE2 A:TYR472 3.8 4.0 1.0 CH3 A:ACT1017 4.0 13.6 1.0 OH A:TYR472 4.0 3.1 1.0 CB A:ALA409 4.1 4.1 1.0 ND1 A:HIS387 4.1 3.0 1.0 ND1 A:HIS383 4.1 3.0 1.0 CG A:HIS387 4.2 9.0 1.0 CG A:HIS383 4.2 3.2 1.0 CG A:GLU406 4.3 7.1 1.0 CZ A:TYR472 4.3 5.2 1.0 OE1 A:GLU350 4.5 4.9 1.0 CA A:GLU406 4.7 4.8 1.0 CB A:GLU406 4.7 6.3 1.0 CD2 A:TYR472 4.7 4.4 1.0 OE2 A:GLU384 4.8 8.8 1.0 O A:HOH1334 4.9 5.0 1.0

Zinc binding site 2 out of 4 in the Structure of the Porcine Aminopeptidase N Ectodomain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Porcine Aminopeptidase N Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:9.6 occ:1.00 OE1 B:GLU406 2.0 7.4 1.0 OXT B:ACT1012 2.0 8.9 1.0 NE2 B:HIS383 2.0 7.4 1.0 NE2 B:HIS387 2.1 7.5 1.0 O B:ACT1012 2.5 15.7 1.0 C B:ACT1012 2.6 12.6 1.0 CD B:GLU406 2.8 10.0 1.0 CE1 B:HIS383 3.0 7.4 1.0 CD2 B:HIS387 3.0 7.5 1.0 OE2 B:GLU406 3.0 11.3 1.0 CD2 B:HIS383 3.0 12.7 1.0 CE1 B:HIS387 3.1 7.6 1.0 O B:HOH1227 3.7 10.8 1.0 CE2 B:TYR472 3.8 13.6 1.0 OH B:TYR472 4.0 7.5 1.0 CH3 B:ACT1012 4.1 13.4 1.0 ND1 B:HIS383 4.1 7.4 1.0 CG B:HIS383 4.2 7.4 1.0 CB B:ALA409 4.2 15.3 1.0 CG B:HIS387 4.2 11.3 1.0 ND1 B:HIS387 4.2 7.7 1.0 CG B:GLU406 4.3 7.4 1.0 CZ B:TYR472 4.3 12.0 1.0 OE1 B:GLU350 4.4 8.3 1.0 CA B:GLU406 4.6 8.7 1.0 CB B:GLU406 4.7 9.7 1.0 CD2 B:TYR472 4.7 14.0 1.0 O B:HOH1258 4.9 10.0 1.0 OE2 B:GLU384 4.9 12.6 1.0

Zinc binding site 3 out of 4 in the Structure of the Porcine Aminopeptidase N Ectodomain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Porcine Aminopeptidase N Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1001 b:9.5 occ:1.00 O C:ACT1011 1.9 12.2 1.0 OE1 C:GLU406 2.0 11.8 1.0 NE2 C:HIS383 2.0 7.3 1.0 NE2 C:HIS387 2.1 11.0 1.0 C C:ACT1011 2.6 15.8 1.0 OXT C:ACT1011 2.6 13.2 1.0 CD C:GLU406 2.8 7.3 1.0 CE1 C:HIS383 3.0 12.8 1.0 CD2 C:HIS387 3.0 7.5 1.0 CD2 C:HIS383 3.0 14.4 1.0 OE2 C:GLU406 3.0 7.8 1.0 CE1 C:HIS387 3.0 7.5 1.0 O C:HOH1192 3.6 5.5 1.0 CE2 C:TYR472 3.9 10.5 1.0 OH C:TYR472 4.0 11.3 1.0 CB C:ALA409 4.0 7.6 1.0 CH3 C:ACT1011 4.0 19.5 1.0 ND1 C:HIS383 4.1 12.8 1.0 CG C:HIS383 4.1 8.0 1.0 CG C:HIS387 4.2 7.6 1.0 ND1 C:HIS387 4.2 7.7 1.0 CZ C:TYR472 4.3 12.7 1.0 CG C:GLU406 4.3 9.6 1.0 OE1 C:GLU350 4.4 7.3 1.0 CA C:GLU406 4.7 14.0 1.0 CB C:GLU406 4.7 15.6 1.0 CD2 C:TYR472 4.8 7.1 1.0 OE2 C:GLU384 4.8 13.3 1.0 OE2 C:GLU350 4.9 9.3 1.0 CD C:GLU350 5.0 7.5 1.0 O C:HOH1314 5.0 7.0 1.0

Zinc binding site 4 out of 4 in the Structure of the Porcine Aminopeptidase N Ectodomain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the Porcine Aminopeptidase N Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1001 b:6.9 occ:1.00 OXT D:ACT1020 1.9 6.2 1.0 OE1 D:GLU406 1.9 7.4 1.0 NE2 D:HIS383 2.0 3.7 1.0 NE2 D:HIS387 2.1 4.9 1.0 C D:ACT1020 2.6 13.9 1.0 O D:ACT1020 2.6 10.6 1.0 CD D:GLU406 2.9 9.8 1.0 CE1 D:HIS383 3.0 4.2 1.0 CD2 D:HIS387 3.0 4.8 1.0 CD2 D:HIS383 3.1 3.7 1.0 CE1 D:HIS387 3.1 6.2 1.0 OE2 D:GLU406 3.1 3.8 1.0 O D:HOH1251 3.4 4.5 1.0 CE2 D:TYR472 3.8 12.1 1.0 OH D:TYR472 4.0 5.1 1.0 CH3 D:ACT1020 4.0 14.9 1.0 ND1 D:HIS383 4.1 3.8 1.0 CG D:HIS387 4.2 3.8 1.0 CG D:HIS383 4.2 4.1 1.0 CB D:ALA409 4.2 3.7 1.0 ND1 D:HIS387 4.2 6.7 1.0 CG D:GLU406 4.3 6.5 1.0 CZ D:TYR472 4.3 10.8 1.0 OE1 D:GLU350 4.4 6.3 1.0 CA D:GLU406 4.6 5.9 1.0 CB D:GLU406 4.7 9.0 1.0 CD2 D:TYR472 4.8 10.2 1.0 OE2 D:GLU384 4.9 10.4 1.0 O D:HOH1220 4.9 6.7 1.0 CD D:GLU350 5.0 3.8 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