Sodium in PDB 8q1w: TTX183B - A C-Type Cytochrome Domain From the Teredinibacter Turnerae Protein TERTU_2913

The structure of TTX183B - A C-Type Cytochrome Domain From the Teredinibacter Turnerae Protein TERTU_2913, PDB code: 8q1w was solved by B.S.Rajagopal, G.R.Hemsworth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.46 / 1.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	38.548, 38.659, 44.049, 90.48, 90.59, 94.48
R / Rfree (%)	19.5 / 24

The structure of TTX183B - A C-Type Cytochrome Domain From the Teredinibacter Turnerae Protein TERTU_2913 also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Iron	(Fe)	3 atoms

The binding sites of Sodium atom in the TTX183B - A C-Type Cytochrome Domain From the Teredinibacter Turnerae Protein TERTU_2913 (pdb code 8q1w). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the TTX183B - A C-Type Cytochrome Domain From the Teredinibacter Turnerae Protein TERTU_2913, PDB code: 8q1w:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the TTX183B - A C-Type Cytochrome Domain From the Teredinibacter Turnerae Protein TERTU_2913


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of TTX183B - A C-Type Cytochrome Domain From the Teredinibacter Turnerae Protein TERTU_2913 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:8.9 occ:1.00 O A:MET56 2.4 7.5 1.0 O A:PRO61 2.4 9.2 1.0 O A:ALA53 2.4 10.4 1.0 O A:ILE52 2.4 8.7 1.0 O A:CYS64 2.4 11.5 1.0 HA A:ALA53 2.9 10.2 1.0 C A:ALA53 3.0 10.4 1.0 HB3 A:CYS64 3.2 13.9 1.0 HA A:PRO61 3.2 10.9 1.0 C A:PRO61 3.3 10.8 1.0 CA A:ALA53 3.4 10.2 1.0 C A:ILE52 3.4 9.2 1.0 H A:CYS64 3.5 12.9 1.0 C A:MET56 3.5 7.0 1.0 C A:CYS64 3.5 12.4 1.0 CA A:PRO61 3.7 10.8 1.0 HB3 A:PRO61 3.7 11.0 1.0 N A:MET56 3.7 7.0 1.0 O A:HOH215 3.8 32.8 1.0 N A:ALA53 3.9 9.6 1.0 H A:ASP55 3.9 9.9 1.0 CB A:CYS64 4.0 13.8 1.0 N A:GLU54 4.0 10.2 1.0 CA A:CYS64 4.0 12.8 1.0 N A:CYS64 4.1 13.0 1.0 CA A:MET56 4.2 7.0 1.0 CB A:PRO61 4.2 11.2 1.0 HD2 A:PRO57 4.2 6.9 1.0 N A:ASP55 4.2 9.8 1.0 HA2 A:GLY65 4.3 12.7 1.0 HB2 A:MET56 4.4 6.7 1.0 HG21 A:ILE52 4.5 9.1 1.0 C A:GLU54 4.5 10.1 1.0 HG22 A:ILE52 4.5 9.1 1.0 N A:ALA62 4.5 11.5 1.0 N A:PRO57 4.5 6.9 1.0 HA A:ALA62 4.5 12.2 1.0 H A:GLU54 4.5 10.4 1.0 HB2 A:PRO61 4.5 11.0 1.0 N A:GLY65 4.6 12.1 1.0 HA A:GLU54 4.6 10.6 1.0 CA A:GLU54 4.7 11.0 1.0 C A:ASP55 4.7 8.5 1.0 HB2 A:CYS64 4.7 13.9 1.0 CD A:PRO57 4.7 7.0 1.0 CB A:ALA53 4.7 10.3 1.0 CA A:ILE52 4.8 9.4 1.0 HA A:ILE52 4.8 9.4 1.0 H A:ALA53 4.8 9.6 1.0 HD3 A:PRO57 4.8 6.9 1.0 HB1 A:ALA53 4.8 10.3 1.0 SG A:CYS64 4.9 15.6 1.0 CG2 A:ILE52 4.9 9.1 1.0 CB A:MET56 4.9 6.6 1.0 CA A:GLY65 4.9 12.8 1.0 CA A:ALA62 4.9 12.1 1.0 HA A:MET56 4.9 6.9 1.0 O A:GLU54 5.0 9.8 1.0

