Sodium in PDB 7r4u: Apoform of Ftra/P19 From Rubrivivax Gelatinosus

The structure of Apoform of Ftra/P19 From Rubrivivax Gelatinosus, PDB code: 7r4u was solved by S.Morera, A.Vigouroux, S.Plancqueel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.25 / 1.23
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.34, 79.97, 82.88, 90, 90, 90
R / Rfree (%)	17 / 18.6

The binding sites of Sodium atom in the Apoform of Ftra/P19 From Rubrivivax Gelatinosus (pdb code 7r4u). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Apoform of Ftra/P19 From Rubrivivax Gelatinosus, PDB code: 7r4u:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Apoform of Ftra/P19 From Rubrivivax Gelatinosus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Apoform of Ftra/P19 From Rubrivivax Gelatinosus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:40.1 occ:1.00 O A:HOH481 2.2 41.1 1.0 O A:HOH500 2.5 44.8 1.0 N A:GLU29 3.0 19.5 1.0 CA A:PRO28 3.6 16.5 1.0 CB A:GLU29 3.7 23.6 1.0 CG A:GLU29 3.7 35.5 1.0 C A:PRO28 3.8 18.7 1.0 CG A:GLU27 3.8 18.3 1.0 CA A:GLU29 4.0 20.6 1.0 CA A:GLU27 4.1 15.8 1.0 CB A:GLU27 4.3 17.0 1.0 O B:HOH450 4.4 42.0 1.0 O A:HOH326 4.4 31.8 1.0 CB A:PRO28 4.5 19.0 1.0 O A:HOH333 4.6 22.8 1.0 N A:PRO28 4.7 15.8 1.0 O A:MET26 4.9 18.5 1.0 C A:GLU27 4.9 16.8 1.0 CD A:GLU27 4.9 19.1 1.0 O A:PRO28 5.0 17.5 1.0

Sodium binding site 2 out of 5 in the Apoform of Ftra/P19 From Rubrivivax Gelatinosus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Apoform of Ftra/P19 From Rubrivivax Gelatinosus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:33.0 occ:1.00 O A:HOH463 2.2 47.6 1.0 O A:HOH417 2.9 29.2 1.0 N A:THR152 3.0 17.4 1.0 O A:HOH401 3.0 28.6 1.0 CB A:PHE151 3.5 17.4 1.0 CA A:PHE151 3.6 16.8 1.0 O A:THR152 3.7 20.2 1.0 C A:PHE151 3.8 18.2 1.0 CA A:THR152 4.0 17.8 1.0 CB A:THR152 4.1 21.2 1.0 O A:PRO4 4.2 18.5 1.0 C A:THR152 4.3 19.7 1.0 OG1 A:THR152 4.5 22.0 1.0 CG A:PHE151 4.5 16.7 1.0 CD2 A:PHE151 4.5 18.6 1.0 O A:HOH422 4.6 30.5 1.0 O A:PHE151 5.0 17.1 1.0 N A:PHE151 5.0 16.6 1.0

Sodium binding site 3 out of 5 in the Apoform of Ftra/P19 From Rubrivivax Gelatinosus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Apoform of Ftra/P19 From Rubrivivax Gelatinosus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:38.5 occ:1.00 O A:HOH451 2.2 34.5 1.0 O A:HOH301 2.5 29.3 1.0 O A:HOH479 2.6 52.0 1.0 O A:HOH488 2.9 37.7 1.0 N A:ASN10 3.0 15.2 1.0 O A:ASN10 3.4 18.2 1.0 CA A:GLN9 3.7 14.2 1.0 C A:GLN9 3.8 15.0 1.0 CA A:ASN10 3.9 15.2 1.0 CB A:GLN9 4.0 14.8 1.0 C A:ASN10 4.1 15.9 1.0 CB A:ASN10 4.1 16.6 1.0 CG A:GLN9 4.6 15.8 1.0 CG A:ASN10 4.9 19.6 1.0 O A:GLN9 5.0 15.6 1.0

Sodium binding site 4 out of 5 in the Apoform of Ftra/P19 From Rubrivivax Gelatinosus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Apoform of Ftra/P19 From Rubrivivax Gelatinosus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na206 b:27.9 occ:1.00 O A:HOH473 2.2 47.5 1.0 O A:HOH371 2.7 19.9 1.0 O A:HOH446 2.8 22.5 1.0 N A:THR7 3.1 16.3 1.0 CA A:GLY6 3.4 17.0 1.0 CD1 A:TRP149 3.7 15.0 1.0 C A:GLY6 3.7 18.5 1.0 O A:THR7 4.0 14.6 1.0 CA A:THR7 4.1 16.9 1.0 CB A:THR7 4.1 19.2 1.0 OG1 A:THR7 4.3 25.9 1.0 O A:HOH375 4.3 27.7 1.0 C A:THR7 4.5 16.7 1.0 NE1 A:TRP149 4.6 13.6 1.0 CG A:TRP149 4.6 13.1 1.0 N A:GLY6 4.7 16.7 1.0 CB A:TRP149 4.8 13.6 1.0 O A:HOH420 4.8 31.5 1.0 O A:GLY6 4.9 21.9 1.0

Sodium binding site 5 out of 5 in the Apoform of Ftra/P19 From Rubrivivax Gelatinosus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Apoform of Ftra/P19 From Rubrivivax Gelatinosus within 5.0Å range: probe atom residue distance (Å) B Occ B:Na203 b:52.5 occ:1.00 O B:HOH472 2.5 24.3 1.0 CG A:PRO28 3.6 22.1 1.0 O B:HOH359 3.6 30.0 1.0 CB A:PRO28 3.8 19.0 1.0 O B:SER125 3.9 16.6 1.0 O A:HOH351 4.1 27.4 1.0 CA B:PRO126 4.3 15.1 1.0 C B:SER125 4.3 16.9 1.0 O B:HOH317 4.4 17.7 1.0 CD A:PRO28 4.4 18.1 1.0 N B:PRO126 4.5 14.7 1.0 O A:HOH333 4.7 22.8 1.0 NE2 A:HIS31 4.8 30.6 1.0 CB B:SER125 4.8 16.0 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