Zinc in PDB 4jbs: Crystal Structure of the Human Endoplasmic Reticulum Aminopeptidase 2 in Complex with Phosphinic Pseudotripeptide Inhibitor.

The structure of Crystal Structure of the Human Endoplasmic Reticulum Aminopeptidase 2 in Complex with Phosphinic Pseudotripeptide Inhibitor., PDB code: 4jbs was solved by E.Saridakis, J.Birtley, E.Stratikos, I.M.Mavridis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.99 / 2.79
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	75.150, 134.770, 128.731, 90.00, 90.28, 90.00
R / Rfree (%)	20.6 / 27.8

The binding sites of Zinc atom in the Crystal Structure of the Human Endoplasmic Reticulum Aminopeptidase 2 in Complex with Phosphinic Pseudotripeptide Inhibitor. (pdb code 4jbs). 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 in Complex with Phosphinic Pseudotripeptide Inhibitor., PDB code: 4jbs:
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 in Complex with Phosphinic Pseudotripeptide Inhibitor.


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 in Complex with Phosphinic Pseudotripeptide Inhibitor. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1008 b:25.7 occ:1.00 OE1 A:GLU393 2.0 31.5 1.0 NE2 A:HIS374 2.1 26.0 1.0 NE2 A:HIS370 2.1 28.6 1.0 O2 A:P521009 2.2 29.2 1.0 O1 A:P521009 2.5 25.2 1.0 P1 A:P521009 2.9 31.9 1.0 CD A:GLU393 2.9 31.6 1.0 CE1 A:HIS374 2.9 27.4 1.0 CD2 A:HIS370 2.9 31.1 1.0 OE2 A:GLU393 3.0 30.6 1.0 CE1 A:HIS370 3.1 29.1 1.0 CD2 A:HIS374 3.1 29.9 1.0 CE2 A:TYR455 3.9 26.8 1.0 OH A:TYR455 3.9 28.5 1.0 N1 A:P521009 3.9 26.8 1.0 C9 A:P521009 4.0 33.9 0.6 ND1 A:HIS374 4.1 28.2 1.0 CG A:HIS370 4.1 27.1 1.0 C11 A:P521009 4.1 29.9 1.0 ND1 A:HIS370 4.2 35.5 1.0 CG A:HIS374 4.2 29.2 1.0 CZ A:TYR455 4.3 25.9 1.0 CG A:GLU393 4.3 34.9 1.0 CB A:ALA396 4.4 30.1 1.0 C12 A:P521009 4.4 34.2 1.0 CA A:GLU393 4.6 32.1 1.0 OE2 A:GLU337 4.7 31.5 1.0 C8 A:P521009 4.7 29.0 1.0 CB A:GLU393 4.7 29.5 1.0 OE1 A:GLU371 4.8 28.6 1.0 C16 A:P521009 4.9 37.7 1.0 CD2 A:TYR455 4.9 28.1 1.0 NZ A:LYS392 4.9 20.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Human Endoplasmic Reticulum Aminopeptidase 2 in Complex with Phosphinic Pseudotripeptide Inhibitor.


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 in Complex with Phosphinic Pseudotripeptide Inhibitor. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1009 b:47.4 occ:1.00 NE2 B:HIS374 2.1 38.3 1.0 OE1 B:GLU393 2.1 55.2 1.0 NE2 B:HIS370 2.1 34.9 1.0 O2 B:P521010 2.4 41.1 1.0 OE2 B:GLU393 2.6 41.3 1.0 CD B:GLU393 2.6 54.8 1.0 CD2 B:HIS374 2.8 47.9 1.0 CD2 B:HIS370 3.0 38.3 1.0 O1 B:P521010 3.1 35.3 1.0 CE1 B:HIS370 3.1 42.0 1.0 CE1 B:HIS374 3.2 46.2 1.0 P1 B:P521010 3.2 56.1 1.0 N1 B:P521010 4.0 35.8 1.0 CG B:HIS374 4.0 50.1 1.0 C16 B:P521010 4.0 41.7 0.3 CG B:GLU393 4.1 68.4 1.0 ND1 B:HIS374 4.2 59.9 1.0 CB B:ALA396 4.2 51.6 1.0 CG B:HIS370 4.2 42.7 1.0 ND1 B:HIS370 4.2 53.0 1.0 CE2 B:TYR455 4.2 63.9 1.0 C9 B:P521010 4.2 46.6 0.7 OH B:TYR455 4.3 56.1 1.0 OE1 B:GLU371 4.5 37.6 1.0 CA B:GLU393 4.5 41.6 1.0 C11 B:P521010 4.6 46.4 1.0 CZ B:TYR455 4.6 64.4 1.0 OE2 B:GLU337 4.6 42.1 1.0 CB B:GLU393 4.7 52.1 1.0 C12 B:P521010 4.8 44.0 1.0 C8 B:P521010 5.0 50.7 1.0 NZ B:LYS392 5.0 42.3 1.0

E.Zervoudi, E.Saridakis, J.R.Birtley, S.S.Seregin, E.Reeves, P.Kokkala, Y.A.Aldhamen, A.Amalfitano, I.M.Mavridis, E.James, D.Georgiadis, E.Stratikos. Rationally Designed Inhibitor Targeting Antigen-Trimming Aminopeptidases Enhances Antigen Presentation and Cytotoxic T-Cell Responses. Proc.Natl.Acad.Sci.Usa V. 110 19890 2013.
ISSN: ISSN 0027-8424
PubMed: 24248368
DOI: 10.1073/PNAS.1309781110