Sodium in PDB 7r3s: Ftra/P19 of Rubrivivax Gelatinosus in Complex with Ni

The structure of Ftra/P19 of Rubrivivax Gelatinosus in Complex with Ni, PDB code: 7r3s was solved by S.Morera, A.Vigouroux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.59 / 1.79
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.28, 79.81, 82.41, 90, 90, 90
R / Rfree (%)	17.6 / 20.1

The structure of Ftra/P19 of Rubrivivax Gelatinosus in Complex with Ni also contains other interesting chemical elements:

Nickel

(Ni)

1 atom

The binding sites of Sodium atom in the Ftra/P19 of Rubrivivax Gelatinosus in Complex with Ni (pdb code 7r3s). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Ftra/P19 of Rubrivivax Gelatinosus in Complex with Ni, PDB code: 7r3s:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Ftra/P19 of Rubrivivax Gelatinosus in Complex with Ni


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ftra/P19 of Rubrivivax Gelatinosus in Complex with Ni within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:58.6 occ:1.00 O A:HOH354 3.0 43.5 1.0 N A:THR152 3.2 32.2 1.0 CA A:PHE151 3.8 29.7 1.0 O A:HOH310 3.9 49.6 1.0 C A:PHE151 4.0 34.3 1.0 CB A:THR152 4.0 41.7 1.0 CA A:THR152 4.1 33.8 1.0 OG1 A:THR152 4.1 43.5 1.0 CB A:PHE151 4.2 30.4 1.0 O A:THR152 4.4 39.8 1.0 C A:THR152 4.7 39.3 1.0 O A:HOH361 4.9 52.6 1.0 O A:ASP150 4.9 33.2 1.0

Sodium binding site 2 out of 2 in the Ftra/P19 of Rubrivivax Gelatinosus in Complex with Ni


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ftra/P19 of Rubrivivax Gelatinosus in Complex with Ni within 5.0Å range: probe atom residue distance (Å) B Occ B:Na203 b:61.3 occ:1.00 N B:GLU29 3.5 39.2 1.0 CA B:PRO28 3.8 33.6 1.0 O B:HOH302 4.1 41.0 1.0 CG B:GLU27 4.2 42.6 1.0 C B:PRO28 4.2 38.6 1.0 CB B:GLU29 4.3 45.0 1.0 CB B:PRO28 4.4 34.5 1.0 CA B:GLU29 4.5 42.0 1.0 CG B:GLU29 4.7 60.0 1.0 OE2 B:GLU27 4.9 47.2 1.0 N B:PRO28 5.0 32.5 1.0

A.S.Steunou, A.Vigouroux, M.Aumont-Nicaise, S.Plancqueel, A.Boussac, S.Ouchane, S.Morera. New Insights Into the Mechanism of Iron Transport Through the Bacterial Ftr System Present in Pathogens. Febs J. V. 289 6286 2022.
ISSN: ISSN 1742-464X
PubMed: 35527501
DOI: 10.1111/FEBS.16476