Sodium in PDB 6top: Structure of the Pore C-Terminal Domain, A Protein of T9SS From Porphyromonas Gingivalis

The structure of Structure of the Pore C-Terminal Domain, A Protein of T9SS From Porphyromonas Gingivalis, PDB code: 6top was solved by T.N.Trinh, C.Cambillau, A.Roussel, P.Leone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.00 / 1.55
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	208.030, 52.220, 66.560, 90.00, 108.38, 90.00
R / Rfree (%)	19 / 21.5

The binding sites of Sodium atom in the Structure of the Pore C-Terminal Domain, A Protein of T9SS From Porphyromonas Gingivalis (pdb code 6top). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of the Pore C-Terminal Domain, A Protein of T9SS From Porphyromonas Gingivalis, PDB code: 6top:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of the Pore C-Terminal Domain, A Protein of T9SS From Porphyromonas Gingivalis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Pore C-Terminal Domain, A Protein of T9SS From Porphyromonas Gingivalis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na702 b:34.7 occ:1.00 O A:ALA627 2.3 33.6 1.0 O A:LEU633 2.4 36.4 1.0 O A:HOH804 2.4 50.3 1.0 O A:HIS630 2.4 34.5 1.0 O A:HOH951 2.5 41.5 1.0 O A:HOH917 2.7 40.3 1.0 C A:ALA627 3.3 33.0 1.0 C A:HIS630 3.5 34.8 1.0 C A:LEU633 3.6 35.2 1.0 CA A:ASP631 3.8 38.2 1.0 O A:ASP631 3.8 41.8 1.0 CA A:ALA627 3.8 32.3 1.0 C A:ASP631 3.8 39.2 1.0 CB A:ALA627 4.0 32.4 1.0 N A:ASP631 4.0 36.0 1.0 N A:LEU633 4.1 34.6 1.0 CA A:LEU633 4.4 34.2 1.0 O A:HOH960 4.4 42.2 1.0 CD A:LYS634 4.4 50.5 1.0 N A:GLU628 4.4 32.3 1.0 NZ A:LYS634 4.5 59.7 1.0 O A:HOH968 4.5 59.8 1.0 N A:LYS634 4.5 34.5 1.0 CA A:HIS630 4.6 33.4 1.0 N A:PHE632 4.6 37.4 1.0 N A:HIS630 4.6 32.7 1.0 CA A:LYS634 4.7 34.4 1.0 CE A:LYS634 4.9 56.1 1.0 CA A:GLU628 4.9 32.4 1.0 CB A:LEU633 4.9 33.4 1.0 O A:HOH905 5.0 38.6 1.0

Sodium binding site 2 out of 4 in the Structure of the Pore C-Terminal Domain, A Protein of T9SS From Porphyromonas Gingivalis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Pore C-Terminal Domain, A Protein of T9SS From Porphyromonas Gingivalis within 5.0Å range: probe atom residue distance (Å) B Occ B:Na702 b:28.9 occ:1.00 O B:LEU633 2.2 30.9 1.0 O B:ALA627 2.3 26.8 1.0 O B:HOH839 2.4 40.5 1.0 O B:HIS630 2.4 29.6 1.0 O B:HOH937 2.4 40.9 1.0 O B:HOH954 2.5 33.0 1.0 C B:ALA627 3.3 26.9 1.0 C B:LEU633 3.4 30.1 1.0 C B:HIS630 3.5 29.7 1.0 CA B:ALA627 3.8 26.3 1.0 CA B:ASP631 3.9 33.4 1.0 CB B:ALA627 4.0 26.7 1.0 C B:ASP631 4.0 34.8 1.0 N B:LEU633 4.0 29.1 1.0 O B:HOH990 4.1 50.3 1.0 O B:ASP631 4.1 38.3 1.0 N B:ASP631 4.1 31.1 1.0 CA B:LEU633 4.3 28.7 1.0 O B:HOH970 4.4 36.1 1.0 N B:LYS634 4.4 30.0 1.0 N B:GLU628 4.5 27.0 1.0 N B:HIS630 4.6 27.1 1.0 CA B:HIS630 4.6 28.4 1.0 CA B:LYS634 4.6 30.4 1.0 N B:PHE632 4.7 32.6 1.0 O B:HOH949 4.7 63.5 1.0 CB B:LEU633 4.8 28.0 1.0 CA B:GLU628 4.9 28.5 1.0 O B:HOH891 5.0 33.0 1.0

