Sodium in PDB 8xf7: High-Resolution Structure of the Siderophore Periplasmic Binding Protein Ftsb From Streptococcus Pyogenes with Ferrioxamine E Bound

The structure of High-Resolution Structure of the Siderophore Periplasmic Binding Protein Ftsb From Streptococcus Pyogenes with Ferrioxamine E Bound, PDB code: 8xf7 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)	40.42 / 1.12
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	76.091, 76.091, 102.375, 90, 90, 120
R / Rfree (%)	12.5 / 14

The structure of High-Resolution Structure of the Siderophore Periplasmic Binding Protein Ftsb From Streptococcus Pyogenes with Ferrioxamine E Bound 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 E Bound (pdb code 8xf7). 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 E Bound, PDB code: 8xf7:
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 E Bound


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 E Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:25.3 occ:1.00 O A:HOH504 1.9 15.7 1.0 O A:HOH845 2.3 23.5 1.0 OE1 A:GLU253 2.6 14.4 1.0 OH A:TYR81 2.7 16.0 1.0 O A:HOH673 2.9 20.3 1.0 OE2 A:GLU253 3.3 20.0 1.0 CD A:GLU253 3.3 15.7 1.0 CZ A:TYR81 3.5 14.5 1.0 O A:HOH799 3.5 27.9 0.6 CE1 A:TYR81 3.6 14.4 1.0 OH A:TYR193 3.9 13.5 1.0 CE1 A:TYR193 3.9 12.4 1.0 CZ A:TYR193 4.4 12.0 1.0 CE2 A:TYR81 4.6 14.2 1.0 O A:HOH511 4.6 17.3 1.0 OH A:TYR287 4.7 12.5 1.0 O A:HOH568 4.7 23.6 1.0 O A:HOH535 4.7 23.1 1.0 CG A:GLU253 4.8 14.9 1.0 CD1 A:TYR81 4.8 13.8 1.0 NZ A:LYS84 4.9 23.9 1.0 CE2 A:TYR287 4.9 11.6 1.0 O A:HOH840 4.9 37.9 1.0 CD1 A:TYR193 5.0 12.4 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 E Bound


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 E Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Na408 b:30.5 occ:1.00 O A:HOH539 2.3 29.8 1.0 O A:HOH868 2.6 28.3 1.0 O A:HOH514 2.8 13.0 1.0 O A:HOH770 2.8 29.1 1.0 OE1 A:GLN213 3.2 13.4 1.0 CB A:GLN213 3.7 11.7 1.0 CD1 A:LEU143 4.0 14.1 1.0 O A:HOH913 4.0 36.4 1.0 CD A:GLN213 4.1 12.0 1.0 CE2 A:TYR142 4.2 10.3 1.0 O A:GLN213 4.3 16.1 1.0 CG A:GLN213 4.3 11.8 1.0 CA A:GLN213 4.5 11.9 1.0 C A:GLN213 4.5 12.4 1.0 O A:HOH815 4.6 29.5 0.5 O A:HOH638 4.7 17.5 1.0 OH A:TYR142 4.7 11.4 1.0 O A:HOH678 4.8 14.0 1.0 CZ A:TYR142 4.9 10.4 1.0 O A:HOH567 5.0 23.0 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