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Sodium in PDB 8b2j: Crystal Structure of Human Sting in Complex with Adu-S100

Protein crystallography data

The structure of Crystal Structure of Human Sting in Complex with Adu-S100, PDB code: 8b2j was solved by A.Nawrotek, L.Vuillard, L.Miallau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 68.16 / 2.17
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.357, 67.368, 136.317, 90, 90, 90
R / Rfree (%) 24.2 / 28.5

Other elements in 8b2j:

The structure of Crystal Structure of Human Sting in Complex with Adu-S100 also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human Sting in Complex with Adu-S100 (pdb code 8b2j). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of Human Sting in Complex with Adu-S100, PDB code: 8b2j:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 8b2j

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Sodium binding site 1 out of 8 in the Crystal Structure of Human Sting in Complex with Adu-S100


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human Sting in Complex with Adu-S100 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:44.6
occ:1.00
 O A:ARG232 2.8 35.1 1.0
NH1 A:ARG238 3.1 33.6 1.0
CD1 A:ILE235 3.4 34.6 1.0
CG A:ARG232 3.4 42.1 1.0
C A:ARG232 3.6 35.0 1.0
CD A:ARG238 3.6 36.2 1.0
OG1 B:THR263 3.7 43.2 1.0
C13 A:GJF401 3.8 42.0 1.0
CB A:ARG232 3.8 37.6 1.0
CG2 B:THR263 3.9 40.1 1.0
CG1 A:ILE235 3.9 33.6 1.0
CB A:ILE235 4.0 33.5 1.0
CB A:ALA233 4.0 34.3 1.0
CZ A:ARG238 4.1 34.5 1.0
NE A:ARG238 4.3 36.1 1.0
CA A:ARG232 4.3 35.4 1.0
N A:ALA233 4.4 34.2 1.0
N6 A:GJF401 4.4 41.7 1.0
CB B:THR263 4.4 39.9 1.0
N5 A:GJF401 4.4 42.5 1.0
CA A:ALA233 4.6 34.2 1.0
O A:ALA233 4.7 34.3 1.0
CD A:ARG232 4.7 44.7 1.0
C A:ALA233 4.8 34.3 1.0
CG A:ARG238 4.8 35.4 1.0
N A:ILE235 4.9 33.7 1.0
CG2 A:ILE235 4.9 33.6 1.0

Sodium binding site 2 out of 8 in 8b2j

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Sodium binding site 2 out of 8 in the Crystal Structure of Human Sting in Complex with Adu-S100


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Human Sting in Complex with Adu-S100 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:52.0
occ:1.00
 O A:ILE171 2.5 37.5 1.0
OE1 A:GLN228 2.6 52.0 1.0
NH1 A:ARG178 3.0 34.2 1.0
N A:LEU175 3.2 41.0 1.0
CD A:ARG178 3.2 35.2 1.0
C A:GLU174 3.4 41.7 1.0
C A:ILE171 3.4 37.1 1.0
CB A:GLU174 3.5 46.8 1.0
CA A:LEU175 3.5 40.7 1.0
CA A:ILE171 3.6 36.8 1.0
CB A:ILE171 3.7 36.8 1.0
O A:GLU174 3.8 41.7 1.0
CD A:GLN228 3.8 50.1 1.0
CA A:GLU174 3.9 42.5 1.0
CZ A:ARG178 3.9 35.4 1.0
NE A:ARG178 4.0 35.1 1.0
CB A:LEU175 4.1 40.7 1.0
N A:GLU174 4.3 41.8 1.0
CD1 A:LEU175 4.3 41.9 1.0
CG A:ARG178 4.4 34.9 1.0
CG A:GLU174 4.5 55.3 1.0
CG2 A:ILE171 4.5 36.8 1.0
NE2 A:GLN228 4.6 50.1 1.0
N A:LEU172 4.7 37.0 1.0
CB A:GLN228 4.7 40.8 1.0
CG A:GLN228 4.7 45.2 1.0
CG1 A:ILE171 4.7 37.5 1.0
CG A:LEU175 4.8 41.8 1.0
C A:LEU175 4.8 40.6 1.0
CB A:ARG178 5.0 35.3 1.0

Sodium binding site 3 out of 8 in 8b2j

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Sodium binding site 3 out of 8 in the Crystal Structure of Human Sting in Complex with Adu-S100


