Sodium in PDB 6fhx: Photorhabdus Asymbiotica Lectin (Phl) in Complex with Synthetic C- Fucoside

The structure of Photorhabdus Asymbiotica Lectin (Phl) in Complex with Synthetic C- Fucoside, PDB code: 6fhx was solved by J.Houser, G.Jancarikova, M.Wimmerova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.58 / 2.34
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	81.568, 81.568, 222.913, 90.00, 90.00, 120.00
R / Rfree (%)	19.2 / 25.2

The structure of Photorhabdus Asymbiotica Lectin (Phl) in Complex with Synthetic C- Fucoside also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Synthetic C- Fucoside (pdb code 6fhx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Synthetic C- Fucoside, PDB code: 6fhx:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Synthetic C- Fucoside


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Photorhabdus Asymbiotica Lectin (Phl) in Complex with Synthetic C- Fucoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:25.7 occ:1.00 OD1 A:ASN134 2.6 14.2 1.0 O A:GLY185 2.7 16.6 1.0 OE1 A:GLN203 3.2 14.5 1.0 N A:ASP207 3.2 20.5 1.0 N A:THR135 3.4 16.0 1.0 CG A:ASN134 3.4 14.9 1.0 CA A:ASN134 3.5 14.9 1.0 CB A:ASN134 3.5 14.8 1.0 OD1 A:ASP207 3.6 19.9 1.0 CA A:PRO206 3.8 21.2 1.0 C A:GLY185 3.9 18.3 1.0 C A:PRO206 3.9 21.0 1.0 C A:ASN134 3.9 15.0 1.0 CG2 A:THR135 4.0 15.6 1.0 CB A:PRO206 4.0 22.5 1.0 CG A:LEU187 4.0 19.2 1.0 CA A:ASP207 4.0 21.0 1.0 CD A:GLN203 4.1 16.4 1.0 CD1 A:ILE181 4.2 15.4 1.0 NE2 A:GLN203 4.2 15.9 1.0 CD2 A:LEU187 4.2 19.6 1.0 OG1 A:THR135 4.2 16.2 1.0 CG A:ASP207 4.4 19.5 1.0 CB A:THR135 4.5 16.2 1.0 N A:LEU187 4.5 18.9 1.0 CA A:THR135 4.5 15.8 1.0 ND2 A:ASN134 4.6 14.8 1.0 CD1 A:LEU187 4.6 19.1 1.0 N A:ASN134 4.7 14.9 1.0 CA A:ARG186 4.7 19.5 1.0 N A:ARG186 4.8 18.4 1.0 CA A:GLY185 4.8 18.3 1.0 CG1 A:ILE181 4.9 15.4 1.0 CB A:ASP207 4.9 20.2 1.0 C A:ARG186 4.9 19.2 1.0 O A:ALA133 4.9 13.4 1.0

Sodium binding site 2 out of 2 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Synthetic C- Fucoside


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Photorhabdus Asymbiotica Lectin (Phl) in Complex with Synthetic C- Fucoside within 5.0Å range: probe atom residue distance (Å) B Occ B:Na407 b:37.8 occ:1.00 OG1 B:THR322 2.7 17.8 1.0 O B:ALA320 2.8 21.6 1.0 N B:ILE32 3.3 30.7 1.0 O B:PHE334 3.4 22.9 1.0 N B:THR322 3.5 20.4 1.0 CB B:THR322 3.5 20.5 1.0 C B:PRO321 3.6 20.6 1.0 OG B:SER319 3.9 23.1 1.0 CA B:GLU31 3.9 34.4 1.0 N B:VAL33 3.9 29.4 1.0 C B:ALA320 3.9 22.1 1.0 CG2 B:ILE32 3.9 32.5 1.0 CA B:PRO321 4.0 20.1 1.0 CB B:GLU31 4.0 35.7 1.0 C B:GLU31 4.0 32.1 1.0 CG2 B:VAL33 4.1 30.2 1.0 CA B:THR322 4.1 20.8 1.0 C B:PHE334 4.2 23.1 1.0 O B:PRO321 4.2 19.2 1.0 CA B:ILE32 4.2 32.2 1.0 CA B:ALA335 4.2 24.9 1.0 CB B:ILE32 4.3 32.8 1.0 CG B:GLU31 4.4 36.3 1.0 N B:PRO321 4.5 19.7 1.0 N B:ALA335 4.5 23.8 1.0 C B:ILE32 4.6 31.9 1.0 O B:VAL33 4.6 23.7 1.0 CB B:SER319 4.7 24.7 1.0 OE1 B:GLU31 4.8 38.5 1.0 CA B:VAL33 4.9 28.9 1.0 CG2 B:THR322 4.9 20.2 1.0 CB B:PHE334 4.9 21.7 1.0 CD1 B:LEU342 4.9 26.0 1.0 N B:ARG336 5.0 27.3 1.0

G.Paulikova, J.Houser, M.Kasakova, B.Oroszova, B.Bertolotti, K.Parkan, J.Moravcova, M.Wimmerova. Fucosylated Inhibitors of Recently Identified Bangle Lectin From Photorhabdus Asymbiotica. Sci Rep V. 9 14904 2019.
ISSN: ESSN 2045-2322
PubMed: 31624296
DOI: 10.1038/S41598-019-51357-9