Sodium in PDB 6gto: Structure of the Atar Antitoxin

The structure of Structure of the Atar Antitoxin, PDB code: 6gto was solved by A.Garcia-Pino, D.Jurenas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.86 / 2.97
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	56.000, 56.000, 165.810, 90.00, 90.00, 120.00
R / Rfree (%)	23.4 / 26.6

The binding sites of Sodium atom in the Structure of the Atar Antitoxin (pdb code 6gto). 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 Atar Antitoxin, PDB code: 6gto:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of the Atar Antitoxin


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 Atar Antitoxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na101 b:0.0 occ:1.00 CB A:SER60 3.9 0.8 1.0 NE1 A:TRP61 4.0 0.2 1.0 OD1 A:ASN57 4.1 0.9 1.0 CD1 A:TRP61 4.3 0.8 1.0 CE2 A:TRP61 4.3 0.2 1.0 OG A:SER60 4.7 0.8 1.0 CG A:TRP61 4.8 1.0 1.0 CZ2 A:TRP61 4.8 0.8 1.0 CD2 A:TRP61 4.8 0.1 1.0 N A:TRP61 4.9 0.8 1.0 C A:SER60 4.9 0.4 1.0

Sodium binding site 2 out of 4 in the Structure of the Atar Antitoxin


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 Atar Antitoxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:0.6 occ:1.00 OE1 A:GLN30 2.8 0.3 1.0 CD A:GLN30 3.7 0.6 1.0 CB A:ASN38 3.8 0.6 1.0 CD1 A:PHE35 4.0 0.7 1.0 NE2 A:GLN30 4.1 0.6 1.0 OD1 A:ASN38 4.2 0.4 1.0 NE2 A:GLN42 4.2 0.5 1.0 CE1 A:PHE35 4.2 0.4 1.0 CG A:ASN38 4.5 1.0 1.0 O A:PHE35 4.7 0.2 1.0 OG A:SER28 4.8 1.0 1.0 CB A:SER28 4.8 1.0 1.0 CA A:PHE35 4.8 0.8 1.0 CG A:PHE35 4.9 0.8 1.0 N A:SER39 4.9 0.7 1.0 CG A:GLN30 5.0 0.1 1.0

Sodium binding site 3 out of 4 in the Structure of the Atar Antitoxin


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 Atar Antitoxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:0.8 occ:1.00 O A:ASP16 3.4 0.1 1.0 CE A:MET20 3.6 0.6 1.0 CG A:MET20 3.7 0.8 1.0 C A:ASP16 4.5 0.5 1.0 SD A:MET20 4.5 0.3 1.0 CB A:ASP16 4.7 0.9 1.0 CA A:ASP16 4.9 0.4 1.0 CB A:MET20 5.0 0.3 1.0

Sodium binding site 4 out of 4 in the Structure of the Atar Antitoxin


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 Atar Antitoxin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na104 b:0.5 occ:1.00 OG A:SER19 3.5 0.4 1.0 CB A:SER19 4.7 0.9 1.0 O A:ASP15 5.0 0.7 1.0

D.Jurenas, L.Van Melderen, A.Garcia-Pino. Mechanism of Regulation and Neutralization of the Atar-Atat Toxin-Antitoxin System. Nat. Chem. Biol. V. 15 285 2019.
ISSN: ESSN 1552-4469
PubMed: 30718814
DOI: 10.1038/S41589-018-0216-Z