Sodium in PDB 8vvn: Cryo-Em Structure of A Type I Zorab Complex From Shewanella Sp. Strain Ana-3

The binding sites of Sodium atom in the Cryo-Em Structure of A Type I Zorab Complex From Shewanella Sp. Strain Ana-3 (pdb code 8vvn). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Cryo-Em Structure of A Type I Zorab Complex From Shewanella Sp. Strain Ana-3, PDB code: 8vvn:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Cryo-Em Structure of A Type I Zorab Complex From Shewanella Sp. Strain Ana-3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cryo-Em Structure of A Type I Zorab Complex From Shewanella Sp. Strain Ana-3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na701 b:23.4 occ:1.00 O D:GLY154 2.3 22.8 1.0 O D:ALA194 2.3 21.1 1.0 OG1 D:THR197 2.3 19.1 1.0 OG1 D:THR158 2.5 23.5 1.0 OG D:SER198 2.7 19.2 1.0 N D:SER198 2.9 19.2 1.0 N D:THR158 3.0 23.5 1.0 CB D:THR197 3.3 19.1 1.0 C D:GLY154 3.3 22.8 1.0 C D:ALA194 3.3 21.1 1.0 CB D:SER198 3.4 19.2 1.0 CB D:THR158 3.4 23.5 1.0 C D:THR197 3.4 19.1 1.0 CA D:SER198 3.5 19.2 1.0 CA D:THR158 3.5 23.5 1.0 C D:GLY157 3.7 21.5 1.0 CA D:ALA194 3.8 21.1 1.0 CA D:THR197 3.8 19.1 1.0 CA D:GLY154 4.0 22.8 1.0 CA D:GLY157 4.1 21.5 1.0 N D:THR197 4.1 19.1 1.0 O D:ILE193 4.2 20.4 1.0 O D:THR197 4.2 19.1 1.0 OD2 B:ASP24 4.4 30.8 1.0 N D:VAL155 4.4 24.5 1.0 O D:GLY157 4.4 21.5 1.0 OD1 B:ASP24 4.5 30.8 1.0 N D:GLY157 4.5 21.5 1.0 N D:PHE195 4.5 20.9 1.0 CG2 D:THR197 4.6 19.1 1.0 CB D:ALA194 4.6 21.1 1.0 CA D:VAL155 4.7 24.5 1.0 CG2 D:THR158 4.7 23.5 1.0 N D:ALA194 4.9 21.1 1.0 CG B:ASP24 4.9 30.8 1.0 C D:ILE193 5.0 20.4 1.0 C D:VAL155 5.0 24.5 1.0 C D:SER198 5.0 19.2 1.0 C D:PHE195 5.0 20.9 1.0 CA D:PHE195 5.0 20.9 1.0

Sodium binding site 2 out of 2 in the Cryo-Em Structure of A Type I Zorab Complex From Shewanella Sp. Strain Ana-3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Cryo-Em Structure of A Type I Zorab Complex From Shewanella Sp. Strain Ana-3 within 5.0Å range: probe atom residue distance (Å) B Occ F:Na701 b:20.6 occ:1.00 O F:GLY154 2.3 20.2 1.0 OG1 F:THR197 2.3 18.3 1.0 O F:ALA194 2.3 19.4 1.0 OG1 F:THR158 2.4 20.3 1.0 OG F:SER198 2.5 19.3 1.0 N F:SER198 2.9 19.3 1.0 N F:THR158 3.0 20.3 1.0 C F:ALA194 3.4 19.4 1.0 C F:GLY154 3.4 20.2 1.0 CB F:THR158 3.4 20.3 1.0 C F:THR197 3.4 18.3 1.0 CA F:THR158 3.5 20.3 1.0 CB F:SER198 3.5 19.3 1.0 CB F:THR197 3.5 18.3 1.0 CA F:SER198 3.5 19.3 1.0 C F:GLY157 3.6 19.1 1.0 CA F:ALA194 3.8 19.4 1.0 CA F:THR197 3.9 18.3 1.0 OD2 A:ASP24 3.9 29.6 1.0 CA F:GLY154 4.0 20.2 1.0 CA F:GLY157 4.0 19.1 1.0 O F:THR197 4.2 18.3 1.0 N F:THR197 4.2 18.3 1.0 O F:ILE193 4.3 19.2 1.0 O F:GLY157 4.3 19.1 1.0 N F:VAL155 4.4 21.3 1.0 N F:GLY157 4.4 19.1 1.0 OD1 A:ASP24 4.5 29.6 1.0 N F:PHE195 4.5 20.8 1.0 CG A:ASP24 4.6 29.6 1.0 CG2 F:THR158 4.6 20.3 1.0 CA F:VAL155 4.7 21.3 1.0 CG2 F:THR197 4.7 18.3 1.0 CB F:ALA194 4.7 19.4 1.0 C F:VAL155 4.8 21.3 1.0 O F:VAL155 4.8 21.3 1.0 CA F:PHE195 4.9 20.8 1.0 C F:PHE195 4.9 20.8 1.0 N F:ALA194 5.0 19.4 1.0 C F:THR158 5.0 20.3 1.0 C F:SER198 5.0 19.3 1.0

G.Mariano, J.C.Deme, T.R.Blower, T.Palmer, S.M.Lea. Modularity of Zorya Defence Systems During Phage Inhibition Nat Commun 2025.
ISSN: ESSN 2041-1723