Sodium in PDB 6flu: 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: 6flu 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)	44.93 / 1.78
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	81.940, 81.940, 224.645, 90.00, 90.00, 120.00
R / Rfree (%)	18.4 / 22.2

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

Chlorine

(Cl)

6 atoms

The binding sites of Sodium atom in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Synthetic C- Fucoside (pdb code 6flu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Synthetic C- Fucoside, PDB code: 6flu:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 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:Na407 b:32.3 occ:1.00 O A:SER25 2.3 22.9 1.0 O A:LYS369 2.3 12.5 1.0 O A:HOH765 2.4 26.3 1.0 O A:HOH708 2.5 15.1 1.0 C A:SER25 3.4 20.3 1.0 C A:LYS369 3.5 13.6 1.0 N A:LYS369 3.8 11.6 1.0 O A:HOH564 3.9 33.9 1.0 O A:HOH538 4.1 39.0 1.0 CA A:LYS369 4.2 13.1 1.0 CA A:THR26 4.3 17.7 1.0 N A:THR26 4.3 18.9 1.0 CG2 A:ILE368 4.3 9.6 1.0 CA A:SER25 4.4 20.8 1.0 OXT A:LYS369 4.4 14.1 1.0 O A:HOH707 4.5 13.5 1.0 CB A:SER25 4.6 22.1 1.0 CG2 A:THR26 4.8 19.1 1.0 C A:ILE368 4.8 10.6 1.0 CB A:LYS369 4.8 14.0 1.0 CA A:ILE368 4.9 9.6 1.0 OG A:SER25 5.0 20.3 1.0 O A:HOH550 5.0 27.5 1.0

Sodium binding site 2 out of 3 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:18.0 occ:1.00 O B:HOH800 2.3 16.8 1.0 O A:HOH591 2.4 15.4 1.0 O B:HOH799 2.4 21.3 1.0 O B:THR38 2.6 11.5 1.0 OD1 B:ASN37 2.6 14.9 1.0 O B:ASN37 3.3 14.8 1.0 CG B:ASN37 3.4 14.6 1.0 C B:THR38 3.6 12.1 1.0 C B:ASN37 3.8 12.7 1.0 O A:HOH833 4.0 24.4 1.0 CB B:ASN37 4.2 13.3 1.0 CA B:GLY41 4.2 12.3 1.0 ND2 B:ASN37 4.2 13.7 1.0 N B:GLY41 4.2 11.1 1.0 N B:THR38 4.2 11.4 1.0 O A:HOH790 4.3 4.7 1.0 O B:HOH551 4.4 25.3 1.0 N B:SER39 4.5 12.3 1.0 CA B:THR38 4.5 12.3 1.0 CA B:SER39 4.5 12.2 1.0 CA B:ASN37 4.5 12.9 1.0 O B:HOH829 4.6 26.0 1.0 O A:ALA231 4.7 10.8 1.0 C B:SER39 4.7 11.4 1.0 O B:HOH822 4.8 9.3 1.0 O B:SER39 4.9 10.3 1.0

Sodium binding site 3 out of 3 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 3 of Photorhabdus Asymbiotica Lectin (Phl) in Complex with Synthetic C- Fucoside within 5.0Å range: probe atom residue distance (Å) B Occ B:Na408 b:22.9 occ:1.00 O B:HOH660 2.3 14.1 1.0 O B:SER168 2.6 10.8 1.0 C B:SER168 3.6 10.4 1.0 N B:SER168 4.1 9.2 1.0 CB B:SER168 4.1 10.6 1.0 CA B:SER168 4.1 10.4 1.0 O B:HOH578 4.1 15.5 1.0 ND2 B:ASN170 4.2 12.7 1.0 OD1 B:ASN170 4.3 12.0 1.0 CG B:ASN170 4.6 12.0 1.0 N B:LEU169 4.7 10.7 1.0 OG B:SER168 4.8 11.2 1.0 CA B:LEU169 5.0 11.6 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