Zinc in PDB 5k1v: Crystal Structure of Endoplasmic Reticulum Aminopeptidase 2 (ERAP2) in Complex with A Diaminobenzoic Acid Derivative Ligand.

The structure of Crystal Structure of Endoplasmic Reticulum Aminopeptidase 2 (ERAP2) in Complex with A Diaminobenzoic Acid Derivative Ligand., PDB code: 5k1v was solved by E.Saridakis, A.Papakyriakou, P.Giastas, A.Mpakali, I.M.Mavridis, E.Stratikos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.35 / 2.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.403, 135.171, 127.489, 90.00, 90.15, 90.00
R / Rfree (%)	20.5 / 27.3

The binding sites of Zinc atom in the Crystal Structure of Endoplasmic Reticulum Aminopeptidase 2 (ERAP2) in Complex with A Diaminobenzoic Acid Derivative Ligand. (pdb code 5k1v). 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 Diaminobenzoic Acid Derivative Ligand., PDB code: 5k1v:
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 Diaminobenzoic Acid 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 Diaminobenzoic Acid Derivative Ligand. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:33.0 occ:1.00 OE1 A:GLU393 1.9 36.8 1.0 O1 A:6PX1002 2.0 38.6 1.0 NE2 A:HIS370 2.0 31.1 1.0 NE2 A:HIS374 2.1 29.6 1.0 OE2 A:GLU393 2.5 35.5 1.0 CD A:GLU393 2.5 33.5 1.0 C2 A:6PX1002 2.8 58.4 1.0 CD2 A:HIS370 2.9 30.9 1.0 CD2 A:HIS374 3.0 34.6 1.0 CE1 A:HIS370 3.1 28.3 1.0 CE1 A:HIS374 3.1 41.2 1.0 N1 A:6PX1002 3.2 64.6 1.0 C1 A:6PX1002 3.6 74.7 1.0 OH A:TYR455 3.8 51.0 1.0 N5 A:6PX1002 3.8 61.6 1.0 CE2 A:TYR455 3.9 52.4 1.0 CG A:GLU393 4.0 32.9 1.0 CG A:HIS370 4.1 31.1 1.0 ND1 A:HIS370 4.1 31.2 1.0 CZ A:TYR455 4.2 50.2 1.0 CG A:HIS374 4.2 34.9 1.0 ND1 A:HIS374 4.2 39.5 1.0 C8 A:6PX1002 4.3 65.6 1.0 NZ A:LYS392 4.5 49.4 1.0 OE2 A:GLU371 4.6 36.7 1.0 CB A:ALA396 4.6 29.2 1.0 OE1 A:GLU337 4.6 44.8 1.0 N6 A:6PX1002 4.7 65.8 1.0 CB A:GLU393 4.7 33.5 1.0 C9 A:6PX1002 4.7 58.9 1.0 CA A:GLU393 4.7 37.5 1.0 C3 A:6PX1002 4.8 60.8 1.0 CD2 A:TYR455 4.9 42.4 1.0 C13 A:6PX1002 5.0 76.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Endoplasmic Reticulum Aminopeptidase 2 (ERAP2) in Complex with A Diaminobenzoic Acid 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 Diaminobenzoic Acid Derivative Ligand. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:54.3 occ:1.00 OE1 B:GLU393 2.0 50.5 1.0 NE2 B:HIS374 2.1 45.3 1.0 NE2 B:HIS370 2.1 50.7 1.0 O B:HOH1114 2.2 44.5 1.0 CD B:GLU393 2.7 58.8 1.0 OE2 B:GLU393 2.7 55.8 1.0 CD2 B:HIS374 2.8 51.5 1.0 CD2 B:HIS370 3.0 49.2 1.0 CE1 B:HIS370 3.1 54.0 1.0 CE1 B:HIS374 3.2 60.3 1.0 OH B:TYR455 3.7 73.7 1.0 CE2 B:TYR455 4.0 66.5 1.0 CG B:HIS374 4.0 55.6 1.0 CG B:GLU393 4.2 64.3 1.0 OE1 B:GLU337 4.2 64.5 1.0 CZ B:TYR455 4.2 68.4 1.0 OE2 B:GLU371 4.2 52.7 1.0 CG B:HIS370 4.2 50.1 1.0 ND1 B:HIS370 4.2 55.4 1.0 ND1 B:HIS374 4.2 65.2 1.0 CB B:ALA396 4.6 61.9 1.0 OE1 B:GLU371 4.6 55.8 1.0 CA B:GLU393 4.7 62.0 1.0 CB B:GLU393 4.7 65.2 1.0 CD B:GLU371 4.8 57.7 1.0 CD B:GLU337 4.9 61.3 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