Sodium in PDB 8fyv: Salmonella Enterica Serovar Typhimurium Chemoreceptor Tsr (Taxis to Serine and Repellents) Ligand-Binding Domain in Complex with L-Serine

The structure of Salmonella Enterica Serovar Typhimurium Chemoreceptor Tsr (Taxis to Serine and Repellents) Ligand-Binding Domain in Complex with L-Serine, PDB code: 8fyv was solved by A.Baylink, Z.Gentry-Lear, S.Glenn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.00 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	125.807, 75.231, 129.588, 90, 116.47, 90
R / Rfree (%)	24.1 / 25.8

The structure of Salmonella Enterica Serovar Typhimurium Chemoreceptor Tsr (Taxis to Serine and Repellents) Ligand-Binding Domain in Complex with L-Serine also contains other interesting chemical elements:

Chlorine

(Cl)

9 atoms

The binding sites of Sodium atom in the Salmonella Enterica Serovar Typhimurium Chemoreceptor Tsr (Taxis to Serine and Repellents) Ligand-Binding Domain in Complex with L-Serine (pdb code 8fyv). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Salmonella Enterica Serovar Typhimurium Chemoreceptor Tsr (Taxis to Serine and Repellents) Ligand-Binding Domain in Complex with L-Serine, PDB code: 8fyv:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Salmonella Enterica Serovar Typhimurium Chemoreceptor Tsr (Taxis to Serine and Repellents) Ligand-Binding Domain in Complex with L-Serine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Salmonella Enterica Serovar Typhimurium Chemoreceptor Tsr (Taxis to Serine and Repellents) Ligand-Binding Domain in Complex with L-Serine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:41.5 occ:1.00 OE1 B:GLU89 2.4 37.2 1.0 O B:HOH356 3.0 41.3 1.0 HB3 B:GLU89 3.1 43.6 1.0 CD B:GLU89 3.2 48.8 1.0 HB1 B:ALA85 3.2 38.8 1.0 HA B:ALA85 3.4 41.0 1.0 HB2 B:ALA85 3.4 38.8 1.0 HB2 B:GLU89 3.4 43.6 1.0 CB B:GLU89 3.6 35.9 1.0 CB B:ALA85 3.7 31.9 1.0 CG B:GLU89 3.8 36.3 1.0 HG2 B:GLU89 3.9 44.2 1.0 H B:THR86 3.9 37.2 1.0 CA B:ALA85 4.0 33.7 1.0 OE2 B:GLU89 4.0 49.0 1.0 O B:HOH350 4.3 48.3 1.0 O B:HOH327 4.4 38.0 1.0 O B:HOH341 4.4 38.7 0.5 O B:HOH345 4.6 33.5 1.0 HB3 B:ALA85 4.6 38.8 1.0 N B:THR86 4.6 30.6 1.0 HG3 B:GLU89 4.7 44.2 1.0 C B:ALA85 4.9 30.6 1.0 HG B:LEU90 5.0 34.1 1.0 CA B:GLU89 5.0 29.7 1.0

Sodium binding site 2 out of 6 in the Salmonella Enterica Serovar Typhimurium Chemoreceptor Tsr (Taxis to Serine and Repellents) Ligand-Binding Domain in Complex with L-Serine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Salmonella Enterica Serovar Typhimurium Chemoreceptor Tsr (Taxis to Serine and Repellents) Ligand-Binding Domain in Complex with L-Serine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:58.9 occ:1.00 O B:SER51 2.6 53.7 1.0 HE1 A:MET171 2.7 90.1 1.0 HA B:SER51 3.0 72.7 1.0 HB2 B:ALA55 3.0 56.2 1.0 OG B:SER51 3.1 78.3 1.0 HB3 B:ASN54 3.2 61.7 1.0 C B:SER51 3.4 57.8 1.0 H B:ALA55 3.4 62.0 1.0 CA B:SER51 3.5 60.1 1.0 OD1 B:ASN54 3.5 62.5 1.0 N B:ALA55 3.7 51.1 1.0 CE A:MET171 3.7 74.6 1.0 HG B:SER51 3.7 94.5 1.0 CB B:SER51 3.8 64.4 1.0 CB B:ALA55 3.9 46.3 1.0 HA B:ALA55 3.9 57.7 1.0 HB2 B:SER51 3.9 77.9 1.0 CB B:ASN54 4.0 51.0 1.0 HE3 A:MET171 4.0 90.1 1.0 CA B:ALA55 4.1 47.6 1.0 HE2 A:MET171 4.2 90.1 1.0 CG B:ASN54 4.2 55.2 1.0 C B:ASN54 4.3 48.0 1.0 HB3 B:ALA55 4.3 56.2 1.0 HE1 A:MET168 4.4 65.6 1.0 HB1 B:ALA55 4.5 56.2 1.0 SD A:MET171 4.5 72.0 1.0 N B:ALA52 4.6 57.4 1.0 HB3 B:SER51 4.6 77.9 1.0 CA B:ASN54 4.7 52.0 1.0 H B:ASN54 4.7 62.4 1.0 HB2 B:ASN54 4.7 61.7 1.0 HA B:ALA52 4.9 73.1 1.0 N B:SER51 4.9 60.9 1.0 O B:GLN50 5.0 56.4 1.0 O B:ASN54 5.0 41.7 1.0 N B:ASN54 5.0 51.6 1.0

