Zinc 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:

Sodium	(Na)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Zinc 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 Zinc atom.
In total 7 binding sites of Zinc where determined in the High-Resolution Structure of the Siderophore Periplasmic Binding Protein Ftsb Mutant Y137A From Streptococcus Pyogenes, PDB code: 8xf9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 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 Zinc with other atoms in the Zn 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:Zn403 b:15.3 occ:1.00 OE2 A:GLU174 2.0 11.8 1.0 ND1 A:HIS216 2.0 13.8 1.0 O A:HOH747 2.0 20.7 1.0 OE1 A:GLU174 2.6 13.2 1.0 CD A:GLU174 2.6 11.4 1.0 CG A:HIS216 3.0 12.8 1.0 CE1 A:HIS216 3.1 17.4 1.0 CB A:HIS216 3.3 11.8 1.0 CG A:GLU174 4.1 10.8 1.0 NE2 A:HIS216 4.2 19.1 1.0 CD2 A:HIS216 4.2 16.1 1.0 O A:HOH801 4.2 29.9 0.6 NZ A:LYS178 4.3 11.3 1.0 O A:HOH560 4.5 15.3 1.0 O A:PHE215 4.5 10.8 1.0 O A:HOH598 4.7 16.7 1.0 CA A:HIS216 4.7 10.8 1.0 O A:HOH693 4.8 23.6 0.6 C A:PHE215 4.9 10.4 1.0

Zinc binding site 2 out of 7 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 Zinc with other atoms in the Zn 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:Zn404 b:12.2 occ:1.00 OE2 A:GLU309 2.0 13.4 1.0 O A:HOH587 2.0 17.0 1.0 NE2 A:HIS277 2.0 11.3 1.0 CD A:GLU309 2.7 13.4 1.0 OE1 A:GLU309 2.8 13.3 1.0 CE1 A:HIS277 3.0 11.8 1.0 CD2 A:HIS277 3.0 10.8 1.0 O A:HOH670 3.8 15.0 1.0 O A:LYS275 4.0 15.3 1.0 O A:SER308 4.1 13.8 1.0 ND1 A:HIS277 4.1 11.5 1.0 CG A:GLU309 4.2 13.7 1.0 CG A:HIS277 4.2 10.8 1.0 OH A:TYR247 4.3 12.5 1.0 C A:SER308 4.8 12.8 1.0 OG A:SER308 4.9 12.6 1.0 CB A:LYS275 4.9 15.6 1.0

Zinc binding site 3 out of 7 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 Zinc with other atoms in the Zn binding site number 3 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:Zn405 b:39.0 occ:0.55 ZN A:ZN405 0.0 39.0 0.6 ZN A:ZN405 2.0 55.7 0.5 OE1 A:GLU128 2.2 51.3 1.0 CD A:GLU128 3.4 40.5 1.0 OE2 A:GLU128 4.0 45.7 1.0 CG A:GLU128 4.5 32.8 1.0 CB A:GLU128 4.7 26.7 1.0 O A:HOH570 4.9 40.4 1.0

Zinc binding site 4 out of 7 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 Zinc with other atoms in the Zn binding site number 4 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:Zn405 b:55.7 occ:0.45 ZN A:ZN405 0.0 55.7 0.5 ZN A:ZN405 2.0 39.0 0.6 OE1 A:GLU128 2.8 51.3 1.0 CD A:GLU128 4.0 40.5 1.0 CG A:GLU128 4.6 32.8 1.0 CB A:GLU128 4.7 26.7 1.0 OE2 A:GLU128 4.9 45.7 1.0

Zinc binding site 5 out of 7 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 Zinc with other atoms in the Zn binding site number 5 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:Zn406 b:23.8 occ:0.75 O A:HOH615 1.9 19.5 0.8 O A:HOH794 2.0 25.0 0.8 OE2 A:GLU253 2.1 17.9 1.0 O A:HOH523 2.4 17.3 0.8 O A:HOH791 2.6 20.3 0.8 CD A:GLU253 3.1 14.5 1.0 OE1 A:GLU253 3.4 14.1 1.0 O A:HOH623 4.0 24.8 1.0 OH A:TYR193 4.2 17.0 1.0 O A:HOH820 4.4 23.4 1.0 CG A:GLU253 4.4 13.6 1.0 NZ A:LYS84 4.4 31.2 1.0 CE1 A:TYR193 4.5 14.9 1.0 O A:HOH585 4.6 16.6 1.0 OH A:TYR81 4.8 23.3 1.0 O A:HOH752 4.8 38.0 1.0 CB A:GLU253 4.8 13.2 1.0 CZ A:TYR193 4.9 15.2 1.0 O A:HOH761 5.0 35.1 1.0

Zinc binding site 6 out of 7 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 Zinc with other atoms in the Zn binding site number 6 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:Zn407 b:26.5 occ:0.35 OD2 A:ASP49 1.6 25.5 1.0 O A:HOH743 2.1 39.3 1.0 CG A:ASP49 2.7 20.8 1.0 O A:HOH727 2.7 22.8 0.5 ZN A:ZN408 2.8 20.9 0.5 O A:HOH697 2.8 29.1 0.6 OD1 A:ASP49 3.1 23.9 1.0 O A:HOH731 3.8 19.3 0.5 CB A:ASP49 4.0 18.1 1.0 CD1 A:LEU35 4.3 16.2 1.0 O A:HOH776 4.3 14.9 0.5 O A:HOH845 4.5 34.7 0.5

Zinc binding site 7 out of 7 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 Zinc with other atoms in the Zn binding site number 7 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:Zn408 b:20.9 occ:0.50 O A:HOH731 1.8 19.3 0.5 O A:HOH776 2.0 14.9 0.5 O A:HOH727 2.2 22.8 0.5 OD2 A:ASP49 2.3 25.5 1.0 ZN A:ZN407 2.8 26.5 0.3 CG A:ASP49 3.3 20.8 1.0 CB A:ASP49 3.6 18.1 1.0 O A:HOH743 4.2 39.3 1.0 O A:HOH764 4.3 27.1 0.6 O A:HOH647 4.4 33.0 1.0 OD1 A:ASP49 4.4 23.9 1.0 CD1 A:LEU35 4.7 16.2 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