Sodium in PDB 8xet: High-Resolution Structure of the Siderophore Periplasmic Binding Protein Ftsb From Streptococcus Pyogenes

The structure of High-Resolution Structure of the Siderophore Periplasmic Binding Protein Ftsb From Streptococcus Pyogenes, PDB code: 8xet 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 / 1.11
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	75.924, 75.924, 102.859, 90, 90, 120
R / Rfree (%)	13.1 / 14.2

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

Zinc	(Zn)	3 atoms
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the High-Resolution Structure of the Siderophore Periplasmic Binding Protein Ftsb From Streptococcus Pyogenes (pdb code 8xet). 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, PDB code: 8xet:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na408 b:15.4 occ:0.60 O A:HOH591 2.1 25.7 0.6 O A:HOH823 2.1 22.4 1.0 O A:HOH567 2.2 26.3 1.0 OE2 A:GLU253 2.3 17.6 1.0 O A:HOH524 2.5 19.1 1.0 CD A:GLU253 3.1 13.8 1.0 OE1 A:GLU253 3.3 13.7 1.0 O A:HOH612 4.0 25.5 1.0 O A:HOH640 4.1 16.5 1.0 O A:HOH882 4.2 27.4 0.6 NZ A:LYS84 4.3 30.8 1.0 O A:HOH702 4.5 21.6 1.0 CG A:GLU253 4.5 13.7 1.0 O A:HOH706 4.5 29.4 1.0 OH A:TYR193 4.5 21.6 1.0 OH A:TYR81 4.6 23.5 1.0 CE1 A:TYR81 4.7 19.3 1.0 CE1 A:TYR193 4.8 17.5 1.0 CD A:LYS84 4.9 21.4 1.0 CB A:GLU253 5.0 13.3 1.0 OD1 A:ASN284 5.0 15.6 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na409 b:19.8 occ:0.30 OE1 A:GLU303 2.3 15.9 0.3 O A:HOH580 2.7 20.0 0.7 CD A:GLU303 2.7 13.7 0.3 OE2 A:GLU303 2.7 15.4 0.3 NH1 A:ARG302 3.0 15.0 1.0 CD2 A:LEU306 3.5 21.6 0.6 CD1 A:LEU306 3.5 15.5 0.4 CG A:GLU303 3.7 13.5 0.7 O A:HOH506 3.8 27.2 1.0 CZ A:ARG302 3.9 14.6 1.0 CG A:GLU303 4.0 12.1 0.3 NH2 A:ARG302 4.0 15.7 1.0 OE1 A:GLU303 4.3 19.7 0.7 CD A:GLU303 4.4 17.1 0.7 CA A:GLU303 4.5 10.7 0.7 CA A:GLU303 4.5 10.6 0.3 O A:HOH869 4.5 26.2 1.0 CB A:GLU303 4.5 11.2 0.7 CB A:GLU303 4.6 11.0 0.3 CG A:LEU306 4.7 14.9 0.4 CG A:LEU306 4.8 19.5 0.6 CB A:LEU306 4.8 14.2 0.4 CB A:LEU306 4.8 16.4 0.6

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