Zinc in PDB 7f5i: X-Ray Structure of Clostridium Perfringens-Specific Amidase Endolysin

The structure of X-Ray Structure of Clostridium Perfringens-Specific Amidase Endolysin, PDB code: 7f5i was solved by S.Kamitori, E.Tamai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.36 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.01, 52.87, 58.61, 90, 90, 90
R / Rfree (%)	13.7 / 20.5

The structure of X-Ray Structure of Clostridium Perfringens-Specific Amidase Endolysin also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Zinc atom in the X-Ray Structure of Clostridium Perfringens-Specific Amidase Endolysin (pdb code 7f5i). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the X-Ray Structure of Clostridium Perfringens-Specific Amidase Endolysin, PDB code: 7f5i:

Zinc binding site 1 out of 1 in the X-Ray Structure of Clostridium Perfringens-Specific Amidase Endolysin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Structure of Clostridium Perfringens-Specific Amidase Endolysin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:27.5 occ:1.00 ND1 A:HIS123 2.0 32.7 1.0 ND1 A:HIS26 2.0 24.1 1.0 SG A:CYS131 2.3 27.8 1.0 CE1 A:HIS26 3.0 23.4 1.0 CE1 A:HIS123 3.0 37.5 1.0 CG A:HIS123 3.0 28.2 1.0 CG A:HIS26 3.1 21.4 1.0 CB A:CYS131 3.2 32.0 1.0 CB A:HIS123 3.3 23.2 1.0 CB A:HIS26 3.5 24.6 1.0 CA A:HIS26 4.0 24.3 1.0 NE2 A:HIS123 4.1 29.9 1.0 CD2 A:HIS123 4.1 32.2 1.0 NE2 A:HIS26 4.1 23.3 1.0 CD2 A:HIS26 4.2 20.4 1.0 O A:HIS27 4.4 28.9 1.0 CA A:CYS131 4.6 27.1 1.0 OH A:TYR51 4.7 34.4 1.0 O A:ASN73 4.8 27.4 1.0 N A:HIS27 4.8 24.1 1.0 CA A:HIS123 4.8 24.9 1.0 O A:ILE25 4.8 21.7 1.0 CE1 A:TYR51 4.8 25.3 1.0 C A:CYS131 5.0 27.1 1.0

H.Sekiya, S.Kamitori, H.Nariya, R.Matsunami, E.Tamai. Structural and Biochemical Characterization of the Clostridium Perfringens-Specific Zn 2+ -Dependent Amidase Endolysin, Psa, Catalytic Domain. Biochem.Biophys.Res.Commun. V. 576 66 2021.
ISSN: ESSN 1090-2104
PubMed: 34482025
DOI: 10.1016/J.BBRC.2021.08.085