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Sodium in PDB 3ffc: Crystal Structure of CF34 Tcr in Complex with Hla-B8/Flr

Protein crystallography data

The structure of Crystal Structure of CF34 Tcr in Complex with Hla-B8/Flr, PDB code: 3ffc was solved by S.Gras, S.R.Burrows, L.Kjer-Nielsen, C.S.Clements, Y.C.Liu, L.C.Sullivan, A.G.Brooks, A.W.Purcell, J.Mccluskey, J.Rossjohn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.80
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 111.564, 171.807, 272.690, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 26.8

Other elements in 3ffc:

The structure of Crystal Structure of CF34 Tcr in Complex with Hla-B8/Flr also contains other interesting chemical elements:

Cadmium (Cd) 10 atoms
Chlorine (Cl) 11 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of CF34 Tcr in Complex with Hla-B8/Flr (pdb code 3ffc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the Crystal Structure of CF34 Tcr in Complex with Hla-B8/Flr, PDB code: 3ffc:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 3ffc

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Sodium binding site 1 out of 10 in the Crystal Structure of CF34 Tcr in Complex with Hla-B8/Flr


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 CF34 Tcr in Complex with Hla-B8/Flr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na281

b:21.1
occ:1.00
 NZ A:LYS243 3.5 22.4 1.0
N A:THR233 3.7 28.1 1.0
CG A:GLU232 3.8 30.9 1.0
CA A:GLU232 4.1 30.2 1.0
OG1 A:THR233 4.2 26.8 1.0
CB A:THR233 4.4 26.8 1.0
C A:GLU232 4.4 29.2 1.0
CB A:GLU232 4.5 30.4 1.0
CA A:THR233 4.7 27.0 1.0
CE A:LYS243 4.8 22.2 1.0

Sodium binding site 2 out of 10 in 3ffc

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Sodium binding site 2 out of 10 in the Crystal Structure of CF34 Tcr in Complex with Hla-B8/Flr


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 CF34 Tcr in Complex with Hla-B8/Flr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na282

b:52.4
occ:1.00
 OD2 A:ASP30 2.7 28.9 1.0
CG A:ASP30 3.5 28.5 1.0
N A:GLU212 3.5 30.6 1.0
CB A:PRO210 3.5 27.9 1.0
OD1 A:ASP30 3.5 30.7 1.0
CB A:GLU212 3.5 31.7 1.0
N A:ALA211 3.8 28.8 1.0
CA A:GLU212 4.1 31.5 1.0
C A:ALA211 4.4 29.9 1.0
C A:PRO210 4.4 28.5 1.0
CA A:ALA211 4.5 29.3 1.0
CA A:PRO210 4.5 28.0 1.0
CG A:PRO210 4.6 27.8 1.0
CB A:ALA211 4.6 29.2 1.0
CG A:GLU212 4.7 33.5 1.0
CB A:ASP30 4.9 27.0 1.0

Sodium binding site 3 out of 10 in 3ffc

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Sodium binding site 3 out of 10 in the Crystal Structure of CF34 Tcr in Complex with Hla-B8/Flr


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 CF34 Tcr in Complex with Hla-B8/Flr within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na103

b:17.8
occ:1.00
 NH2 B:ARG45 3.7 27.3 1.0
N B:LYS48 3.9 31.9 1.0
NH1 B:ARG45 3.9 27.9 1.0
CZ B:ARG45 4.3 27.2 1.0
OE1 F:GLN72 4.5 23.6 0.5
NH1 F:ARG75 4.5 20.6 1.0
CA B:GLU47 4.6 30.0 1.0
CB B:GLU47 4.6 29.9 1.0
CA B:LYS48 4.6 32.9 1.0
C B:GLU47 4.7 30.9 1.0

Sodium binding site 4 out of 10 in 3ffc

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Sodium binding site 4 out of 10 in the Crystal Structure of CF34 Tcr in Complex with Hla-B8/Flr


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 CF34 Tcr in Complex with Hla-B8/Flr within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na104

b:23.5
occ:1.00
 OG1 B:THR4 3.0 24.4 1.0
N B:THR4 3.3 24.5 1.0
CB B:THR4 3.9 23.7 1.0
CA B:ARG3 3.9 25.7 0.5
CA B:ARG3 4.0 25.7 0.5
C B:ARG3 4.2 25.2 0.5
C B:ARG3 4.2 25.1 0.5
CA B:THR4 4.2 23.8 1.0
CG B:ARG3 4.4 25.9 0.5
CB B:ARG3 4.5 25.8 0.5
O B:GLN2 4.6 27.1 1.0
CB B:ARG3 4.8 25.7 0.5
O B:THR4 4.9 23.1 1.0
CG B:ARG3 4.9 26.3 0.5

