Sodium in PDB 6a07: Salmonella Typhi Yfdx in the F222 Space Group at 1.5 A Resolution

The structure of Salmonella Typhi Yfdx in the F222 Space Group at 1.5 A Resolution, PDB code: 6a07 was solved by B.Ku, H.S.Lee, S.J.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.56 / 1.50
Space group	F 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	88.798, 92.207, 95.364, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 21.5

The structure of Salmonella Typhi Yfdx in the F222 Space Group at 1.5 A Resolution also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium atom in the Salmonella Typhi Yfdx in the F222 Space Group at 1.5 A Resolution (pdb code 6a07). 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 Salmonella Typhi Yfdx in the F222 Space Group at 1.5 A Resolution, PDB code: 6a07:

Sodium binding site 1 out of 1 in the Salmonella Typhi Yfdx in the F222 Space Group at 1.5 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Salmonella Typhi Yfdx in the F222 Space Group at 1.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:28.0 occ:1.00 O A:HOH319 2.8 29.8 1.0 OE2 A:GLU43 3.1 21.2 1.0 NZ A:LYS51 3.2 32.7 1.0 CD A:ARG48 3.5 23.4 1.0 OE1 A:GLU43 3.5 16.9 1.0 NE A:ARG48 3.5 38.8 1.0 ND2 A:ASN46 3.6 20.2 1.0 CD A:GLU43 3.7 18.0 1.0 CZ A:ARG48 3.9 37.2 1.0 CE A:LYS51 4.2 30.0 1.0 NH1 A:ARG48 4.2 34.2 1.0 CD A:LYS51 4.4 21.8 1.0 NH2 A:ARG48 4.6 39.0 1.0 CG A:ASN46 4.9 15.8 1.0 CG A:ARG48 5.0 21.1 1.0

H.S.Lee, S.Lee, J.S.Kim, H.R.Lee, H.C.Shin, M.S.Lee, K.S.Jin, C.H.Kim, B.Ku, C.M.Ryu, S.J.Kim. Structural and Physiological Exploration Ofsalmonellatyphi Yfdx Uncovers Its Dual Function in Bacterial Antibiotic Stress and Virulence. Front Microbiol V. 9 3329 2018.
ISSN: ESSN 1664-302X
PubMed: 30692978
DOI: 10.3389/FMICB.2018.03329