Zinc in PDB 5j6s: Crystal Structure of Endoplasmic Reticulum Aminopeptidase 2 (ERAP2) in Complex with A Hydroxamic Derivative Ligand

The structure of Crystal Structure of Endoplasmic Reticulum Aminopeptidase 2 (ERAP2) in Complex with A Hydroxamic Derivative Ligand, PDB code: 5j6s was solved by E.Saridakis, P.Giastas, A.Mpakali, R.Deprez-Poulain, E.Stratikos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	73.51 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.540, 134.330, 127.580, 90.00, 91.71, 90.00
R / Rfree (%)	20.5 / 27.6

The structure of Crystal Structure of Endoplasmic Reticulum Aminopeptidase 2 (ERAP2) in Complex with A Hydroxamic Derivative Ligand also contains other interesting chemical elements:

Fluorine

(F)

3 atoms

The binding sites of Zinc atom in the Crystal Structure of Endoplasmic Reticulum Aminopeptidase 2 (ERAP2) in Complex with A Hydroxamic Derivative Ligand (pdb code 5j6s). 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 Endoplasmic Reticulum Aminopeptidase 2 (ERAP2) in Complex with A Hydroxamic Derivative Ligand, PDB code: 5j6s:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Endoplasmic Reticulum Aminopeptidase 2 (ERAP2) in Complex with A Hydroxamic Derivative 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 Endoplasmic Reticulum Aminopeptidase 2 (ERAP2) in Complex with A Hydroxamic Derivative Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:37.5 occ:1.00 OE2 A:GLU393 2.0 41.5 1.0 O2 A:6GA1015 2.0 41.5 0.4 O15 A:6GA1015 2.0 46.8 0.4 NE2 A:HIS374 2.1 36.6 1.0 NE2 A:HIS370 2.1 43.6 1.0 OE1 A:GLU393 2.1 49.3 1.0 O2 A:6GA1015 2.2 45.6 0.6 CD A:GLU393 2.4 43.1 1.0 O15 A:6GA1015 2.6 48.2 0.6 C12 A:6GA1015 2.7 45.1 0.4 N1 A:6GA1015 2.8 46.0 0.4 CD2 A:HIS374 2.9 38.3 1.0 CD2 A:HIS370 2.9 37.1 1.0 N1 A:6GA1015 3.1 44.7 0.6 CE1 A:HIS370 3.1 37.9 1.0 CE1 A:HIS374 3.1 40.4 1.0 C12 A:6GA1015 3.2 46.5 0.6 CG A:GLU393 3.9 45.0 1.0 CG A:HIS370 4.1 38.7 1.0 CE2 A:TYR455 4.1 46.2 1.0 CG A:HIS374 4.1 42.7 1.0 ND1 A:HIS370 4.2 36.9 1.0 OH A:TYR455 4.2 45.5 1.0 C11 A:6GA1015 4.2 47.0 0.4 ND1 A:HIS374 4.2 42.8 1.0 OE1 A:GLU337 4.4 44.1 1.0 CB A:ALA396 4.5 40.6 1.0 CZ A:TYR455 4.5 49.1 1.0 O10 A:6GA1015 4.6 47.1 0.4 C11 A:6GA1015 4.7 48.7 0.6 C16 A:6GA1015 4.7 49.6 0.4 OE1 A:GLU371 4.8 43.3 1.0 CB A:GLU393 4.8 42.5 1.0 CA A:GLU393 4.8 46.2 1.0 C9 A:6GA1015 4.8 47.8 0.4

Zinc binding site 2 out of 2 in the Crystal Structure of Endoplasmic Reticulum Aminopeptidase 2 (ERAP2) in Complex with A Hydroxamic Derivative 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 Endoplasmic Reticulum Aminopeptidase 2 (ERAP2) in Complex with A Hydroxamic Derivative Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:54.6 occ:1.00 OE1 B:GLU393 2.0 64.5 1.0 NE2 B:HIS370 2.1 52.5 1.0 NE2 B:HIS374 2.1 58.4 1.0 OE2 B:GLU393 2.2 57.7 1.0 O2 B:6GA1015 2.2 67.9 0.9 O15 B:6GA1015 2.2 67.5 0.9 CD B:GLU393 2.4 63.5 1.0 CE1 B:HIS370 2.8 54.2 1.0 CD2 B:HIS374 2.8 57.1 1.0 C12 B:6GA1015 3.1 66.6 0.9 N1 B:6GA1015 3.1 65.2 0.9 CD2 B:HIS370 3.2 54.8 1.0 CE1 B:HIS374 3.2 58.6 1.0 CG B:GLU393 3.9 62.6 1.0 ND1 B:HIS370 4.0 55.6 1.0 OH B:TYR455 4.0 67.1 1.0 OE1 B:GLU337 4.1 63.2 1.0 CG B:HIS374 4.1 56.5 1.0 CE2 B:TYR455 4.2 62.8 1.0 ND1 B:HIS374 4.2 60.4 1.0 CG B:HIS370 4.2 48.4 1.0 OE1 B:GLU371 4.4 55.0 1.0 CZ B:TYR455 4.4 61.9 1.0 CB B:ALA396 4.4 60.5 1.0 C11 B:6GA1015 4.6 74.3 0.9 CB B:GLU393 4.7 65.0 1.0 CA B:GLU393 4.7 62.8 1.0 CD B:GLU337 4.9 66.9 1.0

A.Mpakali, P.Giastas, R.Deprez-Poulain, A.Papakyriakou, D.Koumantou, R.Gealageas, S.Tsoukalidou, D.Vourloumis, I.M.Mavridis, E.Stratikos, E.Saridakis. Crystal Structures of ERAP2 Complexed with Inhibitors Reveal Pharmacophore Requirements For Optimizing Inhibitor Potency. Acs Med Chem Lett V. 8 333 2017.
ISSN: ISSN 1948-5875
PubMed: 28337326
DOI: 10.1021/ACSMEDCHEMLETT.6B00505