Sodium 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:

Zinc

(Zn)

1 atom

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was determined in the X-Ray Structure of Clostridium Perfringens-Specific Amidase Endolysin, PDB code: 7f5i:

Sodium 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 Sodium with other atoms in the Na 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:Na404 b:35.4 occ:1.00 OE1 A:GLN11 2.3 33.8 1.0 O A:VAL6 2.4 28.6 1.0 CD A:GLN11 3.2 32.4 1.0 C A:VAL6 3.5 24.1 1.0 NE2 A:GLN11 3.6 38.0 1.0 N A:LEU8 3.9 27.9 1.0 CA A:TYR7 4.1 35.8 1.0 N A:TYR7 4.2 32.9 1.0 CG A:LEU8 4.3 25.4 1.0 C A:TYR7 4.4 28.7 1.0 N A:VAL6 4.4 26.1 1.0 CD1 A:LEU8 4.5 31.3 1.0 CG A:GLN11 4.5 31.2 1.0 CB A:LEU8 4.6 27.7 1.0 CA A:VAL6 4.6 31.2 1.0 CB A:GLN11 4.7 32.7 1.0 CA A:LEU8 4.9 26.1 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