Zinc in PDB 7pfs: Crystal Structure of ERAP2 Aminopeptidase in Complex with Phosphinic Pseudotripeptide ((1R)-1-Amino-3-Phenylpropyl){2-([1,1:3,1- Terphenyl]-5-Ylmethyl)-3-[((2S)-1-Amino-1-Oxo-3-Phenylpropan-2-Yl)- Amino]-3-Oxopropyl}Phosphinic Acid

The structure of Crystal Structure of ERAP2 Aminopeptidase in Complex with Phosphinic Pseudotripeptide ((1R)-1-Amino-3-Phenylpropyl){2-([1,1:3,1- Terphenyl]-5-Ylmethyl)-3-[((2S)-1-Amino-1-Oxo-3-Phenylpropan-2-Yl)- Amino]-3-Oxopropyl}Phosphinic Acid, PDB code: 7pfs was solved by P.Giastas, E.Stratikos, A.Mpakali, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	65.03 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	75.135, 133.822, 128.703, 90, 90.29, 90
R / Rfree (%)	18.8 / 23.8

The binding sites of Zinc atom in the Crystal Structure of ERAP2 Aminopeptidase in Complex with Phosphinic Pseudotripeptide ((1R)-1-Amino-3-Phenylpropyl){2-([1,1:3,1- Terphenyl]-5-Ylmethyl)-3-[((2S)-1-Amino-1-Oxo-3-Phenylpropan-2-Yl)- Amino]-3-Oxopropyl}Phosphinic Acid (pdb code 7pfs). 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 ERAP2 Aminopeptidase in Complex with Phosphinic Pseudotripeptide ((1R)-1-Amino-3-Phenylpropyl){2-([1,1:3,1- Terphenyl]-5-Ylmethyl)-3-[((2S)-1-Amino-1-Oxo-3-Phenylpropan-2-Yl)- Amino]-3-Oxopropyl}Phosphinic Acid, PDB code: 7pfs:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of ERAP2 Aminopeptidase in Complex with Phosphinic Pseudotripeptide ((1R)-1-Amino-3-Phenylpropyl){2-([1,1:3,1- Terphenyl]-5-Ylmethyl)-3-[((2S)-1-Amino-1-Oxo-3-Phenylpropan-2-Yl)- Amino]-3-Oxopropyl}Phosphinic Acid


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 ERAP2 Aminopeptidase in Complex with Phosphinic Pseudotripeptide ((1R)-1-Amino-3-Phenylpropyl){2-([1,1:3,1- Terphenyl]-5-Ylmethyl)-3-[((2S)-1-Amino-1-Oxo-3-Phenylpropan-2-Yl)- Amino]-3-Oxopropyl}Phosphinic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1011 b:53.0 occ:1.00 OE2 A:GLU393 1.7 55.5 1.0 O37 A:7OO1006 2.0 56.6 1.0 NE2 A:HIS370 2.0 52.2 1.0 NE2 A:HIS374 2.1 37.3 1.0 O04 A:7OO1006 2.1 69.8 1.0 CD A:GLU393 2.3 40.5 1.0 OE1 A:GLU393 2.3 48.5 1.0 P03 A:7OO1006 2.5 77.2 1.0 H011 A:7OO1006 2.7 97.9 1.0 H041 A:7OO1006 2.8 84.0 1.0 CD2 A:HIS370 2.9 49.0 1.0 CD2 A:HIS374 3.0 38.9 1.0 CE1 A:HIS370 3.1 52.8 1.0 CE1 A:HIS374 3.1 46.2 1.0 N01 A:7OO1006 3.4 81.3 1.0 C02 A:7OO1006 3.8 66.9 1.0 CG A:GLU393 3.8 34.4 1.0 CE2 A:TYR455 3.9 29.8 1.0 C05 A:7OO1006 4.0 59.5 1.0 OH A:TYR455 4.0 37.9 1.0 H061 A:7OO1006 4.0 73.6 1.0 H052 A:7OO1006 4.1 71.7 1.0 CG A:HIS370 4.1 41.8 1.0 ND1 A:HIS370 4.1 45.1 1.0 CG A:HIS374 4.2 43.9 1.0 ND1 A:HIS374 4.2 38.8 1.0 H1 A:7OO1006 4.2 97.9 1.0 CZ A:TYR455 4.4 34.8 1.0 H021 A:7OO1006 4.4 80.7 1.0 CB A:ALA396 4.5 43.5 1.0 OE1 A:GLU337 4.5 62.0 1.0 C06 A:7OO1006 4.6 61.1 1.0 CB A:GLU393 4.6 33.1 1.0 CA A:GLU393 4.6 36.0 1.0 H382 A:7OO1006 4.7 80.2 1.0 OE1 A:GLU371 4.7 47.4 1.0 H051 A:7OO1006 4.7 71.7 1.0 OE2 A:GLU371 4.8 50.8 1.0 C38 A:7OO1006 4.8 66.6 1.0 O A:HOH1114 4.8 41.0 1.0 CD2 A:TYR455 4.9 27.4 1.0 H181 A:7OO1006 5.0 79.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of ERAP2 Aminopeptidase in Complex with Phosphinic Pseudotripeptide ((1R)-1-Amino-3-Phenylpropyl){2-([1,1:3,1- Terphenyl]-5-Ylmethyl)-3-[((2S)-1-Amino-1-Oxo-3-Phenylpropan-2-Yl)- Amino]-3-Oxopropyl}Phosphinic Acid


