Zinc in PDB 5a0l: N-Terminal Thioester Domain of Fibronectin-Binding Protein Sfbi From Streptococcus Pyogenes

The structure of N-Terminal Thioester Domain of Fibronectin-Binding Protein Sfbi From Streptococcus Pyogenes, PDB code: 5a0l was solved by M.Walden, J.M.Edwards, A.M.Dziewulska, S.-Y.Kan, U.Schwarz-Linek, M.J.Banfield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.22 / 1.35
Space group	I 41
Cell size a, b, c (Å), α, β, γ (°)	165.120, 165.120, 42.520, 90.00, 90.00, 90.00
R / Rfree (%)	13.1 / 15.3

The binding sites of Zinc atom in the N-Terminal Thioester Domain of Fibronectin-Binding Protein Sfbi From Streptococcus Pyogenes (pdb code 5a0l). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the N-Terminal Thioester Domain of Fibronectin-Binding Protein Sfbi From Streptococcus Pyogenes, PDB code: 5a0l:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the N-Terminal Thioester Domain of Fibronectin-Binding Protein Sfbi 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 N-Terminal Thioester Domain of Fibronectin-Binding Protein Sfbi From Streptococcus Pyogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1271 b:21.7 occ:0.60 O A:HOH2048 2.1 23.1 0.6 O A:HOH2046 2.1 26.3 0.6 O A:HOH2047 2.1 24.5 0.6 CE1 A:HIS93 2.1 23.0 0.4 O A:HOH2290 2.2 30.9 0.6 O A:HOH2035 2.2 31.3 0.6 NE2 A:HIS93 2.2 19.4 0.6 NE2 A:HIS93 2.9 23.8 0.4 O A:HOH2045 2.9 16.2 0.4 CE1 A:HIS93 3.1 21.0 0.6 CD2 A:HIS93 3.2 19.0 0.6 ND1 A:HIS93 3.3 21.1 0.4 CD2 A:HIS93 4.2 20.0 0.4 O A:HOH2025 4.2 26.9 1.0 ND1 A:HIS93 4.2 18.7 0.6 O A:HOH2024 4.3 22.1 1.0 CG A:HIS93 4.3 17.3 0.6 O A:HOH2034 4.3 38.9 1.0 CG A:HIS93 4.3 18.2 0.4 O A:ALA90 4.4 27.4 1.0 O A:HOH2097 4.5 24.0 1.0 CB A:PHE116 4.8 15.1 1.0 CG A:PHE116 4.9 15.2 1.0

Zinc binding site 2 out of 5 in the N-Terminal Thioester Domain of Fibronectin-Binding Protein Sfbi 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 N-Terminal Thioester Domain of Fibronectin-Binding Protein Sfbi From Streptococcus Pyogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1272 b:20.0 occ:0.75 OD2 A:ASP233 2.0 20.4 1.0 O A:HOH2254 2.0 26.6 0.8 O A:HOH2252 2.2 12.5 0.8 CG A:ASP233 2.8 18.0 1.0 OD1 A:ASP233 2.8 18.5 1.0 O A:HOH2253 3.2 42.3 0.8 O A:HOH2256 3.7 46.5 1.0 O A:HOH2265 4.0 36.1 1.0 OD1 A:ASN235 4.0 20.4 1.0 CB A:ASP233 4.2 16.8 1.0 O A:HOH2251 4.3 32.5 1.0 O A:HOH2245 4.6 56.8 1.0 O A:HOH2255 4.7 45.6 1.0 CB A:ASN235 4.7 14.7 1.0 CG A:ASN235 4.8 15.8 1.0 CD A:PRO234 4.9 18.6 1.0

Zinc binding site 3 out of 5 in the N-Terminal Thioester Domain of Fibronectin-Binding Protein Sfbi 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 N-Terminal Thioester Domain of Fibronectin-Binding Protein Sfbi From Streptococcus Pyogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1273 b:16.2 occ:1.00 OE2 A:GLU258 1.9 15.5 1.0 O A:HOH2282 2.0 21.2 1.0 CD A:GLU258 2.6 14.8 1.0 OE1 A:GLU258 2.7 18.0 1.0 O A:HOH2291 3.0 43.2 1.0 CG A:GLU258 4.1 17.8 1.0 CE A:LYS254 4.5 25.6 1.0 NZ A:LYS254 4.8 34.3 1.0

Zinc binding site 4 out of 5 in the N-Terminal Thioester Domain of Fibronectin-Binding Protein Sfbi 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 N-Terminal Thioester Domain of Fibronectin-Binding Protein Sfbi From Streptococcus Pyogenes within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1271 b:28.5 occ:0.40 O B:HOH2025 1.7 39.0 0.4 O B:HOH2037 1.9 30.1 0.4 O B:HOH2035 2.0 32.5 0.4 O B:HOH2036 2.2 28.2 0.4 CE1 B:HIS93 2.4 26.5 0.6 NE2 B:HIS93 2.4 27.9 0.4 O B:HOH2024 2.7 34.8 0.6 NE2 B:HIS93 3.0 28.8 0.6 CE1 B:HIS93 3.2 26.0 0.4 CD2 B:HIS93 3.5 21.3 0.4 ND1 B:HIS93 3.6 24.4 0.6 O B:HOH2023 3.7 39.4 1.0 O B:ALA90 4.1 35.1 1.0 O B:HOH2017 4.3 24.2 1.0 CD2 B:HIS93 4.3 24.1 0.6 ND1 B:HIS93 4.4 24.8 0.4 O B:HOH2069 4.5 32.5 1.0 CG B:HIS93 4.5 21.9 0.4 CG B:HIS93 4.6 21.7 0.6 O B:HOH2016 4.8 86.0 1.0 CB B:PHE116 4.9 17.9 1.0

Zinc binding site 5 out of 5 in the N-Terminal Thioester Domain of Fibronectin-Binding Protein Sfbi 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 N-Terminal Thioester Domain of Fibronectin-Binding Protein Sfbi From Streptococcus Pyogenes within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1272 b:22.7 occ:0.75 OXT B:ACT1274 1.9 31.4 0.8 OE2 B:GLU258 1.9 23.8 1.0 OXT B:ACT1273 2.2 19.7 0.8 C B:ACT1274 2.7 29.2 0.8 CD B:GLU258 2.8 26.8 1.0 O B:ACT1274 2.9 45.1 0.8 OE1 B:GLU258 2.9 27.1 1.0 C B:ACT1273 3.2 25.6 0.8 O B:ACT1273 3.4 34.1 0.8 CE B:LYS254 3.8 40.4 1.0 O B:HOH2166 4.0 33.6 1.0 NZ B:LYS254 4.1 33.7 1.0 CH3 B:ACT1274 4.1 30.3 0.8 CG B:GLU258 4.2 24.7 1.0 CH3 B:ACT1273 4.4 27.1 0.8 O B:HOH2065 4.5 32.4 1.0 O B:HOH2093 4.8 33.4 1.0

M.Walden, J.M.Edwards, A.M.Dziewulska, R.Bergmann, G.Saalbach, S.Y.Kan, O.K.Miller, M.Weckener, R.J.Jackson, S.L.Shirran, C.H.Botting, G.J.Florence, M.Rohde, M.J.Banfield, U.Schwarz-Linek. An Internal Thioester in A Pathogen Surface Protein Mediates Covalent Host Binding. Elife V. 4 2015.
ISSN: ESSN 2050-084X
PubMed: 26032562
DOI: 10.7554/ELIFE.06638