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Sodium in PDB 4udu: Crystal Structure of Staphylococcal Enterotoxin E in Complex with A T Cell Receptor

Protein crystallography data

The structure of Crystal Structure of Staphylococcal Enterotoxin E in Complex with A T Cell Receptor, PDB code: 4udu was solved by K.E.J.Rodstrom, P.Regenthal, K.Lindkvist-Petersson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.33 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.134, 78.544, 180.805, 90.00, 90.00, 90.00
R / Rfree (%) 24.6 / 25.5

Other elements in 4udu:

The structure of Crystal Structure of Staphylococcal Enterotoxin E in Complex with A T Cell Receptor also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Staphylococcal Enterotoxin E in Complex with A T Cell Receptor (pdb code 4udu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Staphylococcal Enterotoxin E in Complex with A T Cell Receptor, PDB code: 4udu:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4udu

Go back to Sodium Binding Sites List in 4udu
Sodium binding site 1 out of 2 in the Crystal Structure of Staphylococcal Enterotoxin E in Complex with A T Cell Receptor


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 Staphylococcal Enterotoxin E in Complex with A T Cell Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1235

b:47.7
occ:1.00
OD1 C:ASP197 2.4 59.3 1.0
O C:ARG13 2.6 53.6 1.0
N C:GLY182 3.1 41.0 1.0
O C:GLY182 3.2 42.3 1.0
CB C:LEU12 3.3 53.7 1.0
CG C:ASP197 3.4 59.9 1.0
N C:ARG13 3.4 52.5 1.0
CD2 C:PHE199 3.5 49.8 1.0
C C:ARG13 3.6 55.1 1.0
CA C:ARG181 3.7 42.5 1.0
N C:PHE199 3.7 44.0 1.0
CB C:PHE199 3.7 46.1 1.0
OD2 C:ASP197 3.8 66.7 1.0
C C:ARG181 3.9 45.5 1.0
CG C:ARG181 3.9 54.8 1.0
CG C:LEU12 3.9 58.2 1.0
CA C:ARG13 4.0 51.8 1.0
C C:GLY182 4.0 43.3 1.0
C C:LEU12 4.0 57.6 1.0
CA C:GLY182 4.0 40.1 1.0
CG C:PHE199 4.1 47.2 1.0
CB C:ARG181 4.2 45.0 1.0
CA C:LEU12 4.2 54.7 1.0
CA C:PHE199 4.2 43.5 1.0
N C:LEU198 4.4 45.2 1.0
CB C:ARG13 4.4 50.6 1.0
CE2 C:PHE199 4.6 52.6 1.0
CB C:ASP197 4.6 49.8 1.0
C C:LEU198 4.7 47.0 1.0
O C:GLN180 4.7 45.8 1.0
C C:ASP197 4.7 49.4 1.0
CD1 C:LEU12 4.8 58.5 1.0
N C:LYS14 4.8 52.8 1.0
N C:ARG181 4.8 43.2 1.0
CA C:LEU198 4.8 43.9 1.0
O C:LEU12 4.8 58.4 1.0
CA C:ASP197 4.9 47.2 1.0
C C:PHE199 4.9 48.0 1.0
CB C:LEU198 4.9 44.4 1.0

Sodium binding site 2 out of 2 in 4udu

Go back to Sodium Binding Sites List in 4udu
Sodium binding site 2 out of 2 in the Crystal Structure of Staphylococcal Enterotoxin E in Complex with A T Cell Receptor


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 Staphylococcal Enterotoxin E in Complex with A T Cell Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1236

b:59.9
occ:1.00
O C:VAL125 2.3 63.0 1.0
O C:ILE140 2.6 64.8 1.0
N C:VAL143 3.2 55.8 1.0
O C:VAL143 3.3 61.3 1.0
C C:ILE140 3.4 66.4 1.0
C C:VAL125 3.4 64.6 1.0
CD1 C:ILE127 3.6 63.8 1.0
CA C:ILE140 3.8 64.2 1.0
N C:LYS142 3.9 58.2 1.0
CA C:VAL143 3.9 54.8 1.0
O C:PRO139 3.9 64.5 1.0
C C:VAL143 4.0 60.3 1.0
N C:VAL125 4.0 62.7 1.0
CB C:VAL143 4.0 57.6 1.0
CA C:VAL125 4.2 61.4 1.0
C C:LYS142 4.2 58.8 1.0
CG1 C:ILE127 4.2 57.2 1.0
N C:PRO126 4.3 61.9 1.0
CA C:LYS142 4.3 55.8 1.0
N C:ASP141 4.3 63.1 1.0
CA C:PRO126 4.4 61.6 1.0
CB C:LYS142 4.5 57.4 1.0
C C:LYS124 4.5 68.8 1.0
C C:ASP141 4.6 63.1 1.0
CG1 C:ILE140 4.6 70.4 1.0
N C:ILE127 4.7 58.4 1.0
N C:ILE140 4.7 64.9 1.0
C C:PRO139 4.7 66.9 1.0
C C:PRO126 4.7 63.0 1.0
CD1 C:ILE140 4.8 77.5 1.0
CG2 C:VAL143 4.8 55.8 1.0
CB C:VAL125 4.8 63.2 1.0
CB C:ILE140 4.8 69.9 1.0
CA C:ASP141 4.9 62.2 1.0
O C:LYS124 4.9 69.7 1.0

Reference:

K.E.J.Rodstrom, P.Regenthal, K.Lindkvist-Petersson. Structure of Staphylococcal Enterotoxin E in Complex with Tcr Defines the Role of Tcr Loop Positioning in Superantigen Recognition. Plos One V. 10 01319 2015.
ISSN: ESSN 1932-6203
PubMed: 26147596
DOI: 10.1371/JOURNAL.PONE.0131988
Page generated: Tue Dec 15 08:06:48 2020

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