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Human Sting in Complex with Adu-S100 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:37.1
occ:1.00
 O A:ARG197 2.4 38.8 1.0
O A:SER195 2.6 40.1 1.0
N A:VAL258 2.9 32.3 1.0
CG1 A:VAL258 3.3 34.0 1.0
C A:SER195 3.3 40.1 1.0
C A:ARG197 3.5 38.7 1.0
N A:ARG197 3.5 42.3 1.0
CB A:CYS257 3.5 34.0 1.0
CA A:CYS257 3.6 33.4 1.0
C A:CYS257 3.7 32.4 1.0
CB A:SER195 3.9 39.4 1.0
CA A:VAL258 3.9 32.5 1.0
O A:VAL258 4.0 30.6 1.0
CA A:SER195 4.0 38.5 1.0
CD1 A:TYR199 4.0 35.7 1.0
N A:GLN196 4.1 41.3 1.0
CE1 A:TYR199 4.1 36.9 1.0
CA A:ARG197 4.1 40.8 1.0
CB A:VAL258 4.2 33.3 1.0
C A:GLN196 4.3 44.1 1.0
N A:SER195 4.3 37.7 1.0
C A:VAL258 4.4 31.1 1.0
CD1 A:ILE179 4.4 36.7 1.0
CG1 A:VAL194 4.5 36.6 1.0
CA A:GLN196 4.6 42.8 1.0
N A:LEU198 4.6 36.7 1.0
O A:THR256 4.9 35.9 1.0
CA A:LEU198 4.9 35.5 1.0
O A:CYS257 4.9 32.1 1.0
N A:CYS257 4.9 34.0 1.0
SG A:CYS257 5.0 36.9 1.0

Sodium binding site 4 out of 8 in 8b2j

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Sodium binding site 4 out of 8 in the Crystal Structure of Human Sting in Complex with Adu-S100


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Human Sting in Complex with Adu-S100 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:58.5
occ:1.00
 OG A:SER243 2.7 31.7 1.0
O B:LYS236 2.7 35.8 1.0
OG A:SER241 2.9 38.3 0.5
C A:ASN242 3.4 33.3 1.0
CD A:LYS224 3.4 46.6 1.0
CG A:LYS224 3.4 41.7 1.0
O A:ASN242 3.5 33.6 1.0
CG2 B:ILE235 3.6 34.6 1.0
N B:LYS236 3.6 33.8 1.0
N A:ASN242 3.7 35.5 1.0
N A:SER243 3.7 31.8 1.0
CB A:SER241 3.7 37.5 0.5
C B:LYS236 3.7 35.8 1.0
CB A:SER241 3.7 37.1 0.5
CB A:SER243 3.9 31.0 1.0
C A:SER241 3.9 36.0 0.5
CA A:ASN242 3.9 34.6 1.0
C A:SER241 4.0 36.1 0.5
CA A:SER243 4.0 30.7 1.0
CB A:LYS224 4.0 38.6 1.0
CA B:LYS236 4.0 34.9 1.0
CB B:LYS236 4.2 36.7 1.0
C B:ILE235 4.3 33.4 1.0
O A:SER241 4.4 36.5 0.5
O A:SER241 4.4 36.6 0.5
CA A:SER241 4.4 36.2 0.5
CA A:SER241 4.5 36.0 0.5
CA B:ILE235 4.5 33.5 1.0
CB B:ILE235 4.7 34.1 1.0
CA A:LYS224 4.7 37.4 1.0
O A:HOH502 4.7 42.5 1.0
OG A:SER241 4.8 39.2 0.5
CE A:LYS224 4.9 50.0 1.0
N B:ASP237 5.0 36.1 1.0

Sodium binding site 5 out of 8 in 8b2j

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Sodium binding site 5 out of 8 in the Crystal Structure of Human Sting in Complex with Adu-S100


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Human Sting in Complex with Adu-S100 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:46.1
occ:1.00
 O B:ARG232 2.9 35.7 1.0
NH1 B:ARG238 3.0 36.7 1.0
CG2 A:THR263 3.3 40.4 1.0
CG B:ARG232 3.5 41.8 1.0
CD1 B:ILE235 3.6 36.4 1.0
CD B:ARG238 3.6 37.5 1.0
C B:ARG232 3.6 35.3 1.0
OG1 A:THR263 3.8 42.8 1.0
CB B:ALA233 3.8 33.3 1.0
CB B:ARG232 3.9 37.6 1.0
CZ B:ARG238 4.1 38.2 1.0
CG1 B:ILE235 4.1 35.1 1.0
C20 A:GJF401 4.1 40.6 1.0
CB A:THR263 4.2 39.8 1.0
CB B:ILE235 4.2 34.1 1.0
NE B:ARG238 4.3 37.9 1.0
N B:ALA233 4.3 34.1 1.0
CA B:ARG232 4.4 35.8 1.0
N2 A:GJF401 4.5 40.9 1.0
CA B:ALA233 4.5 33.6 1.0
CD B:ARG232 4.6 43.8 1.0
O B:ALA233 4.8 33.2 1.0
C B:ALA233 4.8 33.7 1.0
CG B:ARG238 4.9 37.2 1.0
NH1 B:ARG232 4.9 50.5 1.0
N1 A:GJF401 4.9 40.6 1.0

Sodium binding site 6 out of 8 in 8b2j

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Sodium binding site 6 out of 8 in the Crystal Structure of Human Sting in Complex with Adu-S100


