Sodium in PDB 8xf8: High-Resolution Structure of the Siderophore Periplasmic Binding Protein Ftsb From Streptococcus Pyogenes with Ferrioxamine B

The structure of High-Resolution Structure of the Siderophore Periplasmic Binding Protein Ftsb From Streptococcus Pyogenes with Ferrioxamine B, PDB code: 8xf8 was solved by J.M.M.Caaveiro, J.Fernandez-Perez, K.Tsumoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.50 / 1.15
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	76.223, 76.223, 102.502, 90, 90, 120
R / Rfree (%)	13.5 / 15.3

The structure of High-Resolution Structure of the Siderophore Periplasmic Binding Protein Ftsb From Streptococcus Pyogenes with Ferrioxamine B also contains other interesting chemical elements:

Zinc	(Zn)	5 atoms
Iron	(Fe)	1 atom

The binding sites of Sodium atom in the High-Resolution Structure of the Siderophore Periplasmic Binding Protein Ftsb From Streptococcus Pyogenes with Ferrioxamine B (pdb code 8xf8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the High-Resolution Structure of the Siderophore Periplasmic Binding Protein Ftsb From Streptococcus Pyogenes with Ferrioxamine B, PDB code: 8xf8:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the High-Resolution Structure of the Siderophore Periplasmic Binding Protein Ftsb From Streptococcus Pyogenes with Ferrioxamine B


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of High-Resolution Structure of the Siderophore Periplasmic Binding Protein Ftsb From Streptococcus Pyogenes with Ferrioxamine B within 5.0Å range: probe atom residue distance (Å) B Occ A:Na408 b:24.2 occ:1.00 O A:HOH516 2.0 30.1 1.0 O A:HOH846 2.7 25.8 1.0 OG1 A:THR63 2.9 11.8 1.0 O A:HOH679 2.9 12.4 1.0 CB A:THR63 3.5 10.7 1.0 C41 A:0UE401 3.5 21.2 1.0 CB A:ALA61 3.5 11.7 1.0 CE2 A:TYR64 3.6 10.1 1.0 C42 A:0UE401 3.8 22.8 1.0 CA A:GLY117 4.1 10.7 1.0 CD2 A:TYR64 4.2 10.0 1.0 O A:HOH588 4.2 19.4 1.0 CZ A:TYR64 4.3 10.2 1.0 CA A:ALA61 4.3 10.5 1.0 OH A:TYR64 4.3 10.8 1.0 N A:THR63 4.4 10.0 1.0 CG2 A:THR63 4.5 11.2 1.0 C43 A:0UE401 4.5 24.6 1.0 CA A:THR63 4.6 9.9 1.0 C A:ALA61 4.6 9.9 1.0 N A:GLY117 4.7 10.2 1.0 C40 A:0UE401 4.8 19.4 1.0 N A:SER62 4.9 10.4 1.0

Sodium binding site 2 out of 2 in the High-Resolution Structure of the Siderophore Periplasmic Binding Protein Ftsb From Streptococcus Pyogenes with Ferrioxamine B


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of High-Resolution Structure of the Siderophore Periplasmic Binding Protein Ftsb From Streptococcus Pyogenes with Ferrioxamine B within 5.0Å range: probe atom residue distance (Å) B Occ A:Na409 b:31.1 occ:0.60 O A:HOH898 2.5 32.3 0.7 O A:HOH696 2.6 28.4 1.0 O A:HOH563 2.7 28.5 1.0 OD2 A:ASP246 2.7 13.4 1.0 O A:HOH733 3.3 20.8 1.0 O A:HOH827 3.6 30.9 0.6 CG A:ASP246 3.6 12.8 1.0 OD1 A:ASP246 3.8 14.8 1.0 O A:HOH518 3.9 28.1 0.8 OG1 A:THR186 4.1 12.8 1.0 O A:LYS184 4.4 13.5 1.0 CG2 A:THR186 4.4 13.1 1.0 N A:THR186 4.6 10.9 1.0 CB A:THR186 4.8 12.0 1.0 CB A:ASP246 5.0 11.9 1.0 CA A:ALA185 5.0 11.7 1.0

J.Fernandez-Perez, J.M.M.Caaveiro, A.Senoo, M.Nakakido, S.De Vega, I.Nakagawa, K.Tsumoto. Conserved Binding Mechanism For Ligand Promiscuity in the Hydroxamate Siderophore Binding Protein Ftsb From Streptococcus Pyogenes Structure.
ISSN: ISSN 0969-2126
DOI: 10.1016/J.STR.2024.09.018