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 ERAP2 Aminopeptidase in Complex with Phosphinic Pseudotripeptide ((1R)-1-Amino-3-Phenylpropyl){2-([1,1:3,1- Terphenyl]-5-Ylmethyl)-3-[((2S)-1-Amino-1-Oxo-3-Phenylpropan-2-Yl)- Amino]-3-Oxopropyl}Phosphinic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2305 b:65.5 occ:1.00 H041 B:7OO2301 1.7 99.7 1.0 OE1 B:GLU393 2.0 58.9 1.0 NE2 B:HIS374 2.0 54.5 1.0 NE2 B:HIS370 2.0 57.8 1.0 O37 B:7OO2301 2.1 79.1 1.0 O04 B:7OO2301 2.2 82.8 1.0 OE2 B:GLU393 2.5 58.8 1.0 CD B:GLU393 2.5 54.3 1.0 P03 B:7OO2301 2.6 60.2 1.0 CD2 B:HIS370 2.8 54.8 1.0 CD2 B:HIS374 3.0 44.8 1.0 CE1 B:HIS374 3.0 54.3 1.0 CE1 B:HIS370 3.2 59.2 1.0 H011 B:7OO2301 3.4 103.4 1.0 N01 B:7OO2301 3.7 85.9 1.0 C02 B:7OO2301 3.9 67.1 1.0 CG B:GLU393 4.0 52.7 1.0 CG B:HIS370 4.0 52.0 1.0 OH B:TYR455 4.1 71.9 1.0 CE2 B:TYR455 4.1 70.8 1.0 CG B:HIS374 4.1 50.8 1.0 ND1 B:HIS374 4.1 52.1 1.0 C05 B:7OO2301 4.1 57.6 1.0 ND1 B:HIS370 4.2 55.6 1.0 CB B:ALA396 4.3 82.4 1.0 H052 B:7OO2301 4.3 69.4 1.0 H061 B:7OO2301 4.3 81.5 1.0 H382 B:7OO2301 4.4 77.3 1.0 OE2 B:GLU371 4.4 83.7 1.0 CZ B:TYR455 4.4 70.7 1.0 C38 B:7OO2301 4.6 64.2 1.0 H381 B:7OO2301 4.6 77.3 1.0 H1 B:7OO2301 4.6 103.4 1.0 H021 B:7OO2301 4.7 80.9 1.0 CB B:GLU393 4.8 51.7 1.0 C06 B:7OO2301 4.8 67.7 1.0 CA B:GLU393 4.8 46.3 1.0 H051 B:7OO2301 4.9 69.4 1.0 O B:HOH2401 5.0 66.0 1.0

A.Mpakali, D.Georgiadis, E.Stratikos, P.Giastas. Inhibitor-Dependent Usage of the S1' Specificity Pocket of Er Aminopeptidase 2. Acs Med.Chem.Lett. V. 13 218 2022.
ISSN: ISSN 1948-5875
PubMed: 35178178
DOI: 10.1021/ACSMEDCHEMLETT.1C00582