Zinc 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:

Sodium	(Na)	2 atoms
Iron	(Fe)	1 atom

The binding sites of Zinc 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 Zinc atom.
In total 5 binding sites of Zinc 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 Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 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 Zinc with other atoms in the Zn 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:Zn402 b:13.8 occ:0.50 O A:HOH779 1.8 27.4 0.8 OD2 A:ASP49 1.8 19.2 1.0 CG A:ASP49 2.8 17.6 1.0 OD1 A:ASP49 3.1 19.5 1.0 O A:HOH849 4.0 47.8 0.5 O A:HOH742 4.0 23.9 1.0 CB A:ASP49 4.1 15.8 1.0 O A:HOH798 4.5 27.2 0.5 CD1 A:LEU35 4.7 13.8 1.0

Zinc binding site 2 out of 5 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 Zinc with other atoms in the Zn 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:Zn403 b:14.6 occ:0.75 ZN A:ZN403 0.0 14.6 0.8 ZN A:ZN403 1.6 12.4 0.2 OE1 A:GLU121 2.0 28.0 1.0 O A:HOH770 2.1 17.6 0.8 CD A:GLU121 2.5 28.8 1.0 OE2 A:GLU121 2.7 31.4 1.0 CG A:GLU121 3.7 26.8 1.0 O A:HOH625 3.8 29.0 0.5 O A:HOH555 4.2 28.4 0.7 CB A:GLU121 4.9 24.7 1.0

Zinc binding site 3 out of 5 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 Zinc with other atoms in the Zn binding site number 3 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:Zn403 b:12.4 occ:0.25 ZN A:ZN403 0.0 12.4 0.2 ZN A:ZN403 1.6 14.6 0.8 OE2 A:GLU121 2.4 31.4 1.0 OE1 A:GLU121 2.6 28.0 1.0 CD A:GLU121 2.8 28.8 1.0 O A:HOH770 3.7 17.6 0.8 CG A:GLU121 4.2 26.8 1.0 O A:HOH625 5.0 29.0 0.5

Zinc binding site 4 out of 5 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 Zinc with other atoms in the Zn binding site number 4 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:Zn404 b:13.2 occ:1.00 OD2 A:ASP196 1.9 13.0 1.0 O A:HOH759 2.0 24.5 1.0 CG A:ASP196 2.7 12.1 1.0 OD1 A:ASP196 2.9 14.2 1.0 O A:HOH655 3.7 14.6 1.0 O A:HOH737 4.1 22.9 1.0 CB A:ASP196 4.1 12.2 1.0 N A:ASP196 4.6 12.8 1.0 C A:LYS195 4.6 13.9 1.0 CA A:ASP196 4.6 12.1 1.0 O A:HOH508 4.8 23.7 1.0 CB A:LYS195 4.8 17.6 1.0 O A:LYS195 4.8 16.0 1.0

Zinc binding site 5 out of 5 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 Zinc with other atoms in the Zn binding site number 5 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:Zn405 b:39.6 occ:0.60 NE2 A:HIS276 1.8 27.5 1.0 O A:HOH660 1.8 73.1 0.6 CE1 A:HIS276 2.7 28.7 1.0 O A:HOH784 2.9 16.1 0.4 CD2 A:HIS276 2.9 25.4 1.0 ND1 A:HIS276 3.8 28.0 1.0 CG A:HIS276 3.9 22.8 1.0 O A:LYS274 4.1 19.6 1.0 C A:LYS274 5.0 18.4 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