Sodium in PDB 6tqd: D00-D0 Domain of Intimin

The structure of D00-D0 Domain of Intimin, PDB code: 6tqd was solved by J.Weikum, J.C.Leo, J.P.Morth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.83 / 1.48
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	56.039, 65.473, 79.378, 77.78, 76.55, 84.76
R / Rfree (%)	17.9 / 21.6

The structure of D00-D0 Domain of Intimin also contains other interesting chemical elements:

Bromine	(Br)	9 atoms
Chlorine	(Cl)	6 atoms

The binding sites of Sodium atom in the D00-D0 Domain of Intimin (pdb code 6tqd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the D00-D0 Domain of Intimin, PDB code: 6tqd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the D00-D0 Domain of Intimin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of D00-D0 Domain of Intimin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na703 b:23.0 occ:1.00 O A:HOH902 2.2 24.6 1.0 O A:ILE458 2.4 14.4 1.0 O A:HOH993 2.4 53.6 1.0 O B:HOH858 2.5 28.1 1.0 O A:HOH930 2.6 17.8 1.0 O A:HOH1085 2.7 36.7 1.0 O B:HOH846 3.5 92.7 1.0 C A:ILE458 3.6 11.6 1.0 HB A:ILE458 3.8 12.9 1.0 O A:HOH966 4.0 9.5 1.0 O B:HOH862 4.1 27.6 1.0 HA A:PRO459 4.1 18.4 1.0 C A:PRO459 4.2 14.8 1.0 HG22 A:ILE458 4.2 15.4 1.0 O B:HOH1120 4.3 20.9 1.0 OD1 A:ASP461 4.3 19.5 1.0 O A:PRO459 4.3 17.5 1.0 O B:HOH1014 4.3 23.7 1.0 H A:ILE458 4.4 11.3 1.0 O A:LEU543 4.4 12.0 1.0 CA A:PRO459 4.4 15.3 1.0 N A:PRO459 4.5 13.0 1.0 N A:HIS460 4.5 12.5 1.0 CB A:ILE458 4.5 10.7 1.0 O A:HOH840 4.6 29.1 1.0 CA A:ILE458 4.6 11.3 1.0 BR A:BR702 4.7 19.1 0.4 H A:HIS460 4.7 15.0 1.0 HE22 B:GLN500 4.8 20.9 1.0 CG A:ASP461 4.8 23.8 1.0 O A:HOH1069 4.8 32.7 1.0 OE1 B:GLN500 4.8 18.7 1.0 CG2 A:ILE458 4.8 12.8 1.0 OD2 A:ASP461 4.9 27.1 1.0 N A:ILE458 4.9 9.4 1.0 HA A:HIS460 5.0 15.3 1.0 C A:HIS460 5.0 12.5 1.0

Sodium binding site 2 out of 2 in the D00-D0 Domain of Intimin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of D00-D0 Domain of Intimin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na703 b:29.4 occ:1.00 O B:HOH834 2.2 26.5 1.0 O C:HOH808 2.4 34.4 1.0 O B:ILE458 2.5 13.0 1.0 O B:HOH907 2.5 16.4 1.0 C B:ILE458 3.8 12.4 1.0 HB B:ILE458 3.9 9.5 1.0 O C:HOH839 3.9 35.8 1.0 O B:HOH905 4.0 10.8 1.0 O C:HOH947 4.0 26.5 1.0 HA B:PRO459 4.2 16.4 1.0 O B:PRO459 4.2 15.1 1.0 C B:PRO459 4.2 13.3 1.0 O B:HOH1129 4.2 22.4 1.0 OD1 B:ASP461 4.3 19.5 1.0 HG22 B:ILE458 4.4 12.6 1.0 O B:LEU543 4.4 10.8 1.0 BR B:BR701 4.5 19.6 0.3 CA B:PRO459 4.5 13.7 1.0 H B:ILE458 4.5 9.7 0.4 N B:HIS460 4.6 11.5 1.0 H B:ILE458 4.6 9.7 0.6 CB B:ILE458 4.6 7.9 1.0 OE1 C:GLN500 4.6 23.6 1.0 N B:PRO459 4.6 12.2 1.0 O B:HOH934 4.6 29.8 1.0 HE22 C:GLN500 4.7 27.7 1.0 CA B:ILE458 4.7 9.1 1.0 H B:HIS460 4.8 13.8 1.0 CG B:ASP461 4.8 18.0 1.0 OD2 B:ASP461 4.9 23.1 1.0 HA B:HIS460 4.9 14.6 1.0 CG2 B:ILE458 5.0 10.5 1.0 OD1 B:ASN457 5.0 25.3 0.4

J.Weikum, A.Kulakova, G.Tesei, S.Yoshimoto, L.V.Jaegerum, M.Schutz, K.Hori, M.Skepo, P.Harris, J.C.Leo, J.P.Morth. The Extracellular Juncture Domains in the Intimin Passenger Adopt A Constitutively Extended Conformation Inducing Restraints to Its Sphere of Action. Sci Rep V. 10 21249 2020.
ISSN: ESSN 2045-2322
PubMed: 33277518
DOI: 10.1038/S41598-020-77706-7