Zinc in PDB 7p7p: Crystal Structure of ERAP2 Aminopeptidase in Complex with Phosphinic Pseudotripeptide((1R)-1-Amino-3-Phenylpropyl){(2S)-3-[((2S)-1-Amino- 1-Oxo-3-Phenylpropan-2-Yl)Amino]-2-{[3-(2-Hydroxyphenyl)-Isoxazol-5- Yl]Methyl}-3-Oxopropyl}Phosphinic Acid

The structure of Crystal Structure of ERAP2 Aminopeptidase in Complex with Phosphinic Pseudotripeptide((1R)-1-Amino-3-Phenylpropyl){(2S)-3-[((2S)-1-Amino- 1-Oxo-3-Phenylpropan-2-Yl)Amino]-2-{[3-(2-Hydroxyphenyl)-Isoxazol-5- Yl]Methyl}-3-Oxopropyl}Phosphinic Acid, PDB code: 7p7p 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)	50.19 / 3.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	75.342, 134.618, 129.137, 90, 90.48, 90
R / Rfree (%)	18 / 23.1

The binding sites of Zinc atom in the Crystal Structure of ERAP2 Aminopeptidase in Complex with Phosphinic Pseudotripeptide((1R)-1-Amino-3-Phenylpropyl){(2S)-3-[((2S)-1-Amino- 1-Oxo-3-Phenylpropan-2-Yl)Amino]-2-{[3-(2-Hydroxyphenyl)-Isoxazol-5- Yl]Methyl}-3-Oxopropyl}Phosphinic Acid (pdb code 7p7p). 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){(2S)-3-[((2S)-1-Amino- 1-Oxo-3-Phenylpropan-2-Yl)Amino]-2-{[3-(2-Hydroxyphenyl)-Isoxazol-5- Yl]Methyl}-3-Oxopropyl}Phosphinic Acid, PDB code: 7p7p:
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){(2S)-3-[((2S)-1-Amino- 1-Oxo-3-Phenylpropan-2-Yl)Amino]-2-{[3-(2-Hydroxyphenyl)-Isoxazol-5- Yl]Methyl}-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){(2S)-3-[((2S)-1-Amino- 1-Oxo-3-Phenylpropan-2-Yl)Amino]-2-{[3-(2-Hydroxyphenyl)-Isoxazol-5- Yl]Methyl}-3-Oxopropyl}Phosphinic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1119 b:45.3 occ:1.00 OE2 A:GLU393 1.8 42.1 1.0 NE2 A:HIS370 2.0 45.5 1.0 NE2 A:HIS374 2.0 38.3 1.0 O13 A:62S1101 2.0 44.6 1.0 O12 A:62S1101 2.4 61.1 1.0 H131 A:62S1101 2.7 53.7 1.0 CE1 A:HIS374 2.8 39.9 1.0 P11 A:62S1101 2.8 49.3 1.0 CD A:GLU393 2.9 50.6 1.0 CE1 A:HIS370 2.9 41.9 1.0 CD2 A:HIS370 2.9 41.9 1.0 H162 A:62S1101 3.1 135.5 1.0 CD2 A:HIS374 3.1 38.8 1.0 OE1 A:GLU393 3.3 46.6 1.0 CE2 A:TYR455 3.9 46.9 1.0 OH A:TYR455 3.9 44.3 1.0 ND1 A:HIS374 4.0 40.9 1.0 ND1 A:HIS370 4.0 41.3 1.0 C16 A:62S1101 4.1 112.7 1.0 CG A:HIS370 4.1 37.3 1.0 C09 A:62S1101 4.1 72.6 1.0 H1 A:62S1101 4.1 118.7 1.0 N10 A:62S1101 4.1 98.8 1.0 CG A:HIS374 4.2 42.7 1.0 CG A:GLU393 4.2 54.9 1.0 C14 A:62S1101 4.3 65.8 1.0 CB A:ALA396 4.3 35.0 1.0 OE2 A:GLU337 4.3 64.5 1.0 CZ A:TYR455 4.4 43.3 1.0 H141 A:62S1101 4.4 79.1 1.0 CA A:GLU393 4.4 38.4 1.0 CB A:GLU393 4.5 43.0 1.0 H082 A:62S1101 4.5 56.5 1.0 H161 A:62S1101 4.5 135.5 1.0 OE1 A:GLU371 4.6 48.1 1.0 C15 A:62S1101 4.8 81.2 1.0 C17 A:62S1101 4.8 126.7 1.0 H091 A:62S1101 4.8 87.3 1.0 C08 A:62S1101 4.9 46.9 1.0 CD2 A:TYR455 4.9 52.0 1.0 O A:HOH1201 5.0 39.6 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){(2S)-3-[((2S)-1-Amino- 1-Oxo-3-Phenylpropan-2-Yl)Amino]-2-{[3-(2-Hydroxyphenyl)-Isoxazol-5- Yl]Methyl}-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){(2S)-3-[((2S)-1-Amino- 1-Oxo-3-Phenylpropan-2-Yl)Amino]-2-{[3-(2-Hydroxyphenyl)-Isoxazol-5- Yl]Methyl}-3-Oxopropyl}Phosphinic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1509 b:66.8 occ:1.00 OE1 B:GLU393 2.0 82.3 1.0 NE2 B:HIS370 2.0 70.3 1.0 NE2 B:HIS374 2.0 59.4 1.0 O13 B:62S1501 2.2 87.0 1.0 O12 B:62S1501 2.4 100.3 1.0 H131 B:62S1501 2.4 104.6 1.0 P11 B:62S1501 2.8 94.2 1.0 CD B:GLU393 2.8 80.5 1.0 CD2 B:HIS370 2.9 64.8 1.0 CE1 B:HIS374 3.0 66.5 1.0 OE2 B:GLU393 3.0 70.2 1.0 CD2 B:HIS374 3.0 59.4 1.0 CE1 B:HIS370 3.0 69.8 1.0 H151 B:62S1501 3.6 122.8 1.0 H1 B:62S1501 3.9 91.9 1.0 N10 B:62S1501 4.0 76.4 1.0 C09 B:62S1501 4.0 70.0 1.0 CG B:HIS370 4.1 67.9 1.0 ND1 B:HIS370 4.1 73.0 1.0 ND1 B:HIS374 4.1 70.7 1.0 CG B:HIS374 4.1 61.7 1.0 CE2 B:TYR455 4.1 57.9 1.0 C14 B:62S1501 4.1 101.5 1.0 CB B:ALA396 4.2 68.5 1.0 CG B:GLU393 4.2 78.9 1.0 H141 B:62S1501 4.2 122.0 1.0 OH B:TYR455 4.4 59.7 1.0 H161 B:62S1501 4.4 145.8 1.0 H082 B:62S1501 4.4 86.5 1.0 C15 B:62S1501 4.5 102.2 1.0 CA B:GLU393 4.5 55.3 1.0 OE1 B:GLU337 4.6 72.3 1.0 CZ B:TYR455 4.6 54.5 1.0 OE1 B:GLU371 4.7 76.1 1.0 CB B:GLU393 4.7 57.1 1.0 H091 B:62S1501 4.7 84.3 1.0 C08 B:62S1501 4.8 71.9 1.0 H101 B:62S1501 4.9 91.9 1.0 CD2 B:TYR455 5.0 59.1 1.0 H142 B:62S1501 5.0 122.0 1.0 C16 B:62S1501 5.0 121.3 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