Sodium in PDB 6ubv: The Structure of the Streptococcus Gordonii Surface Protein Sspb in Complex with Tev Peptide Provides Clues to the Adherence of Oral Streptococcal Adherence to Salivary Agglutinin

The structure of The Structure of the Streptococcus Gordonii Surface Protein Sspb in Complex with Tev Peptide Provides Clues to the Adherence of Oral Streptococcal Adherence to Salivary Agglutinin, PDB code: 6ubv was solved by N.Schormann, C.Deivanayagam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.72 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.810, 132.697, 243.819, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 25

The structure of The Structure of the Streptococcus Gordonii Surface Protein Sspb in Complex with Tev Peptide Provides Clues to the Adherence of Oral Streptococcal Adherence to Salivary Agglutinin also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Sodium atom in the The Structure of the Streptococcus Gordonii Surface Protein Sspb in Complex with Tev Peptide Provides Clues to the Adherence of Oral Streptococcal Adherence to Salivary Agglutinin (pdb code 6ubv). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the The Structure of the Streptococcus Gordonii Surface Protein Sspb in Complex with Tev Peptide Provides Clues to the Adherence of Oral Streptococcal Adherence to Salivary Agglutinin, PDB code: 6ubv:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the The Structure of the Streptococcus Gordonii Surface Protein Sspb in Complex with Tev Peptide Provides Clues to the Adherence of Oral Streptococcal Adherence to Salivary Agglutinin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of the Streptococcus Gordonii Surface Protein Sspb in Complex with Tev Peptide Provides Clues to the Adherence of Oral Streptococcal Adherence to Salivary Agglutinin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na903 b:27.4 occ:1.00 O A:VAL587 3.1 37.1 1.0 CE2 A:TRP816 3.2 21.6 1.0 CD2 A:TRP816 3.2 22.3 1.0 CZ2 A:TRP816 3.2 34.9 1.0 CE3 A:TRP816 3.2 37.3 1.0 CH2 A:TRP816 3.2 37.9 1.0 CZ3 A:TRP816 3.2 32.8 1.0 C5 A:SNZ902 3.5 52.7 1.0 CA A:VAL587 3.7 21.7 1.0 CG1 A:VAL587 3.7 22.9 1.0 C A:VAL587 3.7 30.7 1.0 C12 A:SNZ902 3.9 52.1 1.0 NE1 A:TRP816 3.9 24.6 1.0 CG A:TRP816 4.0 17.7 1.0 C7 A:SNZ902 4.0 56.4 1.0 C11 A:SNZ902 4.2 54.8 1.0 N1 A:SNZ902 4.2 51.3 1.0 CD1 A:TRP816 4.3 25.4 1.0 CB A:VAL587 4.3 21.0 1.0 C6 A:SNZ902 4.3 44.3 1.0 C8 A:SNZ902 4.4 60.2 1.0 O A:THR586 4.4 27.1 1.0 C10 A:SNZ902 4.6 57.4 1.0 C9 A:SNZ902 4.6 60.6 1.0 N A:VAL587 4.9 27.8 1.0 CB A:TRP816 4.9 13.0 1.0 N A:SER588 5.0 26.2 1.0