Sodium binding site 5 out of 10 in 3ffc

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Sodium binding site 5 out of 10 in the Crystal Structure of CF34 Tcr in Complex with Hla-B8/Flr


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 CF34 Tcr in Complex with Hla-B8/Flr within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na213

b:36.5
occ:0.50
 NH1 D:ARG80 3.2 51.4 1.0
NE2 D:GLN77 3.6 50.7 1.0
CZ D:ARG80 4.4 51.5 1.0
CD D:GLN77 4.5 50.1 1.0
OE1 D:GLN77 4.6 50.2 1.0
NH2 D:ARG80 4.8 51.6 1.0

Sodium binding site 6 out of 10 in 3ffc

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Sodium binding site 6 out of 10 in the Crystal Structure of CF34 Tcr in Complex with Hla-B8/Flr


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 CF34 Tcr in Complex with Hla-B8/Flr within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na263

b:23.6
occ:1.00
 NZ E:LYS11 3.1 23.0 1.0
OG E:SER234 3.3 24.3 1.0
OD1 E:ASN236 3.5 22.7 1.0
CB E:SER234 4.1 24.1 1.0
CG E:ASN236 4.4 22.4 1.0
CE E:LYS11 4.5 21.8 1.0
CB E:ASN236 4.5 22.9 1.0

Sodium binding site 7 out of 10 in 3ffc

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Sodium binding site 7 out of 10 in the Crystal Structure of CF34 Tcr in Complex with Hla-B8/Flr


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 CF34 Tcr in Complex with Hla-B8/Flr within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na103

b:27.1
occ:1.00
 N G:MET0 2.0 31.7 0.5
CA G:MET0 3.4 31.8 0.5
OD2 F:ASP119 3.9 23.0 1.0
CB G:MET0 4.0 31.6 0.5
CE G:MET0 4.0 30.0 0.5
CG G:MET0 4.1 31.7 0.5
C G:MET0 4.3 31.9 0.5
CB F:ASP119 4.4 20.8 1.0
NE2 F:GLN87 4.5 29.4 1.0
CG F:ASP119 4.6 21.6 1.0
N G:ILE1 4.6 31.9 1.0
SD G:MET0 4.9 31.8 0.5

Sodium binding site 8 out of 10 in 3ffc

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Sodium binding site 8 out of 10 in the Crystal Structure of CF34 Tcr in Complex with Hla-B8/Flr


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 CF34 Tcr in Complex with Hla-B8/Flr within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na104

b:35.3
occ:1.00
 NE2 G:HIS51 3.0 39.0 1.0
CD2 G:HIS51 3.9 38.6 1.0
CE1 G:HIS51 4.0 39.3 1.0
O G:VAL49 4.6 34.6 1.0
CD G:CD101 4.9 0.7 1.0

Sodium binding site 9 out of 10 in 3ffc

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Sodium binding site 9 out of 10 in the Crystal Structure of CF34 Tcr in Complex with Hla-B8/Flr


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of CF34 Tcr in Complex with Hla-B8/Flr within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na262

b:25.8
occ:1.00
 NZ J:LYS11 3.3 22.9 1.0
OG J:SER234 3.6 24.8 1.0
CB J:SER234 3.8 23.8 1.0
OD1 J:ASN236 4.1 23.1 1.0
CE J:LYS11 4.7 22.1 1.0

Sodium binding site 10 out of 10 in 3ffc

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Sodium binding site 10 out of 10 in the Crystal Structure of CF34 Tcr in Complex with Hla-B8/Flr


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of CF34 Tcr in Complex with Hla-B8/Flr within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na265

b:50.0
occ:1.00
 CL J:CL266 3.4 60.5 1.0
CD2 J:LEU96 3.4 27.4 1.0
CD J:LYS15 3.5 27.5 1.0
CB J:LYS95 3.8 26.0 1.0
CA J:LYS95 3.9 25.6 1.0
CG J:LYS15 3.9 26.7 1.0
CG J:LYS95 4.0 26.8 1.0
N J:LEU96 4.0 25.1 1.0
C J:LYS95 4.5 25.3 1.0
CE J:LYS15 4.5 28.5 1.0
NZ J:LYS15 4.5 27.9 1.0
CD J:LYS95 4.6 29.6 1.0
CE J:LYS95 4.8 31.8 1.0
CG J:LEU96 4.9 25.8 1.0

Reference:

S.Gras, S.R.Burrows, L.Kjer-Nielsen, C.S.Clements, Y.C.Liu, L.C.Sullivan, M.J.Bell, A.G.Brooks, A.W.Purcell, J.Mccluskey, J.Rossjohn. The Shaping of T Cell Receptor Recognition By Self-Tolerance. Immunity V. 30 193 2009.
ISSN: ISSN 1074-7613
PubMed: 19167249
DOI: 10.1016/J.IMMUNI.2008.11.011
Page generated: Mon Oct 7 09:45:28 2024

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