Sodium binding site 3 out of 4 in the Structure of the Pore C-Terminal Domain, A Protein of T9SS From Porphyromonas Gingivalis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of the Pore C-Terminal Domain, A Protein of T9SS From Porphyromonas Gingivalis within 5.0Å range: probe atom residue distance (Å) B Occ C:Na702 b:44.3 occ:1.00 O C:LEU633 2.2 43.2 1.0 O C:ALA627 2.2 34.2 1.0 O C:HIS630 2.2 39.9 1.0 O C:HOH830 2.7 73.8 1.0 O C:HOH931 2.9 55.7 1.0 C C:ALA627 3.2 33.9 1.0 C C:HIS630 3.3 40.0 1.0 C C:LEU633 3.4 42.5 1.0 CA C:ALA627 3.6 33.4 1.0 CA C:ASP631 3.8 44.9 1.0 O C:ASP631 3.8 47.6 1.0 C C:ASP631 3.8 46.1 1.0 N C:LEU633 3.9 42.4 1.0 CB C:ALA627 3.9 33.7 1.0 N C:ASP631 3.9 41.9 1.0 CA C:LEU633 4.2 42.2 1.0 N C:GLU628 4.4 33.3 1.0 CA C:HIS630 4.4 37.6 1.0 N C:HIS630 4.5 36.0 1.0 N C:LYS634 4.5 41.7 1.0 CD C:LYS634 4.5 57.6 1.0 N C:PHE632 4.5 45.3 1.0 NZ C:LYS634 4.6 66.6 1.0 O C:HOH942 4.6 47.1 1.0 CB C:LEU633 4.7 41.7 1.0 CA C:LYS634 4.7 41.7 1.0 CA C:GLU628 4.9 33.6 1.0 CE C:LYS634 4.9 63.3 1.0 C C:PHE632 4.9 43.6 1.0 N C:ALA627 5.0 32.6 1.0

Sodium binding site 4 out of 4 in the Structure of the Pore C-Terminal Domain, A Protein of T9SS From Porphyromonas Gingivalis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of the Pore C-Terminal Domain, A Protein of T9SS From Porphyromonas Gingivalis within 5.0Å range: probe atom residue distance (Å) B Occ D:Na702 b:36.9 occ:1.00 O D:ALA627 2.2 33.6 1.0 O D:HIS630 2.2 38.4 1.0 O D:LEU633 2.4 36.1 1.0 O D:HOH922 2.7 46.6 1.0 C D:HIS630 3.3 37.6 1.0 C D:ALA627 3.3 32.6 1.0 C D:LEU633 3.6 36.4 1.0 CA D:ASP631 3.7 40.3 1.0 CA D:ALA627 3.8 31.0 1.0 O D:ASP631 3.8 42.7 1.0 C D:ASP631 3.8 41.3 1.0 N D:ASP631 3.9 38.7 1.0 N D:LEU633 4.0 37.8 1.0 CB D:ALA627 4.1 31.2 1.0 CA D:LEU633 4.3 35.9 1.0 CA D:HIS630 4.4 35.9 1.0 N D:HIS630 4.4 35.6 1.0 N D:GLU628 4.4 32.9 1.0 NZ D:LYS634 4.5 55.4 1.0 CD D:LYS634 4.5 48.3 1.0 N D:PHE632 4.6 40.2 1.0 N D:LYS634 4.6 36.1 1.0 O D:HOH901 4.7 51.0 1.0 CA D:GLU628 4.8 34.1 1.0 CB D:LEU633 4.8 34.0 1.0 CA D:LYS634 4.8 36.2 1.0 CE D:LYS634 4.9 52.8 1.0 C D:GLU628 4.9 34.7 1.0

N.T.T.Trinh, H.Q.Tran, Q.Van Dong, C.Cambillau, A.Roussel, P.Leone. Crystal Structure of Type IX Secretion System Pore C-Terminal Domain From Porphyromonas Gingivalis in Complex with A Peptidoglycan Fragment. Sci Rep V. 10 7384 2020.
ISSN: ESSN 2045-2322
PubMed: 32355178
DOI: 10.1038/S41598-020-64115-Z