Sodium in PDB 6rgj: Photorhabdus Asymbiotica Lectin Phl in Complex with D-Glucose

The structure of Photorhabdus Asymbiotica Lectin Phl in Complex with D-Glucose, PDB code: 6rgj was solved by J.Houser, E.Fujdiarova, G.Jancarikova, M.Wimmerova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.03 / 1.80
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	80.638, 80.638, 113.437, 90.00, 90.00, 120.00
R / Rfree (%)	17 / 19.7

The structure of Photorhabdus Asymbiotica Lectin Phl in Complex with D-Glucose also contains other interesting chemical elements:

Chlorine

(Cl)

7 atoms

The binding sites of Sodium atom in the Photorhabdus Asymbiotica Lectin Phl in Complex with D-Glucose (pdb code 6rgj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Photorhabdus Asymbiotica Lectin Phl in Complex with D-Glucose, PDB code: 6rgj:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Photorhabdus Asymbiotica Lectin Phl in Complex with D-Glucose


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 D-Glucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na408 b:21.8 occ:1.00 O A:HOH587 2.2 13.5 1.0 O A:HOH809 2.4 19.4 1.0 O A:HOH712 2.4 11.8 1.0 O A:VAL179 2.4 9.1 1.0 O A:HOH617 2.5 14.0 1.0 OG1 A:THR178 3.2 13.3 1.0 C A:VAL179 3.6 9.8 1.0 O A:HOH812 3.7 20.6 1.0 N A:VAL179 3.8 10.1 1.0 O A:HOH729 4.0 3.8 1.0 O A:HOH699 4.2 11.0 1.0 CA A:VAL179 4.3 9.7 1.0 ND1 A:HIS180 4.4 11.5 1.0 CD2 A:TYR132 4.4 9.5 1.0 O A:HOH821 4.4 29.4 1.0 CG1 A:VAL179 4.5 9.5 1.0 CG1 A:VAL227 4.5 13.5 1.0 CB A:THR178 4.6 12.5 1.0 CE2 A:TYR132 4.6 10.0 1.0 N A:HIS180 4.6 9.8 1.0 O A:ILE131 4.6 7.5 1.0 C A:THR178 4.7 11.1 1.0 CA A:THR178 4.8 11.6 1.0 CA A:HIS180 4.8 10.1 1.0 O A:HOH664 4.9 16.1 1.0

Sodium binding site 2 out of 4 in the Photorhabdus Asymbiotica Lectin Phl in Complex with D-Glucose


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 D-Glucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na409 b:14.3 occ:1.00 O A:GLY185 2.8 8.7 1.0 OD1 A:ASN134 2.8 7.7 1.0 N A:ASP207 3.0 11.4 1.0 N A:THR135 3.1 7.8 1.0 OD1 A:ASP207 3.2 10.4 1.0 CA A:ASN134 3.3 7.5 1.0 CB A:ASN134 3.4 7.5 1.0 OE1 A:GLN203 3.5 9.5 1.0 CG A:ASN134 3.5 7.7 1.0 CG2 A:THR135 3.7 8.2 1.0 C A:ASN134 3.7 7.7 1.0 CA A:PRO206 3.7 10.8 1.0 CA A:ASP207 3.8 12.2 1.0 C A:PRO206 3.8 11.0 1.0 C A:GLY185 4.0 9.2 1.0 CB A:PRO206 4.0 10.8 1.0 CD1 A:ILE181 4.1 9.4 1.0 CG A:ASP207 4.1 11.7 1.0 OG1 A:THR135 4.2 7.7 1.0 CB A:THR135 4.2 7.9 1.0 CA A:THR135 4.3 7.8 1.0 CG A:LEU187 4.3 9.7 1.0 CD A:GLN203 4.3 9.9 1.0 NE2 A:GLN203 4.4 9.8 1.0 CB A:ASP207 4.6 11.9 1.0 N A:ASN134 4.6 7.4 1.0 N A:LEU187 4.7 8.9 1.0 CD2 A:LEU187 4.7 9.9 1.0 ND2 A:ASN134 4.8 7.3 1.0 CA A:GLY185 4.8 9.7 1.0 CA A:ARG186 4.9 8.7 1.0 CG1 A:ILE181 4.9 9.4 1.0 N A:ARG186 4.9 8.9 1.0 CD1 A:LEU187 4.9 10.1 1.0 O A:ASN134 5.0 7.5 1.0

