Sodium in PDB 5d3d: Crystal Structure of Staphylococcal Superantigen-Like Protein 3

The structure of Crystal Structure of Staphylococcal Superantigen-Like Protein 3, PDB code: 5d3d was solved by L.J.Feitsma, E.G.Huizinga, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	61.20 / 1.94
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.000, 79.220, 96.380, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 22.4

The structure of Crystal Structure of Staphylococcal Superantigen-Like Protein 3 also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of Staphylococcal Superantigen-Like Protein 3 (pdb code 5d3d). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Staphylococcal Superantigen-Like Protein 3, PDB code: 5d3d:

Sodium binding site 1 out of 1 in the Crystal Structure of Staphylococcal Superantigen-Like Protein 3


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 Superantigen-Like Protein 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:47.6 occ:1.00 OE2 B:GLU151 2.2 37.8 1.0 OG B:SER149 2.5 25.9 1.0 CD B:GLU151 3.1 38.0 1.0 O B:HOH576 3.4 48.5 1.0 CG B:GLU151 3.5 33.8 1.0 CB B:SER149 3.5 25.7 1.0 CE1 B:PHE201 3.7 26.3 1.0 CB B:GLU151 3.9 30.8 1.0 C B:SER149 3.9 26.0 1.0 O B:SER149 4.0 26.3 1.0 OE1 B:GLU151 4.1 45.3 1.0 N B:GLU151 4.1 25.5 1.0 C B:PHE150 4.2 25.8 1.0 CD1 B:PHE201 4.2 25.1 1.0 N B:PHE150 4.2 25.4 1.0 CE B:LYS266 4.2 31.4 1.0 CA B:SER149 4.3 26.2 1.0 O B:HOH547 4.4 31.9 1.0 CA B:PHE150 4.5 26.0 1.0 O B:PHE150 4.5 26.2 1.0 NZ B:LYS266 4.6 32.1 1.0 CA B:GLU151 4.7 26.9 1.0 CZ B:PHE201 4.7 26.3 1.0 O B:HOH569 4.9 38.0 1.0

K.J.Koymans, L.J.Feitsma, T.H.Brondijk, P.C.Aerts, E.Lukkien, P.Lossl, K.P.Van Kessel, C.J.De Haas, J.A.Van Strijp, E.G.Huizinga. Structural Basis For Inhibition of TLR2 By Staphylococcal Superantigen-Like Protein 3 (SSL3). Proc.Natl.Acad.Sci.Usa V. 112 11018 2015.
ISSN: ESSN 1091-6490
PubMed: 26283364
DOI: 10.1073/PNAS.1502026112