Zinc in PDB 3aho: Pz Peptidase A with Inhibitor 2

The structure of Pz Peptidase A with Inhibitor 2, PDB code: 3aho was solved by H.Nakano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.78 / 1.88
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.813, 194.259, 60.092, 90.00, 106.28, 90.00
R / Rfree (%)	18.9 / 20.4

The binding sites of Zinc atom in the Pz Peptidase A with Inhibitor 2 (pdb code 3aho). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Pz Peptidase A with Inhibitor 2, PDB code: 3aho:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Pz Peptidase A with Inhibitor 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Pz Peptidase A with Inhibitor 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn565 b:23.4 occ:1.00 O22 A:3A2566 2.2 23.8 1.0 NE2 A:HIS360 2.2 19.3 1.0 NE2 A:HIS356 2.2 18.4 1.0 OE1 A:GLU384 2.2 16.5 1.0 O23 A:3A2566 2.4 18.8 1.0 OE2 A:GLU384 2.4 20.1 1.0 CD A:GLU384 2.7 18.0 1.0 P21 A:3A2566 2.7 23.2 1.0 CD2 A:HIS360 3.1 17.9 1.0 CD2 A:HIS356 3.2 17.3 1.0 CE1 A:HIS360 3.2 19.6 1.0 CE1 A:HIS356 3.2 18.0 1.0 OG A:SER387 3.6 17.2 1.0 C24 A:3A2566 3.7 23.9 1.0 CE1 A:TYR490 3.8 18.1 1.0 C25 A:3A2566 3.8 25.6 1.0 C13 A:3A2566 4.0 24.2 1.0 N12 A:3A2566 4.0 24.2 1.0 CB A:SER387 4.1 16.6 1.0 OH A:TYR486 4.2 18.3 1.0 CG A:GLU384 4.2 17.5 1.0 CG A:HIS360 4.3 18.5 1.0 ND1 A:HIS360 4.3 18.7 1.0 ND1 A:HIS356 4.3 18.3 1.0 CG A:HIS356 4.3 18.8 1.0 OH A:TYR490 4.4 17.2 1.0 C7 A:3A2566 4.4 27.0 1.0 CZ A:TYR490 4.6 16.5 1.0 C10 A:3A2566 4.7 25.1 1.0 CD1 A:TYR490 4.7 16.0 1.0 OE1 A:GLU357 4.8 18.5 1.0 C26 A:3A2566 4.8 26.6 1.0 CB A:GLU384 5.0 17.5 1.0 CA A:GLU384 5.0 16.6 1.0

Zinc binding site 2 out of 2 in the Pz Peptidase A with Inhibitor 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Pz Peptidase A with Inhibitor 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn565 b:27.9 occ:1.00 O22 B:3A2566 1.9 27.2 1.0 NE2 B:HIS360 2.1 23.8 1.0 NE2 B:HIS356 2.2 21.0 1.0 OE1 B:GLU384 2.2 23.2 1.0 OE2 B:GLU384 2.5 22.5 1.0 O23 B:3A2566 2.6 28.1 1.0 P21 B:3A2566 2.7 29.7 1.0 CD B:GLU384 2.7 22.6 1.0 CD2 B:HIS360 3.1 21.3 1.0 CE1 B:HIS360 3.1 24.4 1.0 CE1 B:HIS356 3.2 20.2 1.0 CD2 B:HIS356 3.2 21.1 1.0 OG B:SER387 3.5 22.0 1.0 CE1 B:TYR490 3.8 22.7 1.0 C25 B:3A2566 3.9 29.9 1.0 C24 B:3A2566 3.9 28.6 1.0 CB B:SER387 4.1 20.3 1.0 C13 B:3A2566 4.1 29.6 1.0 N12 B:3A2566 4.1 29.0 1.0 OH B:TYR486 4.2 23.7 1.0 CG B:GLU384 4.2 21.5 1.0 ND1 B:HIS360 4.2 24.0 1.0 CG B:HIS360 4.2 22.9 1.0 ND1 B:HIS356 4.3 21.3 1.0 CG B:HIS356 4.3 20.4 1.0 OH B:TYR490 4.4 23.9 1.0 C7 B:3A2566 4.5 33.7 1.0 CZ B:TYR490 4.6 22.1 1.0 CD1 B:TYR490 4.7 21.2 1.0 C10 B:3A2566 4.7 31.2 1.0 OE1 B:GLU357 4.8 22.5 1.0 C26 B:3A2566 4.9 30.4 1.0 CA B:GLU384 4.9 20.8 1.0 CB B:GLU384 5.0 21.2 1.0

A.Kawasaki, H.Nakano, A.Hosokawa, T.Nakatsu, H.Kato, K.Watanabe. The Exquisite Structure and Reaction Mechanism of Bacterial Pz-Peptidase A Toward Collagenous Peptides: X-Ray Crystallographic Structure Analysis of Pz-Peptidase A Reveals Differences From Mammalian Thimet Oligopeptidase. J.Biol.Chem. V. 285 34972 2010.
ISSN: ISSN 0021-9258
PubMed: 20817732
DOI: 10.1074/JBC.M110.141838