Zinc 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:

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

The binding sites of Zinc 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 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 E Bound, PDB code: 8xf7:
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 E Bound


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 E Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:13.2 occ:1.00 O A:HOH690 1.9 21.4 1.0 OE2 A:GLU309 2.0 15.0 1.0 NE2 A:HIS277 2.0 12.1 1.0 CD A:GLU309 2.7 15.5 1.0 OE1 A:GLU309 2.9 16.5 1.0 CE1 A:HIS277 3.0 11.7 1.0 CD2 A:HIS277 3.0 11.1 1.0 O A:HOH653 3.7 13.6 1.0 O A:LYS275 4.0 16.0 1.0 ND1 A:HIS277 4.1 11.6 1.0 CG A:HIS277 4.2 11.1 1.0 CG A:GLU309 4.2 17.0 1.0 O A:SER308 4.2 18.2 1.0 OH A:TYR247 4.3 12.3 1.0 CB A:LYS275 4.9 15.0 1.0 C A:SER308 4.9 16.0 1.0 OG A:SER308 5.0 12.7 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 E Bound


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 E Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:16.2 occ:0.60 O A:HOH700 1.7 26.6 0.6 OE1 A:GLU263 1.8 25.2 1.0 CD A:GLU263 2.8 25.1 1.0 OE2 A:GLU263 3.1 27.6 1.0 O A:HOH574 4.0 24.4 1.0 CG A:GLU263 4.1 23.6 1.0 O A:HOH541 4.8 31.4 0.5

Zinc binding site 3 out of 5 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 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 E Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:35.3 occ:0.75 O A:HOH559 1.9 53.1 0.6 O A:HOH627 2.0 32.5 1.0 NE2 A:HIS276 2.0 28.1 1.0 O A:HOH780 2.5 21.6 0.6 O A:HOH757 2.7 27.2 0.4 CE1 A:HIS276 3.0 29.9 1.0 CD2 A:HIS276 3.0 26.0 1.0 ND1 A:HIS276 4.1 29.1 1.0 CG A:HIS276 4.2 23.4 1.0 O A:LYS274 4.3 17.9 1.0 O A:HOH507 4.9 32.0 1.0 O A:VAL273 5.0 17.2 1.0

Zinc binding site 4 out of 5 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 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 E Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn406 b:12.9 occ:0.70 ZN A:ZN406 0.0 12.9 0.7 ZN A:ZN406 1.5 16.8 0.3 OE2 A:GLU174 2.1 12.4 1.0 O A:HOH786 2.1 20.1 1.0 ND1 A:HIS216 2.1 15.6 1.0 OE1 A:GLU174 2.6 14.4 1.0 CD A:GLU174 2.7 12.0 1.0 CE1 A:HIS216 3.1 17.6 1.0 CG A:HIS216 3.1 13.8 1.0 CB A:HIS216 3.3 12.5 1.0 O A:HOH830 4.1 36.7 1.0 CG A:GLU174 4.2 11.4 1.0 NE2 A:HIS216 4.2 17.8 1.0 CD2 A:HIS216 4.2 15.6 1.0 NZ A:LYS178 4.2 12.6 1.0 O A:HOH577 4.5 15.2 1.0 O A:HOH717 4.6 27.3 1.0 O A:HOH663 4.7 17.7 1.0 O A:PHE215 4.7 11.3 1.0 CA A:HIS216 4.7 11.7 1.0 C A:PHE215 5.0 10.7 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 E Bound


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 E Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn406 b:16.8 occ:0.30 ZN A:ZN406 0.0 16.8 0.3 ZN A:ZN406 1.5 12.9 0.7 OE1 A:GLU174 1.9 14.4 1.0 ND1 A:HIS216 1.9 15.6 1.0 CE1 A:HIS216 2.5 17.6 1.0 CD A:GLU174 2.6 12.0 1.0 OE2 A:GLU174 2.6 12.4 1.0 O A:HOH577 2.9 15.2 1.0 CG A:HIS216 3.1 13.8 1.0 O A:HOH786 3.6 20.1 1.0 NE2 A:HIS216 3.7 17.8 1.0 CB A:HIS216 3.7 12.5 1.0 CD2 A:HIS216 3.9 15.6 1.0 CG A:GLU174 4.0 11.4 1.0 O A:HOH638 4.2 17.5 1.0 O A:HOH663 4.3 17.7 1.0 O A:ALA214 4.4 13.7 1.0 CB A:GLU174 4.6 11.1 1.0 O A:HOH816 4.6 31.9 1.0 O A:PHE215 4.7 11.3 1.0 C A:PHE215 4.8 10.7 1.0 N A:HIS216 4.8 11.0 1.0 CA A:HIS216 4.9 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