Sodium in PDB 8vl8: Salmonella Enterica Typhimurium Taxis to Serine and Repellents (Tsr) Ligand-Binding Domain with L-Ser, pH 7

Protein crystallography data

The structure of Salmonella Enterica Typhimurium Taxis to Serine and Repellents (Tsr) Ligand-Binding Domain with L-Ser, pH 7, PDB code: 8vl8 was solved by S.Glenn, A.Baylink, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 61.50 / 2.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 126.022, 74.771, 128.931, 90, 116.14, 90
R / Rfree (%) 22.6 / 27.3

Other elements in 8vl8:

The structure of Salmonella Enterica Typhimurium Taxis to Serine and Repellents (Tsr) Ligand-Binding Domain with L-Ser, pH 7 also contains other interesting chemical elements:

Potassium (K) 1 atom
Chlorine (Cl) 7 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Salmonella Enterica Typhimurium Taxis to Serine and Repellents (Tsr) Ligand-Binding Domain with L-Ser, pH 7 (pdb code 8vl8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the Salmonella Enterica Typhimurium Taxis to Serine and Repellents (Tsr) Ligand-Binding Domain with L-Ser, pH 7, PDB code: 8vl8:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 8vl8

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Sodium binding site 1 out of 10 in the Salmonella Enterica Typhimurium Taxis to Serine and Repellents (Tsr) Ligand-Binding Domain with L-Ser, pH 7


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Salmonella Enterica Typhimurium Taxis to Serine and Repellents (Tsr) Ligand-Binding Domain with L-Ser, pH 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:37.7
occ:1.00
 OD2 A:ASP161 2.0 25.3 1.0
CG A:ASP161 2.8 19.0 1.0
OD1 A:ASP161 3.2 24.5 1.0
CG A:GLN157 3.8 17.7 1.0
NE2 A:GLN157 3.9 20.0 1.0
CB A:ASP161 4.1 19.9 1.0
CD A:GLN157 4.4 18.3 1.0
O A:GLN157 4.8 24.4 1.0

Sodium binding site 2 out of 10 in 8vl8

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Sodium binding site 2 out of 10 in the Salmonella Enterica Typhimurium Taxis to Serine and Repellents (Tsr) Ligand-Binding Domain with L-Ser, pH 7


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Salmonella Enterica Typhimurium Taxis to Serine and Repellents (Tsr) Ligand-Binding Domain with L-Ser, pH 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na201

b:42.7
occ:1.00
 OE1 B:GLU89 2.5 20.4 1.0
CB B:ALA85 3.4 13.4 1.0
CD B:GLU89 3.4 34.6 1.0
CB B:GLU89 3.8 18.0 1.0
CA B:ALA85 3.9 13.8 1.0
CG B:GLU89 4.0 33.8 1.0
O B:HOH332 4.3 24.3 1.0
OE2 B:GLU89 4.3 45.1 1.0
O B:HOH334 4.4 26.9 1.0
O B:HOH328 4.6 22.6 1.0
N B:THR86 4.7 20.1 1.0
O B:HOH345 4.8 29.8 1.0
C B:ALA85 4.9 25.3 1.0
N B:ALA85 4.9 13.9 1.0

Sodium binding site 3 out of 10 in 8vl8

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Sodium binding site 3 out of 10 in the Salmonella Enterica Typhimurium Taxis to Serine and Repellents (Tsr) Ligand-Binding Domain with L-Ser, pH 7


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Salmonella Enterica Typhimurium Taxis to Serine and Repellents (Tsr) Ligand-Binding Domain with L-Ser, pH 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na202

b:42.2
occ:1.00
 O B:SER51 2.7 28.3 1.0
OG B:SER51 3.0 46.7 1.0
O B:HOH335 3.3 40.1 1.0
CA B:SER51 3.3 31.3 1.0
C B:SER51 3.4 29.9 1.0
CB B:SER51 3.5 34.8 1.0
ND2 B:ASN54 3.8 44.0 1.0
CE A:MET171 3.8 59.9 1.0
N B:ALA55 3.9 34.7 1.0
CB B:ASN54 4.0 28.9 1.0
CB B:ALA55 4.1 26.5 1.0
CA B:ALA55 4.3 32.4 1.0
CG B:ASN54 4.4 48.7 1.0
C B:ASN54 4.5 35.3 1.0
N B:ALA52 4.6 30.7 1.0
N B:SER51 4.7 42.4 1.0
CA B:ASN54 4.8 28.4 1.0
O B:GLN50 4.9 40.9 1.0

Sodium binding site 4 out of 10 in 8vl8

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Sodium binding site 4 out of 10 in the Salmonella Enterica Typhimurium Taxis to Serine and Repellents (Tsr) Ligand-Binding Domain with L-Ser, pH 7


