Sodium in PDB 6nw9: Crystal Structure of A Tailspike Protein 3 (TSP3, ORF212) From Escherichia Coli O157:H7 Bacteriophage CBA120

The structure of Crystal Structure of A Tailspike Protein 3 (TSP3, ORF212) From Escherichia Coli O157:H7 Bacteriophage CBA120, PDB code: 6nw9 was solved by J.Y.Greenfield, O.Herzberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.16 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	99.439, 66.770, 161.600, 90.00, 103.58, 90.00
R / Rfree (%)	15.1 / 18.4

The structure of Crystal Structure of A Tailspike Protein 3 (TSP3, ORF212) From Escherichia Coli O157:H7 Bacteriophage CBA120 also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	6 atoms

The binding sites of Sodium atom in the Crystal Structure of A Tailspike Protein 3 (TSP3, ORF212) From Escherichia Coli O157:H7 Bacteriophage CBA120 (pdb code 6nw9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of A Tailspike Protein 3 (TSP3, ORF212) From Escherichia Coli O157:H7 Bacteriophage CBA120, PDB code: 6nw9:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of A Tailspike Protein 3 (TSP3, ORF212) From Escherichia Coli O157:H7 Bacteriophage CBA120


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of A Tailspike Protein 3 (TSP3, ORF212) From Escherichia Coli O157:H7 Bacteriophage CBA120 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na702 b:26.1 occ:1.00 O A:HOH1290 2.3 25.1 1.0 O A:SER272 2.3 12.7 1.0 O A:HOH1287 2.4 22.0 1.0 O A:HOH1325 2.4 32.4 1.0 O A:HOH1153 2.5 24.5 1.0 OG1 A:THR274 2.6 12.7 1.0 CB A:THR274 3.4 12.7 1.0 C A:SER272 3.5 9.1 1.0 N A:THR274 3.9 11.0 1.0 O A:HOH1303 4.0 22.4 1.0 O A:HOH1015 4.1 23.1 1.0 C A:PHE273 4.1 13.8 1.0 O A:HOH859 4.1 13.5 1.0 CA A:THR274 4.2 9.8 1.0 CA A:SER272 4.3 13.9 1.0 O A:HOH875 4.3 36.7 1.0 O A:PHE273 4.4 10.2 1.0 O A:HOH1429 4.5 39.7 1.0 N A:PHE273 4.5 10.7 1.0 CG2 A:THR274 4.5 13.4 1.0 OD1 A:ASP246 4.6 17.3 1.0 CA A:PHE273 4.6 11.2 1.0 CB A:SER272 4.7 18.7 1.0 NH1 A:ARG245 4.8 20.8 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of A Tailspike Protein 3 (TSP3, ORF212) From Escherichia Coli O157:H7 Bacteriophage CBA120


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of A Tailspike Protein 3 (TSP3, ORF212) From Escherichia Coli O157:H7 Bacteriophage CBA120 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na703 b:26.7 occ:0.61 O A:HOH823 2.3 32.4 1.0 OG A:SER540 2.5 27.3 1.0 CB A:SER540 3.5 17.4 1.0 O A:HOH1273 3.7 31.1 1.0 CA A:SER540 4.3 14.7 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of A Tailspike Protein 3 (TSP3, ORF212) From Escherichia Coli O157:H7 Bacteriophage CBA120


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of A Tailspike Protein 3 (TSP3, ORF212) From Escherichia Coli O157:H7 Bacteriophage CBA120 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na704 b:24.9 occ:1.00 O B:SER272 2.3 16.3 1.0 O B:HOH1274 2.4 31.6 1.0 O B:HOH1232 2.4 24.2 1.0 O B:HOH1111 2.4 24.1 1.0 OG1 B:THR274 2.4 15.2 1.0 O B:HOH1262 2.5 23.4 1.0 CB B:THR274 3.4 12.6 1.0 C B:SER272 3.4 13.1 1.0 O B:HOH921 3.9 13.4 1.0 N B:THR274 3.9 13.9 1.0 C B:PHE273 4.0 14.2 1.0 O B:HOH1267 4.1 32.2 1.0 O B:HOH896 4.1 27.3 1.0 CA B:THR274 4.2 11.4 1.0 CA B:SER272 4.3 17.3 1.0 O B:HOH1364 4.3 36.1 1.0 O B:PHE273 4.3 13.2 1.0 N B:PHE273 4.4 16.4 1.0 O B:HOH876 4.4 41.5 1.0 CA B:PHE273 4.5 16.6 1.0 CG2 B:THR274 4.6 15.4 1.0 OD1 B:ASP246 4.6 20.7 1.0 NH1 B:ARG245 4.6 21.6 1.0 CB B:SER272 4.6 18.6 1.0

J.Greenfield, X.Shang, H.Luo, Y.Zhou, R.D.Heselpoth, D.C.Nelson, O.Herzberg. Structure and Tailspike Glycosidase Machinery of ORF212 From E. Coli O157:H7 Phage CBA120 (TSP3). Sci Rep V. 9 7349 2019.
ISSN: ESSN 2045-2322
PubMed: 31089181
DOI: 10.1038/S41598-019-43748-9