Sodium binding site 3 out of 6 in the Salmonella Enterica Serovar Typhimurium Chemoreceptor Tsr (Taxis to Serine and Repellents) Ligand-Binding Domain in Complex with L-Serine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Salmonella Enterica Serovar Typhimurium Chemoreceptor Tsr (Taxis to Serine and Repellents) Ligand-Binding Domain in Complex with L-Serine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na203 b:44.1 occ:1.00 OE1 B:GLN78 2.3 42.5 1.0 HG2 B:GLN78 2.5 47.2 1.0 CD B:GLN78 2.8 53.0 1.0 CG B:GLN78 3.1 38.9 1.0 NE1 B:TRP74 3.1 38.5 1.0 CE2 B:TRP74 3.2 40.8 1.0 O B:HOH336 3.2 36.1 1.0 O B:TRP74 3.2 33.4 1.0 CD1 B:TRP74 3.4 38.0 1.0 HB2 B:ASP77 3.4 42.5 1.0 CD2 B:TRP74 3.4 40.3 1.0 HE1 B:TRP74 3.4 46.8 1.0 HG3 B:GLN78 3.5 47.2 1.0 CG B:TRP74 3.5 35.9 1.0 O B:HOH320 3.6 36.8 1.0 HA B:TRP74 3.7 37.0 1.0 CZ2 B:TRP74 3.7 40.7 1.0 H B:GLN78 3.8 39.0 1.0 HD1 B:TRP74 3.8 46.2 1.0 NE2 B:GLN78 3.9 49.9 1.0 HB3 B:ASP77 3.9 42.5 1.0 C B:TRP74 4.0 31.7 1.0 HZ2 B:TRP74 4.1 49.4 1.0 CB B:ASP77 4.1 35.0 1.0 CE3 B:TRP74 4.1 39.4 1.0 N B:GLN78 4.1 32.0 1.0 CA B:TRP74 4.2 30.4 1.0 O B:HOH344 4.2 46.8 1.0 HE22 B:GLN78 4.2 60.4 1.0 CB B:GLN78 4.3 37.3 1.0 CH2 B:TRP74 4.4 44.6 1.0 HE21 B:GLN78 4.5 60.4 1.0 HA B:GLN78 4.5 49.1 1.0 CB B:TRP74 4.5 35.3 1.0 CZ3 B:TRP74 4.6 44.1 1.0 CA B:GLN78 4.6 40.5 1.0 HE3 B:TRP74 4.7 47.9 1.0 C B:ASP77 4.7 33.7 1.0 HB2 B:GLN78 4.8 45.3 1.0 CA B:ASP77 5.0 37.3 1.0

Sodium binding site 4 out of 6 in the Salmonella Enterica Serovar Typhimurium Chemoreceptor Tsr (Taxis to Serine and Repellents) Ligand-Binding Domain in Complex with L-Serine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Salmonella Enterica Serovar Typhimurium Chemoreceptor Tsr (Taxis to Serine and Repellents) Ligand-Binding Domain in Complex with L-Serine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na204 b:49.7 occ:1.00 OD2 B:ASP130 2.6 43.7 1.0 HA B:ARG127 2.9 49.9 1.0 HB2 B:ASP130 2.9 47.8 1.0 CG B:ASP130 3.4 38.7 1.0 CB B:ASP130 3.5 39.3 1.0 HB3 B:ASP130 3.6 47.8 1.0 HG2 B:LYS126 3.7 67.1 1.0 CA B:ARG127 3.8 41.1 1.0 HE3 B:LYS126 3.8 123.1 1.0 HG3 B:ARG127 4.0 50.2 1.0 O B:LYS126 4.2 35.1 1.0 O D:HOH356 4.2 47.9 1.0 O B:ARG127 4.4 38.9 1.0 N B:ARG127 4.4 44.7 1.0 HB2 B:ARG127 4.4 52.2 1.0 HG3 B:LYS126 4.5 67.1 1.0 CG B:LYS126 4.5 55.5 1.0 C B:LYS126 4.5 43.6 1.0 CB B:ARG127 4.6 43.0 1.0 C B:ARG127 4.6 40.4 1.0 OD1 B:ASP130 4.6 40.5 1.0 O D:HOH336 4.7 43.4 1.0 CE B:LYS126 4.7 102.1 1.0 H B:ASP130 4.7 44.1 1.0 CG B:ARG127 4.7 41.4 1.0 HE2 B:LYS126 4.8 123.1 1.0 CA B:ASP130 4.9 37.0 1.0 H B:ARG127 5.0 54.2 1.0 O D:HOH350 5.0 47.8 1.0