Sodium binding site 2 out of 3 in the TTX183B - A C-Type Cytochrome Domain From the Teredinibacter Turnerae Protein TERTU_2913


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of TTX183B - A C-Type Cytochrome Domain From the Teredinibacter Turnerae Protein TERTU_2913 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na102 b:10.1 occ:1.00 O B:MET56 2.3 7.4 1.0 O B:CYS64 2.4 11.9 1.0 O B:PRO61 2.4 12.2 1.0 O B:ALA53 2.4 11.0 1.0 O B:ILE52 2.4 8.8 1.0 HA B:ALA53 2.8 11.2 1.0 C B:ALA53 3.0 11.6 1.0 HB3 B:CYS64 3.1 14.1 1.0 HA B:PRO61 3.3 11.4 1.0 C B:PRO61 3.3 12.0 1.0 CA B:ALA53 3.3 11.2 1.0 H B:CYS64 3.4 14.2 1.0 C B:ILE52 3.4 9.5 1.0 C B:CYS64 3.4 13.2 1.0 C B:MET56 3.4 7.0 1.0 HB3 B:PRO61 3.6 11.1 1.0 CA B:PRO61 3.7 11.4 1.0 N B:MET56 3.7 7.2 1.0 N B:ALA53 3.8 10.4 1.0 CB B:CYS64 3.9 14.2 1.0 CA B:CYS64 4.0 14.0 1.0 N B:CYS64 4.0 14.2 1.0 N B:GLU54 4.0 12.2 1.0 H B:ASP55 4.1 10.9 1.0 CB B:PRO61 4.1 11.0 1.0 HD2 B:PRO57 4.1 7.3 1.0 CA B:MET56 4.2 6.6 1.0 HA2 B:GLY65 4.2 12.9 1.0 HG22 B:ILE52 4.3 8.8 1.0 N B:ASP55 4.3 10.6 1.0 HB2 B:PRO61 4.4 11.1 1.0 HG21 B:ILE52 4.4 8.8 1.0 HB2 B:MET56 4.4 5.9 1.0 N B:PRO57 4.4 7.1 1.0 N B:GLY65 4.5 12.6 1.0 N B:ALA62 4.5 12.4 1.0 C B:GLU54 4.5 11.6 1.0 HA B:ALA62 4.5 13.2 1.0 H B:GLU54 4.6 12.3 1.0 HB2 B:CYS64 4.7 14.2 1.0 CD B:PRO57 4.7 7.3 1.0 CB B:ALA53 4.7 11.6 1.0 CA B:GLU54 4.7 13.0 1.0 C B:ASP55 4.7 8.8 1.0 HA B:GLU54 4.7 12.9 1.0 H B:ALA53 4.7 10.3 1.0 CA B:ILE52 4.7 9.1 1.0 HA B:ILE52 4.8 9.2 1.0 HD3 B:PRO57 4.8 7.3 1.0 HB1 B:ALA53 4.8 11.6 1.0 SG B:CYS64 4.8 14.4 1.0 CG2 B:ILE52 4.8 8.9 1.0 CA B:GLY65 4.8 13.1 1.0 CB B:MET56 4.9 5.8 1.0 HB2 B:ALA69 4.9 7.8 1.0 CA B:ALA62 4.9 13.3 1.0 HA B:CYS64 5.0 13.9 1.0 HA B:MET56 5.0 6.7 1.0

