Zinc in PDB 3ahm: Pz Peptidase A

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

Resolution Low / High (Å)	29.17 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.634, 193.841, 60.242, 90.00, 106.54, 90.00
R / Rfree (%)	19.2 / 20.4

The binding sites of Zinc atom in the Pz Peptidase A (pdb code 3ahm). 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, PDB code: 3ahm:
Jump to Zinc binding site number: 1; 2;

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn565 b:27.6 occ:1.00 NE2 A:HIS360 2.1 21.7 1.0 O A:HOH790 2.2 25.3 1.0 NE2 A:HIS356 2.2 17.2 1.0 OE1 A:GLU384 2.3 20.4 1.0 OE2 A:GLU384 2.6 22.6 1.0 CD A:GLU384 2.8 18.6 1.0 O A:HOH797 2.8 29.6 1.0 CD2 A:HIS360 3.0 22.3 1.0 CE1 A:HIS356 3.1 19.9 1.0 CE1 A:HIS360 3.2 23.3 1.0 CD2 A:HIS356 3.2 14.9 1.0 OG A:SER387 3.6 16.6 1.0 CE1 A:TYR490 3.8 16.8 1.0 CB A:SER387 4.0 17.2 1.0 CG A:HIS360 4.2 20.3 1.0 OH A:TYR486 4.2 20.8 1.0 ND1 A:HIS360 4.2 22.9 1.0 ND1 A:HIS356 4.2 16.4 1.0 CG A:GLU384 4.3 17.6 1.0 OH A:TYR490 4.3 20.5 1.0 CG A:HIS356 4.3 19.3 1.0 O A:HOH787 4.5 23.3 1.0 CZ A:TYR490 4.6 19.1 1.0 OE2 A:GLU357 4.8 21.3 1.0 CD1 A:TYR490 4.8 15.5 1.0 OE1 A:GLU357 4.8 21.4 1.0 O A:HOH799 4.9 20.0 1.0 CA A:GLU384 5.0 17.8 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn565 b:31.3 occ:1.00 NE2 B:HIS360 2.1 20.1 1.0 NE2 B:HIS356 2.2 27.2 1.0 OE1 B:GLU384 2.2 20.5 1.0 O B:HOH801 2.4 20.0 1.0 O B:HOH789 2.6 28.4 1.0 OE2 B:GLU384 2.6 21.7 1.0 CD B:GLU384 2.8 21.0 1.0 CE1 B:HIS360 3.0 26.2 1.0 CE1 B:HIS356 3.1 23.0 1.0 CD2 B:HIS360 3.2 19.7 1.0 CD2 B:HIS356 3.2 22.4 1.0 OG B:SER387 3.6 22.2 1.0 CE1 B:TYR490 3.8 25.7 1.0 CB B:SER387 4.1 20.3 1.0 ND1 B:HIS360 4.1 26.2 1.0 OH B:TYR486 4.2 26.3 1.0 ND1 B:HIS356 4.2 27.5 1.0 CG B:HIS360 4.2 24.1 1.0 CG B:GLU384 4.3 21.5 1.0 CG B:HIS356 4.3 23.2 1.0 OH B:TYR490 4.4 26.1 1.0 O B:HOH784 4.4 27.1 1.0 CZ B:TYR490 4.6 26.3 1.0 CD1 B:TYR490 4.7 23.4 1.0 OE2 B:GLU357 4.7 24.0 1.0 CA B:GLU384 4.8 23.5 1.0 O B:HOH1083 4.9 38.0 1.0 CB B:GLU384 4.9 22.9 1.0 OE1 B:GLU357 5.0 26.1 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