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Salmonella Enterica Typhimurium Taxis to Serine and Repellents (Tsr) Ligand-Binding Domain with L-Ser, pH 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na203

b:40.4
occ:1.00
 OE1 B:GLN78 2.8 39.1 1.0
CE2 B:TRP74 2.9 29.1 1.0
NE1 B:TRP74 3.0 24.4 1.0
CD B:GLN78 3.1 43.1 1.0
CG B:GLN78 3.1 18.9 1.0
O B:HOH333 3.2 33.9 1.0
CD2 B:TRP74 3.2 30.0 1.0
CD1 B:TRP74 3.2 26.3 1.0
CG B:TRP74 3.4 25.9 1.0
O B:TRP74 3.6 15.2 1.0
O B:HOH320 3.6 18.3 1.0
CZ2 B:TRP74 3.6 29.8 1.0
CE3 B:TRP74 4.0 23.0 1.0
NE2 B:GLN78 4.1 33.4 1.0
O B:HOH325 4.1 31.1 1.0
C B:TRP74 4.2 19.7 1.0
CH2 B:TRP74 4.2 26.7 1.0
CB B:ASP77 4.2 17.3 1.0
CA B:TRP74 4.2 13.6 1.0
N B:GLN78 4.4 17.3 1.0
CB B:GLN78 4.4 19.1 1.0
CB B:TRP74 4.4 13.8 1.0
CZ3 B:TRP74 4.4 21.4 1.0
CA B:GLN78 4.7 27.7 1.0
C B:ASP77 5.0 25.3 1.0

Sodium binding site 5 out of 10 in 8vl8

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Sodium binding site 5 out of 10 in the Salmonella Enterica Typhimurium Taxis to Serine and Repellents (Tsr) Ligand-Binding Domain with L-Ser, pH 7


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Salmonella Enterica Typhimurium Taxis to Serine and Repellents (Tsr) Ligand-Binding Domain with L-Ser, pH 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na204

b:46.4
occ:1.00
 OD2 B:ASP130 2.7 24.2 1.0
CG B:ASP130 3.5 33.0 1.0
CB B:ASP130 3.6 21.1 1.0
CA B:ARG127 3.7 27.7 1.0
O B:LYS126 3.9 19.3 1.0
N B:ARG127 4.2 27.4 1.0
C B:LYS126 4.2 19.5 1.0
CG B:LYS126 4.3 24.1 1.0
O B:ARG127 4.3 23.9 1.0
O D:HOH337 4.4 39.2 1.0
O D:HOH346 4.5 18.4 1.0
CB B:ARG127 4.5 20.1 1.0
C B:ARG127 4.5 20.3 1.0
O D:HOH348 4.7 25.3 1.0
OD1 B:ASP130 4.7 42.0 1.0
CG B:ARG127 4.7 20.9 1.0
CA B:ASP130 5.0 18.9 1.0

Sodium binding site 6 out of 10 in 8vl8

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Sodium binding site 6 out of 10 in the Salmonella Enterica Typhimurium Taxis to Serine and Repellents (Tsr) Ligand-Binding Domain with L-Ser, pH 7


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Salmonella Enterica Typhimurium Taxis to Serine and Repellents (Tsr) Ligand-Binding Domain with L-Ser, pH 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na205

b:42.1
occ:1.00
 OD1 B:ASN96 2.2 27.6 1.0
O B:ASN96 3.1 23.4 1.0
CG B:ASN96 3.3 25.5 1.0
O B:HOH316 3.4 37.5 1.0
CA B:ASN96 3.5 22.2 1.0
C B:ASN96 3.7 21.8 1.0
CB B:ASN96 3.8 23.0 1.0
CB B:LYS99 3.9 36.5 1.0
ND2 B:ASN96 4.4 26.0 1.0
CG B:LEU100 4.5 37.5 1.0
N B:LEU100 4.6 25.7 1.0
CD B:LYS99 4.6 46.1 1.0
CD2 B:LEU100 4.7 41.1 1.0
CE B:LYS99 4.8 41.7 1.0
N B:ASN96 4.8 22.2 1.0
CG B:LYS99 4.9 39.7 1.0
CA B:LYS99 4.9 29.4 1.0
O B:THR95 4.9 21.1 1.0
N B:THR97 5.0 20.2 1.0

Sodium binding site 7 out of 10 in 8vl8

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Sodium binding site 7 out of 10 in the Salmonella Enterica Typhimurium Taxis to Serine and Repellents (Tsr) Ligand-Binding Domain with L-Ser, pH 7


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Salmonella Enterica Typhimurium Taxis to Serine and Repellents (Tsr) Ligand-Binding Domain with L-Ser, pH 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na201

b:36.7
occ:1.00
 OD2 C:ASP161 2.2 24.6 1.0
O B:HOH324 2.6 29.1 1.0
CG C:ASP161 3.1 31.3 1.0
OD1 C:ASP161 3.3 17.1 1.0
O B:HOH338 3.4 20.9 1.0
CB B:ALA162 3.7 15.0 1.0
CG C:GLN157 3.8 16.2 1.0
NE2 C:GLN157 3.9 22.9 1.0
CA B:ALA162 3.9 16.7 1.0
CD B:LYS165 3.9 18.2 1.0
O C:HOH316 4.2 19.4 1.0
CD C:GLN157 4.2 21.2 1.0
O B:ALA162 4.4 21.4 1.0
CB C:ASP161 4.5 20.7 1.0
CE B:LYS165 4.5 25.7 1.0
C B:ALA162 4.6 24.8 1.0
O C:HOH334 4.8 32.0 1.0
CB B:LYS165 4.8 17.9 1.0
NE2 B:GLN166 4.9 21.2 1.0
N B:ALA162 5.0 19.8 1.0

