Zinc in PDB 3se6: Crystal Structure of the Human Endoplasmic Reticulum Aminopeptidase 2

The structure of Crystal Structure of the Human Endoplasmic Reticulum Aminopeptidase 2, PDB code: 3se6 was solved by J.R.Birtley, E.Saridakis, E.Stratikos, I.M.Mavridis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	11.00 / 3.08
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.579, 134.362, 128.009, 90.00, 90.71, 90.00
R / Rfree (%)	21.2 / 27.7

The binding sites of Zinc atom in the Crystal Structure of the Human Endoplasmic Reticulum Aminopeptidase 2 (pdb code 3se6). 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 the Human Endoplasmic Reticulum Aminopeptidase 2, PDB code: 3se6:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Human Endoplasmic Reticulum Aminopeptidase 2


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 the Human Endoplasmic Reticulum Aminopeptidase 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn5000 b:31.1 occ:1.00 OE1 A:GLU393 2.0 40.3 1.0 NE2 A:HIS374 2.1 36.5 1.0 NE2 A:HIS370 2.1 39.9 1.0 OXT A:LYS968 2.1 32.9 1.0 CD A:GLU393 2.8 45.5 1.0 C A:LYS968 2.9 45.4 1.0 OE2 A:GLU393 3.0 46.3 1.0 CE1 A:HIS370 3.0 40.1 1.0 CD2 A:HIS374 3.0 36.8 1.0 CE1 A:HIS374 3.1 40.1 1.0 CD2 A:HIS370 3.2 38.9 1.0 O A:LYS968 3.4 51.6 1.0 N A:LYS968 3.9 37.8 1.0 CA A:LYS968 3.9 46.9 1.0 CE2 A:TYR455 3.9 49.3 1.0 OH A:TYR455 4.0 53.1 1.0 OE2 A:GLU337 4.1 43.0 1.0 CG A:GLU393 4.1 48.0 1.0 ND1 A:HIS370 4.1 44.8 1.0 OE1 A:GLU371 4.2 32.3 1.0 CG A:HIS374 4.2 38.9 1.0 ND1 A:HIS374 4.2 43.1 1.0 CG A:HIS370 4.3 38.7 1.0 CA A:GLU393 4.4 47.3 1.0 CZ A:TYR455 4.4 51.6 1.0 CB A:GLU393 4.4 48.2 1.0 CB A:ALA396 4.5 38.2 1.0 CB A:LYS968 4.8 39.5 1.0 CD2 A:TYR455 4.9 51.4 1.0 CD A:GLU337 4.9 48.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Human Endoplasmic Reticulum Aminopeptidase 2


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 the Human Endoplasmic Reticulum Aminopeptidase 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn6000 b:36.6 occ:1.00 OE1 B:GLU393 2.0 48.0 1.0 NE2 B:HIS374 2.1 38.9 1.0 OXT B:LYS968 2.1 36.0 1.0 NE2 B:HIS370 2.1 43.0 1.0 CD B:GLU393 2.7 50.5 1.0 C B:LYS968 2.7 43.6 1.0 O B:LYS968 2.9 42.1 1.0 CE1 B:HIS370 2.9 43.6 1.0 OE2 B:GLU393 2.9 45.3 1.0 CE1 B:HIS374 3.1 43.9 1.0 CD2 B:HIS374 3.1 38.8 1.0 CD2 B:HIS370 3.2 39.7 1.0 CE2 B:TYR455 3.9 49.9 1.0 CA B:LYS968 4.0 52.9 1.0 CG B:GLU393 4.0 55.9 1.0 OH B:TYR455 4.1 54.1 1.0 N B:LYS968 4.1 52.0 1.0 ND1 B:HIS370 4.1 45.4 1.0 CA B:GLU393 4.2 51.6 1.0 ND1 B:HIS374 4.2 44.9 1.0 CG B:HIS374 4.2 41.5 1.0 CB B:GLU393 4.2 54.0 1.0 CG B:HIS370 4.3 37.2 1.0 OE2 B:GLU337 4.3 51.4 1.0 CB B:ALA396 4.3 38.3 1.0 CZ B:TYR455 4.3 53.1 1.0 OE1 B:GLU371 4.4 32.8 1.0 CD2 B:TYR455 4.8 52.0 1.0 O B:GLU393 4.8 59.7 1.0 CB B:LYS968 4.9 51.5 1.0 O B:ASN392 5.0 52.6 1.0

J.R.Birtley, E.Saridakis, E.Stratikos, I.M.Mavridis. The Crystal Structure of Human Endoplasmic Reticulum Aminopeptidase 2 Reveals the Atomic Basis For Distinct Roles in Antigen Processing. Biochemistry V. 51 286 2012.
ISSN: ISSN 0006-2960
PubMed: 22106953
DOI: 10.1021/BI201230P