Fluorine 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:

Zinc

(Zn)

2 atoms

The binding sites of Fluorine 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 Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Endoplasmic Reticulum Aminopeptidase 2 (ERAP2) in Complex with A Hydroxamic Derivative Ligand, PDB code: 5j6s:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 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 Fluorine with other atoms in the F 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:F1015 b:52.0 occ:0.40 F29 A:6GA1015 0.0 52.0 0.4 C20 A:6GA1015 1.4 50.5 0.4 C21 A:6GA1015 2.4 51.0 0.4 C19 A:6GA1015 2.4 49.7 0.4 OD2 A:ASP198 2.7 53.9 1.0 F29 A:6GA1015 3.1 50.3 0.6 O A:GLU200 3.1 53.7 1.0 C20 A:6GA1015 3.2 51.6 0.6 C19 A:6GA1015 3.2 48.6 0.6 C22 A:6GA1015 3.6 51.5 0.4 CG A:ASP198 3.7 52.5 1.0 C18 A:6GA1015 3.7 47.4 0.4 CG A:PRO333 3.8 45.7 1.0 OD1 A:ASP198 3.9 51.1 1.0 C A:GLU200 4.0 50.0 1.0 C21 A:6GA1015 4.0 52.4 0.6 CB A:GLU200 4.1 41.8 1.0 C18 A:6GA1015 4.1 49.8 0.6 C17 A:6GA1015 4.2 50.0 0.4 SD A:MET336 4.4 34.4 1.0 CB A:PRO333 4.4 44.7 1.0 CA A:GLU200 4.4 47.1 1.0 CD A:PRO333 4.6 45.4 1.0 N A:GLU200 4.6 44.1 1.0 OE1 A:GLU200 4.7 53.6 1.0 C22 A:6GA1015 4.7 49.6 0.6 C17 A:6GA1015 4.8 50.3 0.6 CG A:GLU200 4.8 44.1 1.0

Fluorine binding site 2 out of 3 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 Fluorine with other atoms in the F 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 A:F1015 b:50.3 occ:0.60 F29 A:6GA1015 0.0 50.3 0.6 C20 A:6GA1015 1.3 51.6 0.6 C19 A:6GA1015 2.4 48.6 0.6 C21 A:6GA1015 2.4 52.4 0.6 C21 A:6GA1015 2.5 51.0 0.4 C20 A:6GA1015 2.8 50.5 0.4 F29 A:6GA1015 3.1 52.0 0.4 C22 A:6GA1015 3.2 51.5 0.4 CE2 A:PHE450 3.4 46.8 1.0 C19 A:6GA1015 3.6 49.7 0.4 CG A:GLU200 3.6 44.1 1.0 O A:GLU200 3.6 53.7 1.0 C18 A:6GA1015 3.6 49.8 0.6 CZ A:PHE450 3.6 45.5 1.0 C22 A:6GA1015 3.7 49.6 0.6 OE1 A:GLU200 3.7 53.6 1.0 CD2 A:PHE450 3.8 46.1 1.0 CD A:GLU200 3.8 47.1 1.0 C A:GLU200 3.9 50.0 1.0 CB A:GLU200 3.9 41.8 1.0 C17 A:6GA1015 4.0 50.0 0.4 C18 A:6GA1015 4.1 47.4 0.4 CD A:PRO201 4.1 43.5 1.0 C17 A:6GA1015 4.2 50.3 0.6 CE1 A:PHE450 4.2 43.1 1.0 N A:PRO201 4.2 45.6 1.0 CG A:PHE450 4.3 39.8 1.0 CD1 A:PHE450 4.5 41.1 1.0 CG A:PRO201 4.5 39.1 1.0 CA A:GLU200 4.5 47.1 1.0 OE2 A:GLU200 4.6 53.8 1.0 OH A:TYR892 4.8 48.1 0.5

Fluorine binding site 3 out of 3 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 Fluorine with other atoms in the F binding site number 3 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:F1015 b:74.5 occ:0.87 F29 B:6GA1015 0.0 74.5 0.9 C20 B:6GA1015 1.4 75.1 0.9 O B:GLU200 2.3 58.8 1.0 C19 B:6GA1015 2.4 70.8 0.9 C21 B:6GA1015 2.4 79.2 0.9 OD1 B:ASP198 3.1 57.1 1.0 C B:GLU200 3.3 61.3 1.0 C18 B:6GA1015 3.6 68.5 0.9 C22 B:6GA1015 3.7 77.9 0.9 CB B:GLU200 3.8 60.6 1.0 CA B:GLU200 3.9 66.0 1.0 CG B:PRO333 4.0 55.8 1.0 N B:GLU200 4.0 61.9 1.0 C17 B:6GA1015 4.1 74.3 0.9 CG B:ASP198 4.2 54.3 1.0 OE1 B:GLN203 4.4 66.7 1.0 N B:PRO201 4.4 60.6 1.0 OD2 B:ASP198 4.5 53.6 1.0 CD B:PRO201 4.6 66.8 1.0 CG B:GLU200 4.6 63.4 1.0 OE1 B:GLU200 4.9 61.4 1.0 NE2 B:GLN203 4.9 73.9 1.0 SD B:MET336 5.0 53.4 1.0 CD B:PRO333 5.0 53.6 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