Sodium in PDB 8yrc: Chlorinated Yabj From Staphylococcus Aureus

The structure of Chlorinated Yabj From Staphylococcus Aureus, PDB code: 8yrc was solved by C.Jeong, H.J.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.51 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.69, 75.35, 52.83, 90, 103.05, 90
R / Rfree (%)	18.3 / 20.9

The structure of Chlorinated Yabj From Staphylococcus Aureus also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Chlorinated Yabj From Staphylococcus Aureus (pdb code 8yrc). 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 Chlorinated Yabj From Staphylococcus Aureus, PDB code: 8yrc:

Sodium binding site 1 out of 1 in the Chlorinated Yabj From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Chlorinated Yabj From Staphylococcus Aureus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:44.3 occ:1.00 O A:O201 2.6 49.1 1.0 CL A:CL203 2.8 52.0 1.0 OE1 A:GLN31 2.8 32.4 1.0 N A:ILE32 3.2 28.7 1.0 CG1 A:ILE32 3.4 28.0 1.0 CD A:GLN31 3.5 33.5 1.0 O A:ILE32 3.6 28.2 1.0 NE2 A:GLN31 3.7 32.6 1.0 CA A:GLN31 3.8 25.6 1.0 C A:GLN31 4.0 27.3 1.0 CA A:ILE32 4.1 25.1 1.0 C A:ILE32 4.2 27.7 1.0 O A:GLY30 4.3 29.5 1.0 CB A:ILE32 4.3 25.5 1.0 CG A:PRO10 4.4 40.6 1.0 CB A:GLN31 4.4 26.9 1.0 CD1 A:ILE32 4.4 32.7 1.0 CG A:GLN31 4.5 29.7 1.0 ND2 A:ASN55 4.7 26.8 1.0 CD1 A:LEU34 4.9 35.7 1.0 CG A:LEU34 4.9 35.0 1.0 N A:GLN31 4.9 26.0 1.0

C.Jeong, H.J.Kim. Yabj From Staphylococcus Aureus Entraps Chlorides Within Its Pocket. Biochem.Biophys.Res.Commun. V. 710 49892 2024.
ISSN: ESSN 1090-2104
PubMed: 38581951
DOI: 10.1016/J.BBRC.2024.149892