Sodium binding site 3 out of 3 in the TTX183B - A C-Type Cytochrome Domain From the Teredinibacter Turnerae Protein TERTU_2913


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of TTX183B - A C-Type Cytochrome Domain From the Teredinibacter Turnerae Protein TERTU_2913 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na103 b:9.7 occ:1.00 O C:MET56 2.3 8.0 1.0 O C:ALA53 2.4 9.9 1.0 O C:CYS64 2.4 10.6 1.0 O C:PRO61 2.4 10.6 1.0 O C:ILE52 2.4 8.3 1.0 HA C:ALA53 2.8 9.4 1.0 C C:ALA53 2.9 9.7 1.0 HB3 C:CYS64 3.2 11.3 1.0 CA C:ALA53 3.3 9.4 1.0 HA C:PRO61 3.3 10.3 1.0 C C:PRO61 3.4 10.6 1.0 C C:ILE52 3.4 8.6 1.0 C C:CYS64 3.4 10.9 1.0 H C:CYS64 3.5 11.9 1.0 C C:MET56 3.5 7.3 1.0 HB3 C:PRO61 3.6 10.3 1.0 CA C:PRO61 3.7 10.4 1.0 N C:MET56 3.8 7.1 1.0 N C:ALA53 3.8 8.9 1.0 O C:HOH212 3.8 26.4 1.0 CB C:CYS64 4.0 11.4 1.0 N C:GLU54 4.0 10.6 1.0 H C:ASP55 4.0 10.7 1.0 CA C:CYS64 4.0 11.2 1.0 N C:CYS64 4.1 11.9 1.0 HA2 C:GLY65 4.1 11.3 1.0 CB C:PRO61 4.1 10.3 1.0 CA C:MET56 4.2 6.8 1.0 HD2 C:PRO57 4.2 7.9 1.0 N C:ASP55 4.3 10.5 1.0 HG22 C:ILE52 4.3 8.4 1.0 HB2 C:MET56 4.3 6.3 1.0 C C:GLU54 4.5 11.2 1.0 HB2 C:PRO61 4.5 10.3 1.0 N C:PRO57 4.5 7.6 1.0 N C:GLY65 4.5 10.9 1.0 HG21 C:ILE52 4.5 8.4 1.0 H C:GLU54 4.5 10.7 1.0 N C:ALA62 4.6 11.6 1.0 CB C:ALA53 4.6 9.7 1.0 CA C:GLU54 4.6 12.0 1.0 HA C:ALA62 4.6 12.6 1.0 HA C:GLU54 4.6 11.9 1.0 HB2 C:CYS64 4.7 11.3 1.0 H C:ALA53 4.7 8.9 1.0 CD C:PRO57 4.7 8.0 1.0 HB1 C:ALA53 4.7 9.6 1.0 C C:ASP55 4.7 8.8 1.0 CA C:GLY65 4.8 11.3 1.0 CA C:ILE52 4.8 8.6 1.0 HD3 C:PRO57 4.8 7.9 1.0 SG C:CYS64 4.8 11.6 1.0 HA C:ILE52 4.8 8.6 1.0 CB C:MET56 4.8 6.2 1.0 CG2 C:ILE52 4.9 8.5 1.0 HB2 C:ALA69 5.0 8.6 1.0 HA C:CYS64 5.0 11.3 1.0 HA C:MET56 5.0 6.8 1.0 O C:GLU54 5.0 10.3 1.0

B.S.Rajagopal, N.Yates, J.Smith, A.Paradisi, C.Tetard-Jones, W.G.T.Willats, S.Marcus, P.J.Knox, M.Firdaus-Raih, B.Henrissat, G.J.Davies, P.H.Walton, A.Parkin, G.R.Hemsworth. Structural Dissection of Two Redox Proteins From the Shipworm Symbiont Teredinibacter Turnerae Iucrj 2024.
ISSN: ESSN 2052-2525
DOI: 10.1107/S2052252524001386