Zinc in PDB 2yd0: Crystal Structure of the Soluble Domain of Human Endoplasmic Reticulum Aminopeptidase 1 ERAP1

The structure of Crystal Structure of the Soluble Domain of Human Endoplasmic Reticulum Aminopeptidase 1 ERAP1, PDB code: 2yd0 was solved by M.Vollmar, G.Kochan, T.Krojer, E.Ugochukwu, J.R.C.Muniz, J.Raynor, A.Chaikuad, C.Allerston, F.Von Delft, C.Bountra, C.H.Arrowsmith, J.Weigelt, A.Edwards, S.Knapp, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.94 / 2.70
Space group	P 6 2 2
Cell size a, b, c (Å), α, β, γ (°)	200.948, 200.948, 114.222, 90.00, 90.00, 120.00
R / Rfree (%)	15.2 / 21.5

The structure of Crystal Structure of the Soluble Domain of Human Endoplasmic Reticulum Aminopeptidase 1 ERAP1 also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of the Soluble Domain of Human Endoplasmic Reticulum Aminopeptidase 1 ERAP1 (pdb code 2yd0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of the Soluble Domain of Human Endoplasmic Reticulum Aminopeptidase 1 ERAP1, PDB code: 2yd0:

Zinc binding site 1 out of 1 in the Crystal Structure of the Soluble Domain of Human Endoplasmic Reticulum Aminopeptidase 1 ERAP1


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 Soluble Domain of Human Endoplasmic Reticulum Aminopeptidase 1 ERAP1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1946 b:25.9 occ:1.00 O2 A:BES1950 1.9 66.3 1.0 O3 A:BES1950 1.9 48.0 1.0 OE1 A:GLU376 2.0 19.2 1.0 NE2 A:HIS357 2.1 15.9 1.0 NE2 A:HIS353 2.1 18.3 1.0 C3 A:BES1950 2.6 51.5 1.0 CD A:GLU376 2.7 18.4 1.0 C2 A:BES1950 2.8 58.7 1.0 OE2 A:GLU376 2.8 26.5 1.0 CD2 A:HIS353 3.1 15.2 1.0 CE1 A:HIS357 3.1 12.8 1.0 CD2 A:HIS357 3.1 12.9 1.0 CE1 A:HIS353 3.1 17.4 1.0 C1 A:BES1950 3.5 30.7 1.0 N1 A:BES1950 3.8 46.5 1.0 N2 A:BES1950 3.8 8.2 1.0 CE2 A:TYR438 3.9 18.1 1.0 OH A:TYR438 3.9 14.2 1.0 CG A:GLU376 4.2 18.2 1.0 ND1 A:HIS357 4.2 13.9 1.0 ND1 A:HIS353 4.2 13.6 1.0 CG A:HIS353 4.2 9.0 1.0 CG A:HIS357 4.2 13.1 1.0 CZ A:TYR438 4.2 18.9 1.0 CB A:ALA379 4.3 13.5 1.0 OE1 A:GLU320 4.4 20.1 1.0 C4 A:BES1950 4.5 65.9 1.0 CA A:GLU376 4.6 12.6 1.0 OE2 A:GLU354 4.6 19.0 1.0 CB A:GLU376 4.7 17.3 1.0 CD2 A:TYR438 4.9 14.7 1.0 C6 A:BES1950 4.9 52.5 1.0 OE2 A:GLU320 4.9 17.6 1.0 CD A:GLU320 4.9 20.6 1.0 O A:HOH2056 5.0 13.3 1.0

G.Kochan, T.Krojer, D.Harvey, R.Fischer, L.Chen, M.Vollmar, F.Von Delft, K.L.Kavanagh, M.A.Brown, P.Bowness, P.Wordsworth, B.M.Kessler, U.Oppermann. Crystal Structures of the Endoplasmic Reticulum Aminopeptidase-1 (ERAP1) Reveal the Molecular Basis For N-Terminal Peptide Trimming. Proc.Natl.Acad.Sci.Usa V. 108 7745 2011.
ISSN: ISSN 0027-8424
PubMed: 21508329
DOI: 10.1073/PNAS.1101262108