Sodium binding site 8 out of 10 in 8vl8

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Sodium binding site 8 out of 10 in the Salmonella Enterica Typhimurium Taxis to Serine and Repellents (Tsr) Ligand-Binding Domain with L-Ser, pH 7


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Salmonella Enterica Typhimurium Taxis to Serine and Repellents (Tsr) Ligand-Binding Domain with L-Ser, pH 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na202

b:40.8
occ:1.00
 OE1 C:GLN166 2.6 44.0 1.0
O B:HOH306 3.0 22.2 1.0
O C:ALA162 3.1 33.5 1.0
CG C:GLN166 3.1 33.5 1.0
CD C:GLN166 3.2 29.1 1.0
CB C:LYS165 3.7 21.5 1.0
CG2 C:THR128 3.9 16.0 1.0
C C:ALA162 3.9 36.0 1.0
CA C:ALA162 4.0 19.7 1.0
N C:GLN166 4.0 23.8 1.0
CG C:LYS165 4.0 23.1 1.0
CD C:LYS165 4.1 22.9 1.0
CB C:ALA162 4.2 18.9 1.0
CE C:LYS165 4.2 26.8 1.0
CB C:GLN166 4.4 26.1 1.0
NE2 C:GLN166 4.4 29.2 1.0
C C:LYS165 4.6 30.9 1.0
NH2 C:ARG127 4.6 17.8 1.0
CA C:GLN166 4.7 28.0 1.0
CA C:LYS165 4.7 24.0 1.0
OD2 B:ASP161 4.8 21.7 1.0
K A:K205 4.8 55.0 1.0

Sodium binding site 9 out of 10 in 8vl8

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Sodium binding site 9 out of 10 in the Salmonella Enterica Typhimurium Taxis to Serine and Repellents (Tsr) Ligand-Binding Domain with L-Ser, pH 7


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Salmonella Enterica Typhimurium Taxis to Serine and Repellents (Tsr) Ligand-Binding Domain with L-Ser, pH 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na201

b:32.6
occ:1.00
 O D:ILE131 2.4 29.9 1.0
N D:ALA135 3.0 25.5 1.0
C D:ILE131 3.3 26.8 1.0
C D:GLY134 3.6 33.7 1.0
CA D:ALA135 3.6 22.7 1.0
CA D:ILE131 3.6 23.8 1.0
CB D:ALA135 3.7 18.6 1.0
CG2 D:ILE131 3.9 22.6 1.0
CA D:GLY134 4.0 21.7 1.0
CB D:ILE131 4.2 34.4 1.0
O D:GLY134 4.3 27.6 1.0
N D:GLY134 4.4 25.5 1.0
O D:ASP130 4.5 35.1 1.0
N D:TYR132 4.6 20.9 1.0
CE2 D:TYR159 4.6 20.1 1.0
CG1 D:ILE131 4.6 25.2 1.0
CD2 D:TYR159 4.8 22.5 1.0
CZ D:TYR159 4.9 25.4 1.0
N D:ILE131 4.9 39.3 1.0

Sodium binding site 10 out of 10 in 8vl8

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Sodium binding site 10 out of 10 in the Salmonella Enterica Typhimurium Taxis to Serine and Repellents (Tsr) Ligand-Binding Domain with L-Ser, pH 7


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Salmonella Enterica Typhimurium Taxis to Serine and Repellents (Tsr) Ligand-Binding Domain with L-Ser, pH 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na201

b:52.9
occ:1.00
 O E:ALA88 2.3 39.5 1.0
N E:GLN92 3.1 42.5 1.0
CB E:GLN92 3.1 34.9 1.0
C E:ALA88 3.4 39.5 1.0
CA E:GLN92 3.5 35.4 1.0
OE1 E:GLN92 3.8 43.8 1.0
CB E:MET91 3.8 36.4 1.0
CG E:GLN92 3.8 33.3 1.0
C E:MET91 3.8 33.9 1.0
CA E:ALA88 3.8 40.2 1.0
CD E:GLN92 4.2 35.6 1.0
CA E:MET91 4.2 37.5 1.0
CB E:ALA88 4.4 38.5 1.0
N E:MET91 4.5 32.1 1.0
N E:GLU89 4.5 36.0 1.0
O E:MET91 4.6 33.7 1.0
O E:VAL87 4.8 35.1 1.0
CA E:GLU89 4.9 36.3 1.0
CG E:MET91 5.0 37.8 1.0

Reference:

S.Glenn, Z.Gentry-Lear, M.Shavlik, M.J.Harms, T.J.Asaki, A.Baylink. Human Serum Is A Potent Chemoattractant For Enterobacteriaceae Species Associated with Gastrointestinal Bleeding Elife 2024.
ISSN: ESSN 2050-084X
DOI: 10.7554/ELIFE.93178.1
Page generated: Wed Oct 9 14:03:09 2024

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