Zinc in PDB 3mdj: Er Aminopeptidase, ERAP1, Bound to the Zinc Aminopeptidase Inhibitor, Bestatin

The structure of Er Aminopeptidase, ERAP1, Bound to the Zinc Aminopeptidase Inhibitor, Bestatin, PDB code: 3mdj was solved by T.T.Nguyen, L.J.Stern, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.11 / 2.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	71.029, 234.635, 95.860, 90.00, 103.59, 90.00
R / Rfree (%)	19.9 / 26.4

The binding sites of Zinc atom in the Er Aminopeptidase, ERAP1, Bound to the Zinc Aminopeptidase Inhibitor, Bestatin (pdb code 3mdj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Er Aminopeptidase, ERAP1, Bound to the Zinc Aminopeptidase Inhibitor, Bestatin, PDB code: 3mdj:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Er Aminopeptidase, ERAP1, Bound to the Zinc Aminopeptidase Inhibitor, Bestatin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Er Aminopeptidase, ERAP1, Bound to the Zinc Aminopeptidase Inhibitor, Bestatin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1000 b:40.5 occ:1.00 NE2 A:HIS353 2.1 20.9 1.0 OE1 A:GLU376 2.1 40.9 1.0 NE2 A:HIS357 2.2 34.5 1.0 O2 A:BES1001 2.2 0.5 1.0 OE2 A:GLU376 2.5 46.3 1.0 CD A:GLU376 2.6 57.0 1.0 CD2 A:HIS357 2.8 31.9 1.0 CD2 A:HIS353 2.9 28.4 1.0 O3 A:BES1001 2.9 1.0 1.0 C2 A:BES1001 3.1 0.9 1.0 CE1 A:HIS353 3.3 46.4 1.0 CE1 A:HIS357 3.4 46.5 1.0 C3 A:BES1001 3.4 0.5 1.0 C1 A:BES1001 3.6 0.8 1.0 CG A:HIS357 4.1 26.1 1.0 N2 A:BES1001 4.1 0.9 1.0 CG A:GLU376 4.1 44.3 1.0 CG A:HIS353 4.1 32.0 1.0 CB A:ALA379 4.2 39.5 1.0 OE1 A:GLU354 4.2 82.0 1.0 ND1 A:HIS353 4.3 57.6 1.0 ND1 A:HIS357 4.3 18.9 1.0 OE2 A:GLU354 4.4 64.9 1.0 CA A:GLU376 4.6 60.1 1.0 N1 A:BES1001 4.7 0.7 1.0 CD A:GLU354 4.7 54.9 1.0 CB A:GLU376 4.8 47.8 1.0 ND2 A:ASN375 5.0 71.2 1.0 C6 A:BES1001 5.0 0.3 1.0

Zinc binding site 2 out of 3 in the Er Aminopeptidase, ERAP1, Bound to the Zinc Aminopeptidase Inhibitor, Bestatin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Er Aminopeptidase, ERAP1, Bound to the Zinc Aminopeptidase Inhibitor, Bestatin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1000 b:38.2 occ:1.00 O2 B:BES1001 2.1 0.4 1.0 NE2 B:HIS353 2.2 22.0 1.0 OE1 B:GLU376 2.2 47.3 1.0 NE2 B:HIS357 2.3 18.3 1.0 OE2 B:GLU376 2.5 53.3 1.0 CD B:GLU376 2.7 48.4 1.0 CD2 B:HIS353 2.9 19.0 1.0 CD2 B:HIS357 3.0 13.8 1.0 O3 B:BES1001 3.1 0.6 1.0 C2 B:BES1001 3.2 0.1 1.0 C3 B:BES1001 3.3 0.1 1.0 CE1 B:HIS353 3.4 33.2 1.0 CE1 B:HIS357 3.4 48.0 1.0 OE2 B:GLU354 4.0 66.5 1.0 C1 B:BES1001 4.1 0.1 1.0 OE1 B:GLU354 4.1 81.0 1.0 CG B:GLU376 4.2 37.3 1.0 CG B:HIS353 4.2 17.5 1.0 CG B:HIS357 4.2 22.2 1.0 CB B:ALA379 4.2 34.6 1.0 ND1 B:HIS353 4.3 40.5 1.0 ND1 B:HIS357 4.4 28.7 1.0 N1 B:BES1001 4.4 0.6 1.0 CD B:GLU354 4.5 49.0 1.0 CA B:GLU376 4.6 57.3 1.0 N2 B:BES1001 4.6 0.7 1.0 CB B:GLU376 4.8 42.7 1.0 OE1 B:GLU320 4.9 0.4 1.0 C13 B:BES1001 5.0 0.9 1.0

Zinc binding site 3 out of 3 in the Er Aminopeptidase, ERAP1, Bound to the Zinc Aminopeptidase Inhibitor, Bestatin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Er Aminopeptidase, ERAP1, Bound to the Zinc Aminopeptidase Inhibitor, Bestatin within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1000 b:38.7 occ:1.00 NE2 C:HIS353 2.1 18.5 1.0 OE1 C:GLU376 2.2 15.6 1.0 NE2 C:HIS357 2.3 19.5 1.0 O2 C:BES1001 2.4 0.3 1.0 OE2 C:GLU376 2.5 25.6 1.0 CD C:GLU376 2.7 39.4 1.0 CD2 C:HIS357 2.7 29.8 1.0 CD2 C:HIS353 2.8 26.1 1.0 O3 C:BES1001 2.9 0.4 1.0 CE1 C:HIS353 3.3 45.9 1.0 C2 C:BES1001 3.5 0.0 1.0 C3 C:BES1001 3.5 0.8 1.0 CE1 C:HIS357 3.5 39.7 1.0 OE2 C:GLU354 4.0 63.3 1.0 CG C:HIS357 4.0 24.9 1.0 OE1 C:GLU354 4.0 90.6 1.0 CG C:HIS353 4.1 20.5 1.0 CG C:GLU376 4.2 34.4 1.0 CB C:ALA379 4.2 34.7 1.0 ND1 C:HIS353 4.3 50.0 1.0 C1 C:BES1001 4.3 0.4 1.0 ND1 C:HIS357 4.4 29.3 1.0 CD C:GLU354 4.4 50.8 1.0 OE1 C:GLU320 4.7 0.4 1.0 N1 C:BES1001 4.7 0.4 1.0 CA C:GLU376 4.7 52.7 1.0 N2 C:BES1001 4.8 0.6 1.0 CB C:GLU376 4.9 36.3 1.0

T.T.Nguyen, S.C.Chang, I.Evnouchidou, I.A.York, C.Zikos, K.L.Rock, A.L.Goldberg, E.Stratikos, L.J.Stern. Structural Basis For Antigenic Peptide Precursor Processing By the Endoplasmic Reticulum Aminopeptidase ERAP1. Nat.Struct.Mol.Biol. V. 18 604 2011.
ISSN: ISSN 1545-9993
PubMed: 21478864
DOI: 10.1038/NSMB.2021