Sodium in PDB 6ksn: Structure of A Zn-Bound Camelid Single Domain Antibody

The structure of Structure of A Zn-Bound Camelid Single Domain Antibody, PDB code: 6ksn was solved by S.Kumar, A.Athreya, A.Penmatsa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.28 / 2.15
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	106.880, 106.880, 70.580, 90.00, 90.00, 120.00
R / Rfree (%)	19.3 / 23.2

The structure of Structure of A Zn-Bound Camelid Single Domain Antibody also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Sodium atom in the Structure of A Zn-Bound Camelid Single Domain Antibody (pdb code 6ksn). 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 Structure of A Zn-Bound Camelid Single Domain Antibody, PDB code: 6ksn:

Sodium binding site 1 out of 1 in the Structure of A Zn-Bound Camelid Single Domain Antibody


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of A Zn-Bound Camelid Single Domain Antibody within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:49.1 occ:1.00 O B:SER34 2.3 50.2 1.0 O B:SER37 2.3 47.6 1.0 O2 B:EDO203 2.4 48.3 1.0 O1 B:EDO203 2.4 50.0 1.0 O B:HOH345 2.5 55.1 1.0 O B:HOH358 2.5 55.7 1.0 C1 B:EDO203 3.1 53.3 1.0 C2 B:EDO203 3.2 47.9 1.0 C B:SER37 3.4 48.5 1.0 C B:SER34 3.5 51.2 1.0 N B:SER34 4.1 52.0 1.0 CA B:SER37 4.2 46.7 1.0 N B:SER37 4.2 47.9 1.0 O B:HOH340 4.2 49.2 1.0 CA B:SER34 4.2 54.0 1.0 N B:THR38 4.2 45.6 1.0 CB B:SER37 4.3 46.5 1.0 CA B:THR38 4.4 45.6 1.0 N B:THR35 4.5 52.1 1.0 CB B:SER34 4.5 57.1 1.0 CA B:THR35 4.6 52.2 1.0 O B:HOH316 4.7 66.0 1.0 C B:THR35 4.8 51.0 1.0 OG B:SER34 4.8 57.0 1.0 O B:MET32 4.9 52.3 1.0 O B:HOH357 4.9 52.7 1.0

S.Kumar, M.Ithayaraja, A.Athreya, R.Ranjan, A.Penmatsa. Isolation and Structural Characterization of A ZN2+-Bound Single-Domain Antibody Against Norc, A Putative Multi-Drug Efflux Transporter in Bacteria. J.Biol.Chem. 2019.
ISSN: ESSN 1083-351X
PubMed: 31699895
DOI: 10.1074/JBC.RA119.010902