Sodium binding site 5 out of 6 in the Salmonella Enterica Serovar Typhimurium Chemoreceptor Tsr (Taxis to Serine and Repellents) Ligand-Binding Domain in Complex with L-Serine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Salmonella Enterica Serovar Typhimurium Chemoreceptor Tsr (Taxis to Serine and Repellents) Ligand-Binding Domain in Complex with L-Serine within 5.0Å range: probe atom residue distance (Å) B Occ C:Na201 b:39.1 occ:1.00 OD2 C:ASP161 2.5 32.4 1.0 O B:HOH315 2.5 35.9 1.0 HG3 C:GLN157 3.1 38.8 1.0 HE21 C:GLN157 3.2 38.6 1.0 HD3 B:LYS165 3.3 47.8 1.0 HA B:ALA162 3.3 35.3 1.0 HB1 B:ALA162 3.3 33.5 1.0 HG2 C:GLN157 3.4 38.8 1.0 CG C:ASP161 3.4 34.6 1.0 O B:HOH347 3.5 38.8 1.0 HB2 B:ALA162 3.6 33.5 1.0 CG C:GLN157 3.7 31.9 1.0 OD1 C:ASP161 3.7 31.4 1.0 CB B:ALA162 3.8 27.4 1.0 NE2 C:GLN157 3.8 31.7 1.0 CA B:ALA162 4.0 28.9 1.0 HE21 B:GLN166 4.1 51.7 1.0 HH22 B:ARG127 4.1 58.5 1.0 CD C:GLN157 4.2 30.5 1.0 CD B:LYS165 4.2 39.4 1.0 HB3 B:LYS165 4.4 40.1 1.0 HE2 B:LYS165 4.4 52.6 1.0 HD2 B:LYS165 4.4 47.8 1.0 HE22 C:GLN157 4.4 38.6 1.0 O C:HOH355 4.5 34.7 1.0 O B:ALA162 4.5 32.8 1.0 HB3 B:ALA162 4.7 33.5 1.0 HG21 B:THR128 4.7 48.8 1.0 O B:HOH361 4.7 44.8 1.0 CE B:LYS165 4.7 43.4 1.0 C B:ALA162 4.8 30.5 1.0 O B:HOH321 4.8 28.3 1.0 HE3 B:LYS165 4.8 52.6 1.0 CB C:ASP161 4.8 30.8 1.0 NE2 B:GLN166 4.9 42.6 1.0 HG22 B:THR128 4.9 48.8 1.0 NH2 B:ARG127 4.9 48.3 1.0 HB3 C:ASP161 5.0 37.5 1.0

Sodium binding site 6 out of 6 in the Salmonella Enterica Serovar Typhimurium Chemoreceptor Tsr (Taxis to Serine and Repellents) Ligand-Binding Domain in Complex with L-Serine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Salmonella Enterica Serovar Typhimurium Chemoreceptor Tsr (Taxis to Serine and Repellents) Ligand-Binding Domain in Complex with L-Serine within 5.0Å range: probe atom residue distance (Å) B Occ D:Na201 b:43.1 occ:1.00 O D:ILE131 2.4 36.8 1.0 H D:ALA135 2.8 46.2 1.0 HA D:ILE131 2.9 47.2 1.0 N D:ALA135 3.0 38.0 1.0 HG23 D:ILE131 3.0 40.6 1.0 HB2 D:ALA135 3.0 40.1 1.0 HA3 D:GLY134 3.2 46.4 1.0 C D:ILE131 3.3 36.6 1.0 C D:GLY134 3.5 42.4 1.0 CA D:ILE131 3.5 38.9 1.0 HA D:ALA135 3.6 50.0 1.0 CA D:ALA135 3.7 41.2 1.0 CA D:GLY134 3.7 38.1 1.0 CB D:ALA135 3.8 33.0 1.0 CG2 D:ILE131 3.9 33.4 1.0 H D:GLY134 4.0 45.5 1.0 HB3 D:ALA135 4.2 40.1 1.0 N D:GLY134 4.2 37.5 1.0 HG22 D:ILE131 4.2 40.6 1.0 CB D:ILE131 4.2 36.7 1.0 O D:ASP130 4.2 38.8 1.0 O D:GLY134 4.3 39.2 1.0 HG12 D:ILE131 4.3 42.8 1.0 HB1 D:ALA135 4.5 40.1 1.0 N D:TYR132 4.5 33.1 1.0 HA2 D:GLY134 4.6 46.4 1.0 HG21 D:ILE131 4.6 40.6 1.0 N D:ILE131 4.7 38.1 1.0 CG1 D:ILE131 4.8 35.2 1.0 CE2 D:TYR159 4.8 33.0 1.0 HA D:TYR132 4.8 38.0 1.0 HE2 D:TYR159 4.8 40.2 1.0 CD2 D:TYR159 4.9 35.2 1.0 C D:ASP130 4.9 37.6 1.0

A.Baylink, Z.Gentry-Lear, S.Glenn. Bacterial Vampirism Mediated By Chemotaxis To Be Published.