Zinc 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:

Chlorine	(Cl)	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 (pdb code 8xet). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the High-Resolution Structure of the Siderophore Periplasmic Binding Protein Ftsb From Streptococcus Pyogenes, PDB code: 8xet:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 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 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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:15.4 occ:1.00 OE2 A:GLU174 2.0 12.2 1.0 ND1 A:HIS216 2.1 13.4 1.0 O A:HOH758 2.1 20.4 1.0 OE1 A:GLU174 2.6 13.7 1.0 CD A:GLU174 2.6 11.6 1.0 CG A:HIS216 3.0 12.6 1.0 CE1 A:HIS216 3.1 16.8 1.0 CB A:HIS216 3.3 11.7 1.0 O A:HOH792 3.7 21.8 0.6 CG A:GLU174 4.1 11.3 1.0 O A:HOH821 4.2 37.3 1.0 CD2 A:HIS216 4.2 15.0 1.0 NE2 A:HIS216 4.2 16.9 1.0 NZ A:LYS178 4.3 11.2 1.0 O A:HOH739 4.5 37.8 1.0 O A:HOH588 4.6 14.6 1.0 O A:PHE215 4.6 10.7 1.0 CA A:HIS216 4.7 10.6 1.0 O A:HOH791 4.8 32.6 1.0 O A:HOH619 4.9 18.7 1.0 C A:PHE215 4.9 10.3 1.0 N A:HIS216 5.0 10.2 1.0

Zinc binding site 2 out of 3 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 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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn406 b:11.9 occ:1.00 OE2 A:GLU309 1.9 13.3 1.0 O A:HOH579 2.0 16.7 1.0 NE2 A:HIS277 2.0 11.5 1.0 CD A:GLU309 2.7 12.6 1.0 OE1 A:GLU309 2.8 13.2 1.0 CE1 A:HIS277 3.0 11.9 1.0 CD2 A:HIS277 3.0 11.2 1.0 O A:HOH651 3.8 15.4 1.0 O A:LYS275 4.0 15.6 1.0 O A:SER308 4.1 14.0 1.0 ND1 A:HIS277 4.1 12.2 1.0 CG A:GLU309 4.2 13.3 1.0 CG A:HIS277 4.2 11.1 1.0 OH A:TYR247 4.3 12.3 1.0 O A:HOH857 4.6 18.9 1.0 C A:SER308 4.8 12.7 1.0 OG A:SER308 4.8 12.3 1.0 CB A:LYS275 4.9 16.5 1.0

Zinc binding site 3 out of 3 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 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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn407 b:26.2 occ:0.50 O A:HOH814 1.7 22.4 0.5 OE1 A:GLU104 2.0 31.5 1.0 OE2 A:GLU104 2.5 34.9 1.0 CD A:GLU104 2.5 28.2 1.0 O A:HOH779 4.0 25.4 1.0 CG A:GLU104 4.1 25.0 1.0 O A:HOH670 4.2 25.9 1.0 CB A:GLU104 4.8 19.9 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