Zinc in PDB 5ab2: Crystal Structure of Aminopeptidase ERAP2 with Ligand

The structure of Crystal Structure of Aminopeptidase ERAP2 with Ligand, PDB code: 5ab2 was solved by A.Mpakali, P.Giastas, E.Saridakis, I.M.Mavridis, E.Stratikos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.01 / 2.73
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	75.650, 135.465, 128.212, 90.00, 90.24, 90.00
R / Rfree (%)	22.3 / 28.6

The binding sites of Zinc atom in the Crystal Structure of Aminopeptidase ERAP2 with Ligand (pdb code 5ab2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Aminopeptidase ERAP2 with Ligand, PDB code: 5ab2:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Aminopeptidase ERAP2 with Ligand


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 Aminopeptidase ERAP2 with Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1119 b:29.0 occ:1.00 OE1 A:GLU393 2.0 37.9 1.0 O C:GLY1 2.0 39.4 1.0 NE2 A:HIS370 2.1 22.5 1.0 NE2 A:HIS374 2.1 33.5 1.0 C C:GLY1 2.4 41.0 1.0 CA C:GLY1 2.8 52.9 1.0 CD A:GLU393 2.9 36.2 1.0 CD2 A:HIS370 3.0 28.4 1.0 CD2 A:HIS374 3.0 31.8 1.0 CE1 A:HIS370 3.1 28.9 1.0 CE1 A:HIS374 3.1 36.2 1.0 OE2 A:GLU393 3.2 41.6 1.0 N C:PRO2 3.3 48.0 0.5 O C:PRO2 3.3 48.1 0.5 N C:PRO2 3.4 48.1 0.5 N C:GLY1 3.7 36.4 1.0 CD C:PRO2 3.8 44.9 0.5 CE2 A:TYR455 3.9 42.8 1.0 OH A:TYR455 4.0 49.8 1.0 ND1 A:HIS370 4.2 25.3 1.0 ND1 A:HIS374 4.2 29.0 1.0 CG A:HIS370 4.2 28.6 1.0 CG A:HIS374 4.2 29.5 1.0 C C:PRO2 4.2 44.4 0.5 CG A:GLU393 4.3 31.8 1.0 CA C:PRO2 4.3 45.2 0.5 CZ A:TYR455 4.3 45.2 1.0 CD C:PRO2 4.4 50.4 0.5 CA C:PRO2 4.4 50.8 0.5 CB A:ALA396 4.5 31.4 1.0 CB A:GLU393 4.6 30.8 1.0 CA A:GLU393 4.6 31.3 1.0 OE2 A:GLU371 4.6 34.7 1.0 OE1 A:GLU337 4.7 34.3 1.0 CD2 A:TYR455 4.8 43.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Aminopeptidase ERAP2 with Ligand


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Aminopeptidase ERAP2 with Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1119 b:60.8 occ:1.00 NE2 B:HIS370 2.0 49.0 1.0 NE2 B:HIS374 2.0 66.2 1.0 OE1 B:GLU393 2.0 78.0 1.0 O D:GLY1 2.0 74.5 0.8 OE2 B:GLU393 2.5 64.1 1.0 CD B:GLU393 2.6 70.7 1.0 C D:GLY1 2.6 74.5 0.8 CD2 B:HIS374 2.8 61.4 1.0 CE1 B:HIS370 3.0 60.8 1.0 CD2 B:HIS370 3.0 58.1 1.0 CA D:GLY1 3.2 78.8 0.8 CE1 B:HIS374 3.2 66.5 1.0 N D:PRO2 3.5 74.2 0.8 CD D:PRO2 3.8 70.7 0.8 OE1 B:GLU337 4.0 72.7 1.0 N D:GLY1 4.0 69.9 0.8 CG B:HIS374 4.0 67.3 1.0 ND1 B:HIS370 4.1 66.9 1.0 CG B:GLU393 4.1 74.9 1.0 CG B:HIS370 4.1 56.3 1.0 ND1 B:HIS374 4.2 73.6 1.0 CB B:ALA396 4.3 68.4 1.0 CE2 B:TYR455 4.4 77.5 1.0 OH B:TYR455 4.4 85.5 1.0 OE2 B:GLU371 4.5 53.0 1.0 CA B:GLU393 4.6 71.0 1.0 CB B:GLU393 4.7 73.9 1.0 CZ B:TYR455 4.7 80.5 1.0 CA D:PRO2 4.7 83.0 0.8 CD B:GLU337 4.8 69.7 1.0

A.Mpakali, P.Giastas, N.Mathioudakis, I.M.Mavridis, E.Saridakis, E.Stratikos. Structural Basis For Antigenic Peptide Recognition and Processing By Endoplasmic Reticulum (Er) Aminopeptidase 2. J.Biol.Chem. V. 290 26021 2015.
ISSN: ISSN 0021-9258
PubMed: 26381406
DOI: 10.1074/JBC.M115.685909