Zinc in PDB 7skm: Complex Between S. Aureus Aureolysin and Wt Impi.

All present enzymatic activity of Complex Between S. Aureus Aureolysin and Wt Impi.:
3.4.24.29;

The structure of Complex Between S. Aureus Aureolysin and Wt Impi., PDB code: 7skm was solved by S.R.Mendes, U.Eckhard, A.Rodriguez-Banqueri, T.Guevara, F.X.Gomis-Ruth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.69 / 1.85
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	68.14, 68.14, 166.18, 90, 90, 90
R / Rfree (%)	16.4 / 21.9

The structure of Complex Between S. Aureus Aureolysin and Wt Impi. also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

The binding sites of Zinc atom in the Complex Between S. Aureus Aureolysin and Wt Impi. (pdb code 7skm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Complex Between S. Aureus Aureolysin and Wt Impi., PDB code: 7skm:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Complex Between S. Aureus Aureolysin and Wt Impi.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Complex Between S. Aureus Aureolysin and Wt Impi. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn604 b:29.4 occ:1.00 NE2 A:HIS356 2.0 25.7 1.0 NE2 A:HIS352 2.0 25.9 1.0 OXT B:ASN56 2.1 35.8 1.0 OE2 A:GLU376 2.1 31.3 1.0 O B:ASN56 2.3 34.5 1.0 C B:ASN56 2.6 33.2 1.0 CD A:GLU376 2.8 29.5 1.0 OE1 A:GLU376 2.9 31.2 1.0 CE1 A:HIS356 3.0 25.1 1.0 CE1 A:HIS352 3.0 26.0 1.0 CD2 A:HIS356 3.0 26.1 1.0 CD2 A:HIS352 3.0 26.6 1.0 CA B:ASN56 4.1 32.8 1.0 ND1 A:HIS356 4.1 24.9 1.0 ND1 A:HIS352 4.1 25.0 1.0 CG A:HIS356 4.1 25.6 1.0 CG A:HIS352 4.2 25.5 1.0 OH A:TYR367 4.2 39.1 1.0 NE2 A:HIS436 4.2 30.0 1.0 CG A:GLU376 4.3 27.7 1.0 CB A:SER379 4.6 27.4 1.0 N B:ASN56 4.6 31.6 1.0 CA E:ILE57 4.7 29.4 1.0 OE1 A:GLU353 4.7 28.4 1.0 N E:ILE57 4.7 29.5 1.0 CA A:GLU376 4.8 25.1 1.0 CD2 A:HIS436 4.8 31.2 1.0 CG2 B:ILE55 4.8 34.7 1.0 OG A:SER379 4.9 27.9 1.0 CB B:ASN56 4.9 31.2 1.0 O B:ILE55 5.0 31.1 1.0 C E:ILE57 5.0 29.0 1.0 C B:ILE55 5.0 30.7 1.0

Zinc binding site 2 out of 2 in the Complex Between S. Aureus Aureolysin and Wt Impi.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Complex Between S. Aureus Aureolysin and Wt Impi. within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn604 b:28.7 occ:1.00 NE2 C:HIS356 1.9 24.6 1.0 OE2 C:GLU376 2.0 30.2 1.0 NE2 C:HIS352 2.1 28.6 1.0 OXT D:ASN56 2.1 33.2 1.0 O D:ASN56 2.4 29.1 1.0 C D:ASN56 2.7 33.3 1.0 CD C:GLU376 2.7 29.1 1.0 OE1 C:GLU376 2.8 30.0 1.0 CE1 C:HIS356 2.9 25.2 1.0 CD2 C:HIS356 3.0 26.5 1.0 CE1 C:HIS352 3.0 28.0 1.0 CD2 C:HIS352 3.0 28.6 1.0 ND1 C:HIS356 4.0 25.2 1.0 OH C:TYR367 4.1 30.6 1.0 CG C:HIS356 4.1 26.3 1.0 ND1 C:HIS352 4.1 26.9 1.0 CG C:GLU376 4.2 26.6 1.0 CG C:HIS352 4.2 28.2 1.0 CA D:ASN56 4.2 33.0 1.0 NE2 C:HIS436 4.4 29.2 1.0 N F:ILE57 4.5 30.3 1.0 CB C:SER379 4.6 25.8 1.0 CA F:ILE57 4.6 33.0 1.0 OE1 C:GLU353 4.6 30.6 1.0 N D:ASN56 4.7 32.1 1.0 CA C:GLU376 4.7 25.3 1.0 OG C:SER379 4.8 27.2 1.0 CD2 C:HIS436 4.9 28.5 1.0 OE2 C:GLU353 4.9 31.6 1.0 CG2 D:ILE55 4.9 34.3 1.0 CB C:GLU376 4.9 24.1 1.0 C F:ILE57 5.0 33.4 1.0 CZ C:TYR367 5.0 28.5 1.0

S.R.Mendes, U.Eckhard, A.Rodriguez-Banqueri, T.Guevara, P.Czermak, E.Marcos, A.Vilcinskas. An Engineered Protein-Based Submicromolar Competitive Inhibitor of the Staphylococcus Aureus Virulence Factor Aureolysin Comput Struct Biotechnol J V. 20 534 2022.
ISSN: ESSN 2001-0370
DOI: 10.1016/J.CSBJ.2022.01.001