Zinc in PDB 7tj4: Structure of the S. Aureus Amidase Lyth and Activator Acth Extracellular Domains

All present enzymatic activity of Structure of the S. Aureus Amidase Lyth and Activator Acth Extracellular Domains:
3.4.21.105;

The structure of Structure of the S. Aureus Amidase Lyth and Activator Acth Extracellular Domains, PDB code: 7tj4 was solved by J.E.Page, M.A.Skiba, A.C.Kruse, S.Walker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.39 / 1.80
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.6, 71.26, 190.4, 90, 90, 90
R / Rfree (%)	18.6 / 22.9

The binding sites of Zinc atom in the Structure of the S. Aureus Amidase Lyth and Activator Acth Extracellular Domains (pdb code 7tj4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of the S. Aureus Amidase Lyth and Activator Acth Extracellular Domains, PDB code: 7tj4:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of the S. Aureus Amidase Lyth and Activator Acth Extracellular Domains


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the S. Aureus Amidase Lyth and Activator Acth Extracellular Domains within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn500 b:32.8 occ:0.69 OD1 B:ASP195 2.0 42.7 1.0 NE2 B:HIS128 2.1 36.5 1.0 ND1 B:HIS193 2.1 30.9 1.0 OE2 B:GLU145 2.2 30.9 1.0 O B:HOH704 2.6 40.0 1.0 CG B:ASP195 2.8 37.5 1.0 OD2 B:ASP195 2.8 38.5 1.0 CD2 B:HIS128 2.9 33.7 1.0 CD B:GLU145 3.0 30.5 1.0 CE1 B:HIS193 3.0 30.0 1.0 OE1 B:GLU145 3.1 31.3 1.0 CG B:HIS193 3.2 31.1 1.0 CE1 B:HIS128 3.2 34.1 1.0 O B:HOH603 3.5 37.0 1.0 CB B:HIS193 3.5 31.1 1.0 CG B:HIS128 4.1 34.7 1.0 NE2 B:HIS193 4.2 27.8 1.0 CB B:ASP195 4.2 36.4 1.0 ND1 B:HIS128 4.2 34.0 1.0 CD2 B:HIS193 4.3 29.4 1.0 CA B:HIS193 4.3 27.9 1.0 CG B:GLU145 4.4 30.1 1.0 N B:ASN194 4.5 27.1 1.0 CA B:ASP195 4.5 36.8 1.0 N B:ASP195 4.6 35.1 1.0 C B:HIS193 4.9 28.7 1.0 C B:ASN194 5.0 32.3 1.0

Zinc binding site 2 out of 2 in the Structure of the S. Aureus Amidase Lyth and Activator Acth Extracellular Domains


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the S. Aureus Amidase Lyth and Activator Acth Extracellular Domains within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn500 b:35.1 occ:0.76 OD2 B:ASP212 2.0 38.9 1.0 ND1 D:HIS193 2.0 34.8 1.0 O D:HOH626 2.2 33.0 1.0 OE2 D:GLU145 2.2 35.8 1.0 NE2 D:HIS128 2.2 37.3 1.0 O D:HOH623 2.4 40.7 1.0 CE1 D:HIS193 2.9 35.6 1.0 CG B:ASP212 2.9 40.0 1.0 CD D:GLU145 3.0 35.4 1.0 CD2 D:HIS128 3.1 34.5 1.0 CG D:HIS193 3.1 33.5 1.0 OE1 D:GLU145 3.2 33.6 1.0 CE1 D:HIS128 3.3 38.4 1.0 OD1 B:ASP212 3.5 46.8 1.0 CB D:HIS193 3.6 29.0 1.0 CB B:ASP212 3.9 37.0 1.0 O D:ASN194 4.0 35.5 1.0 NE2 D:HIS193 4.1 34.0 1.0 CD2 D:HIS193 4.2 32.9 1.0 CG D:HIS128 4.3 36.9 1.0 ND1 D:HIS128 4.3 37.2 1.0 CG D:GLU145 4.4 33.0 1.0 CA D:HIS193 4.5 32.2 1.0 OE2 D:GLU255 4.5 35.8 1.0 N D:ASN194 4.5 31.2 1.0 O B:HOH717 4.6 43.0 1.0 O B:HOH688 4.7 33.1 1.0 O B:HOH707 4.7 44.2 1.0 OE1 D:GLU255 5.0 33.7 1.0 C D:ASN194 5.0 33.9 1.0

J.E.Page, M.A.Skiba, T.Do, A.C.Kruse, S.Walker. Metal Cofactor Stabilization By A Partner Protein Is A Widespread Strategy Employed For Amidase Activation. Proc.Natl.Acad.Sci.Usa V. 119 41119 2022.
ISSN: ESSN 1091-6490
PubMed: 35733252
DOI: 10.1073/PNAS.2201141119