Sodium in PDB 8xf9: High-Resolution Structure of the Siderophore Periplasmic Binding Protein Ftsb Mutant Y137A From Streptococcus Pyogenes

The structure of High-Resolution Structure of the Siderophore Periplasmic Binding Protein Ftsb Mutant Y137A From Streptococcus Pyogenes, PDB code: 8xf9 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)	40.40 / 1.15
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	75.847, 75.847, 102.622, 90, 90, 120
R / Rfree (%)	13.1 / 14.7

The structure of High-Resolution Structure of the Siderophore Periplasmic Binding Protein Ftsb Mutant Y137A From Streptococcus Pyogenes also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Zinc	(Zn)	7 atoms

The binding sites of Sodium atom in the High-Resolution Structure of the Siderophore Periplasmic Binding Protein Ftsb Mutant Y137A From Streptococcus Pyogenes (pdb code 8xf9). 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 Mutant Y137A From Streptococcus Pyogenes, PDB code: 8xf9:
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 Mutant Y137A 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 Mutant Y137A From Streptococcus Pyogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:Na412 b:44.0 occ:1.00 O A:HOH712 2.4 22.0 1.0 OG1 A:THR63 2.5 23.9 1.0 O A:HOH803 2.6 31.1 1.0 O A:HOH588 2.6 19.0 1.0 O A:HOH815 2.7 32.4 1.0 CB A:THR63 3.3 18.7 1.0 OH A:TYR64 3.4 15.6 1.0 CG2 A:THR63 3.4 19.5 1.0 CB A:ALA137 3.7 18.0 1.0 O A:HOH505 3.7 24.2 1.0 CZ A:TYR64 3.9 13.7 1.0 CE2 A:TYR64 3.9 13.4 1.0 O A:HOH851 4.0 25.9 1.0 CA A:ALA137 4.4 15.6 1.0 O A:HOH782 4.7 24.1 0.5 CA A:THR63 4.7 13.8 1.0 O A:HOH836 4.8 40.0 1.0 CE1 A:TYR64 4.9 12.8 1.0 CD2 A:TYR64 4.9 13.1 1.0 O A:HOH607 4.9 24.3 1.0 N A:ALA137 4.9 15.3 1.0

Sodium binding site 2 out of 2 in the High-Resolution Structure of the Siderophore Periplasmic Binding Protein Ftsb Mutant Y137A 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 Mutant Y137A From Streptococcus Pyogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:Na413 b:32.9 occ:0.50 OD1 A:ASN310 2.5 26.5 1.0 O A:LEU306 2.6 17.5 1.0 C A:GLU309 3.4 14.8 1.0 N A:ASN310 3.4 16.4 1.0 CG A:ASN310 3.5 23.2 1.0 C A:LEU306 3.6 14.5 1.0 O A:GLU309 3.6 15.1 1.0 CA A:ASN310 3.9 19.0 1.0 CA A:SER307 3.9 15.1 1.0 CA A:GLU309 4.0 13.1 1.0 CB A:GLU309 4.0 13.5 1.0 N A:GLU309 4.1 12.4 1.0 N A:SER307 4.2 14.1 1.0 C A:SER307 4.2 14.4 1.0 CB A:ASN310 4.3 21.4 1.0 ND2 A:ASN310 4.3 28.1 1.0 O A:SER307 4.4 14.7 1.0 O A:HOH773 4.5 34.3 1.0 CA A:LEU306 4.7 14.3 0.5 CA A:LEU306 4.7 13.9 0.5 N A:SER308 4.9 13.6 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