Sodium binding site 2 out of 3 in the The Structure of the Streptococcus Gordonii Surface Protein Sspb in Complex with Tev Peptide Provides Clues to the Adherence of Oral Streptococcal Adherence to Salivary Agglutinin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Structure of the Streptococcus Gordonii Surface Protein Sspb in Complex with Tev Peptide Provides Clues to the Adherence of Oral Streptococcal Adherence to Salivary Agglutinin within 5.0Å range: probe atom residue distance (Å) B Occ C:Na903 b:34.2 occ:1.00 CD2 C:TRP816 3.0 23.6 1.0 CE2 C:TRP816 3.0 20.6 1.0 CE3 C:TRP816 3.3 30.8 1.0 CG C:TRP816 3.4 19.7 1.0 NE1 C:TRP816 3.5 20.5 1.0 CZ2 C:TRP816 3.5 25.6 1.0 C12 C:SNZ902 3.6 71.9 1.0 CA C:VAL587 3.6 34.4 1.0 CD1 C:TRP816 3.7 22.7 1.0 CZ3 C:TRP816 3.7 22.9 1.0 CH2 C:TRP816 3.8 29.1 1.0 O C:VAL587 3.8 49.1 1.0 C11 C:SNZ902 3.9 72.4 1.0 C7 C:SNZ902 3.9 70.5 1.0 O C:THR586 4.0 32.0 1.0 CG1 C:VAL587 4.1 36.2 1.0 C5 C:SNZ902 4.1 57.6 1.0 C C:VAL587 4.2 42.1 1.0 CB C:VAL587 4.2 40.3 1.0 CB C:TRP816 4.3 17.1 1.0 CG2 C:VAL587 4.3 28.6 1.0 C6 C:SNZ902 4.3 61.5 1.0 C10 C:SNZ902 4.5 73.8 1.0 C8 C:SNZ902 4.5 73.2 1.0 N C:VAL587 4.6 27.2 1.0 N1 C:SNZ902 4.6 49.9 1.0 C C:THR586 4.6 26.0 1.0 C9 C:SNZ902 4.8 77.9 1.0

Sodium binding site 3 out of 3 in the The Structure of the Streptococcus Gordonii Surface Protein Sspb in Complex with Tev Peptide Provides Clues to the Adherence of Oral Streptococcal Adherence to Salivary Agglutinin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Structure of the Streptococcus Gordonii Surface Protein Sspb in Complex with Tev Peptide Provides Clues to the Adherence of Oral Streptococcal Adherence to Salivary Agglutinin within 5.0Å range: probe atom residue distance (Å) B Occ D:Na904 b:33.2 occ:1.00 CD2 D:TRP816 2.9 31.3 1.0 CE2 D:TRP816 3.0 28.2 1.0 CE3 D:TRP816 3.2 41.7 1.0 CZ2 D:TRP816 3.3 48.1 1.0 CZ3 D:TRP816 3.4 36.1 1.0 CH2 D:TRP816 3.5 45.9 1.0 O D:VAL587 3.5 40.9 1.0 CG D:TRP816 3.5 24.2 1.0 NE1 D:TRP816 3.5 34.6 1.0 CA D:VAL587 3.6 27.4 1.0 CD1 D:TRP816 3.8 35.1 1.0 CG1 D:VAL587 3.9 29.0 1.0 C D:VAL587 4.0 30.8 1.0 C7 D:SNZ903 4.0 54.0 1.0 C8 D:SNZ903 4.1 60.2 1.0 N1 D:SNZ903 4.1 52.8 1.0 CB D:VAL587 4.1 24.8 1.0 O D:THR586 4.2 29.5 1.0 C12 D:SNZ903 4.2 46.0 1.0 C9 D:SNZ903 4.3 72.8 1.0 CG2 D:VAL587 4.4 19.7 1.0 C11 D:SNZ903 4.4 57.2 1.0 CB D:TRP816 4.4 21.2 1.0 C10 D:SNZ903 4.5 67.9 1.0 N D:SNZ903 4.6 55.9 0.5 C6 D:SNZ903 4.6 55.6 1.0 N D:VAL587 4.6 26.0 1.0 C5 D:SNZ903 4.7 47.5 1.0 C D:THR586 4.8 28.9 1.0 C4 D:SNZ903 4.9 45.3 1.0 O2 D:SNZ903 5.0 64.0 1.0

N.Schormann, C.Deivanayagam. The Structure of the Streptococcus Gordonii Surface Protein Sspb in Complex with Tev Peptide Provides Clues to the Adherence of Oral Streptococcal Adherence to Salivary Agglutinin To Be Published.