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Human Sting in Complex with Adu-S100 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:41.0
occ:1.00
 O B:GLN266 2.7 35.1 1.0
O B:GLY207 3.0 46.3 1.0
C B:GLN266 3.5 34.7 1.0
CB B:PHE269 3.6 41.9 1.0
CG B:GLN266 3.6 32.5 1.0
CA B:GLN266 3.7 33.1 1.0
N B:ALA270 3.8 40.1 1.0
C B:GLY207 4.1 45.5 1.0
C B:PHE269 4.1 41.2 1.0
CB B:GLN266 4.3 32.8 1.0
CA B:PHE269 4.3 41.1 1.0
CB B:ALA270 4.3 39.2 1.0
CA B:ALA270 4.4 39.6 1.0
CD2 B:PHE269 4.6 44.9 1.0
CG B:PHE269 4.6 43.6 1.0
CB B:VAL208 4.6 41.8 1.0
N B:PHE269 4.7 40.5 1.0
O B:PHE269 4.8 42.3 1.0
O B:VAL208 4.8 39.8 1.0
O B:LEU265 4.8 32.9 1.0
N B:THR267 4.8 35.4 1.0
CA B:GLY207 4.9 46.7 1.0
CD B:GLN266 4.9 32.0 1.0
N B:GLN266 4.9 32.8 1.0
CG2 B:VAL208 5.0 41.9 1.0
N B:VAL208 5.0 43.3 1.0

Sodium binding site 7 out of 8 in 8b2j

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Sodium binding site 7 out of 8 in the Crystal Structure of Human Sting in Complex with Adu-S100


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Human Sting in Complex with Adu-S100 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na404

b:42.7
occ:1.00
 O B:ARG197 2.4 38.7 1.0
O B:SER195 2.7 40.1 1.0
N B:VAL258 2.9 32.5 1.0
C B:SER195 3.3 40.1 1.0
N B:ARG197 3.5 41.7 1.0
C B:ARG197 3.5 38.5 1.0
CG2 B:VAL258 3.6 33.3 1.0
CB B:CYS257 3.6 35.3 1.0
CA B:CYS257 3.6 34.2 1.0
CB B:VAL258 3.7 33.0 1.0
C B:CYS257 3.8 33.0 1.0
CB B:SER195 3.8 39.9 1.0
CA B:VAL258 3.8 32.5 1.0
CD1 B:TYR199 4.0 36.2 1.0
CA B:SER195 4.0 38.8 1.0
O B:VAL258 4.0 32.0 1.0
CA B:ARG197 4.1 40.6 1.0
CE1 B:TYR199 4.1 37.2 1.0
N B:GLN196 4.1 40.9 1.0
C B:GLN196 4.2 43.3 1.0
N B:SER195 4.2 37.8 1.0
CD1 B:ILE179 4.4 31.5 1.0
C B:VAL258 4.4 32.1 1.0
CG1 B:VAL194 4.4 36.5 1.0
CA B:GLN196 4.5 42.2 1.0
N B:LEU198 4.6 36.9 1.0
O B:THR256 4.9 36.0 1.0
O B:CYS257 4.9 32.5 1.0
OG B:SER195 4.9 42.5 1.0
CA B:LEU198 5.0 35.6 1.0
N B:CYS257 5.0 34.9 1.0

Sodium binding site 8 out of 8 in 8b2j

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Sodium binding site 8 out of 8 in the Crystal Structure of Human Sting in Complex with Adu-S100


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Human Sting in Complex with Adu-S100 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na405

b:49.2
occ:1.00
 O B:ILE171 2.5 35.5 1.0
OE1 B:GLN228 2.5 53.3 1.0
NH1 B:ARG178 3.0 35.0 1.0
N B:LEU175 3.1 40.5 1.0
C B:GLU174 3.3 41.7 1.0
C B:ILE171 3.3 35.1 1.0
CD B:ARG178 3.4 34.1 1.0
CA B:ILE171 3.5 34.7 1.0
CA B:LEU175 3.5 39.9 1.0
CB B:ILE171 3.6 35.6 1.0
CB B:GLU174 3.7 47.6 1.0
CD B:GLN228 3.7 50.9 1.0
O B:GLU174 3.8 41.9 1.0
CA B:GLU174 3.9 42.8 1.0
CZ B:ARG178 4.0 35.5 1.0
CG B:GLU174 4.0 57.3 1.0
CB B:LEU175 4.1 39.5 1.0
NE B:ARG178 4.1 35.0 1.0
N B:GLU174 4.2 42.0 1.0
CG2 B:ILE171 4.4 36.1 1.0
NE2 B:GLN228 4.5 50.8 1.0
CD2 B:LEU175 4.5 40.5 1.0
CG B:ARG178 4.5 33.7 1.0
N B:LEU172 4.6 35.2 1.0
CB B:GLN228 4.7 41.4 1.0
CG1 B:ILE171 4.7 36.3 1.0
CG B:GLN228 4.7 45.8 1.0
CG B:LEU175 4.7 40.2 1.0
C B:LEU175 4.9 39.6 1.0
N B:ILE171 4.9 33.8 1.0
O B:LEU170 4.9 33.1 1.0

Reference:

A.Nawrotek, L.Vuillard, L.Miallau. Crystal Structure of Human Sting in Complex with Adu-S100 To Be Published.
Page generated: Wed Oct 9 10:34:33 2024

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