Sodium binding site 3 out of 4 in the Photorhabdus Asymbiotica Lectin Phl in Complex with D-Glucose


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 D-Glucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na410 b:24.5 occ:1.00 O A:HOH784 2.3 26.5 1.0 O A:HOH793 2.3 39.4 1.0 OD1 A:ASN37 2.5 14.1 0.5 O A:THR38 2.6 12.2 1.0 O A:HOH502 3.0 33.7 1.0 O A:ASN37 3.3 15.8 0.5 CG A:ASN37 3.4 14.4 0.5 O A:HOH855 3.5 23.9 1.0 CB A:ASN37 3.6 18.8 0.5 C A:THR38 3.8 12.8 1.0 C A:ASN37 3.8 15.4 0.5 ND2 A:ASN37 4.0 14.2 0.5 CA A:GLY41 4.1 11.2 1.0 C A:ASN37 4.1 16.5 0.5 N A:GLY41 4.2 11.2 1.0 O A:ASN37 4.2 16.2 0.5 CB A:ASN37 4.3 14.5 0.5 N A:THR38 4.4 14.9 1.0 CA A:ASN37 4.5 17.2 0.5 CA A:SER39 4.5 13.5 1.0 N A:SER39 4.6 13.3 1.0 O A:HOH516 4.6 20.9 1.0 CA A:ASN37 4.6 15.0 0.5 C A:SER39 4.6 12.8 1.0 O A:SER39 4.7 13.0 1.0 O A:HOH829 4.7 23.5 1.0 O A:HOH523 4.7 34.2 1.0 CA A:THR38 4.8 14.2 1.0 CG A:ASN37 4.8 19.6 0.5

Sodium binding site 4 out of 4 in the Photorhabdus Asymbiotica Lectin Phl in Complex with D-Glucose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Photorhabdus Asymbiotica Lectin Phl in Complex with D-Glucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na411 b:39.6 occ:1.00 O A:HOH603 2.2 17.3 1.0 O A:HOH777 2.2 26.8 1.0 O A:HOH604 2.5 31.9 1.0 O A:HOH660 2.5 19.6 1.0 O A:HOH801 2.5 25.4 1.0 O A:HOH566 3.3 30.8 1.0 NZ A:LYS81 3.6 20.6 1.0 O A:HOH691 3.6 16.3 1.0 O A:HOH668 3.7 16.2 1.0 O A:HOH622 3.9 19.2 1.0 O A:HOH664 4.2 16.1 1.0 O A:HOH716 4.3 16.2 1.0 OE2 A:GLU31 4.4 18.3 1.0 OD2 A:ASP224 4.5 14.3 1.0 O A:HOH519 4.8 18.5 1.0 CB A:ASP224 4.9 14.1 1.0 CG1 A:VAL226 4.9 19.1 1.0 CE A:LYS81 4.9 20.6 1.0 CD A:GLU31 4.9 17.9 1.0

E.Fujdiarova, J.Houser, P.Dobes, G.Paulikova, N.Kondakov, L.Kononov, P.Hyrsl, M.Wimmerova. Heptabladed Beta-Propeller Lectins PLL2 and Phl From Photorhabdus Spp. Recognize O-Methylated Sugars and Influence the Host Immune System. Febs J. 2020.
ISSN: ISSN 1742-464X
PubMed: 32559333
DOI: 10.1111/FEBS.15457