Sodium in PDB 6rgu: Photorhabdus Asymbiotica Lectin Phl in Complex with 3-O-Methyl-D- Glucose

The structure of Photorhabdus Asymbiotica Lectin Phl in Complex with 3-O-Methyl-D- Glucose, PDB code: 6rgu 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)	40.45 / 1.75
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	80.828, 80.828, 113.243, 90.00, 90.00, 120.00
R / Rfree (%)	16.9 / 19.7

The structure of Photorhabdus Asymbiotica Lectin Phl in Complex with 3-O-Methyl-D- Glucose also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Sodium atom in the Photorhabdus Asymbiotica Lectin Phl in Complex with 3-O-Methyl-D- Glucose (pdb code 6rgu). 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 3-O-Methyl-D- Glucose, PDB code: 6rgu:
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 3-O-Methyl-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 3-O-Methyl-D- Glucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na414 b:28.0 occ:1.00 OD1 A:ASN37 2.4 27.3 1.0 O A:THR38 2.4 22.7 1.0 O A:HOH744 2.4 30.3 1.0 O A:HOH756 2.5 33.0 1.0 O A:HOH536 2.5 34.3 1.0 CG A:ASN37 3.4 26.8 1.0 C A:THR38 3.5 23.4 1.0 O A:ASN37 3.6 26.2 1.0 O A:HOH781 3.6 28.1 1.0 C A:ASN37 3.8 27.0 1.0 ND2 A:ASN37 4.1 27.4 1.0 N A:THR38 4.1 24.2 1.0 N A:GLY41 4.1 23.5 1.0 CA A:GLY41 4.1 24.7 1.0 CL A:CL409 4.3 32.9 1.0 CB A:ASN37 4.3 26.7 1.0 O A:HOH766 4.3 40.4 1.0 N A:SER39 4.3 24.3 1.0 CA A:SER39 4.4 25.0 1.0 CA A:THR38 4.4 24.3 1.0 C A:SER39 4.6 25.1 1.0 CA A:ASN37 4.6 25.9 1.0 CL A:CL413 4.6 39.3 1.0 O A:HOH516 4.7 26.9 1.0 O A:SER39 4.8 25.4 1.0

Sodium binding site 2 out of 3 in the Photorhabdus Asymbiotica Lectin Phl in Complex with 3-O-Methyl-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 3-O-Methyl-D- Glucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na415 b:31.3 occ:1.00 N A:ASP229 3.4 26.4 1.0 CE1 A:HIS180 3.4 28.7 1.0 CA A:ILE228 3.7 28.7 1.0 NZ A:LYS277 3.7 30.9 1.0 CB A:ILE228 3.7 31.7 1.0 NE2 A:HIS180 3.8 28.8 1.0 CE A:LYS277 3.8 33.2 1.0 O A:ASP229 3.9 28.6 1.0 C A:ILE228 4.0 28.1 1.0 CG2 A:ILE228 4.2 31.5 1.0 CA A:ASP229 4.4 28.2 1.0 ND1 A:HIS180 4.5 27.9 1.0 C A:ASP229 4.6 27.6 1.0 CB A:ASP229 4.7 29.6 1.0 CD A:LYS277 4.9 32.7 1.0 O A:VAL227 5.0 25.5 1.0 O A:HOH733 5.0 44.5 1.0

Sodium binding site 3 out of 3 in the Photorhabdus Asymbiotica Lectin Phl in Complex with 3-O-Methyl-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 3-O-Methyl-D- Glucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na416 b:35.6 occ:0.50 O A:HOH750 2.8 44.2 1.0 O A:THR135 2.9 21.8 1.0 N A:GLY137 3.6 19.8 1.0 C A:THR135 3.7 19.8 1.0 CA A:GLY137 3.9 20.4 1.0 CG2 A:THR88 4.1 23.3 1.0 C A:ASP136 4.2 19.2 1.0 O A:HOH779 4.3 50.2 1.0 N A:ASP136 4.4 19.9 1.0 O A:ASN134 4.4 19.2 1.0 CA A:ASP136 4.5 19.9 1.0 CB A:THR88 4.5 22.1 1.0 CA A:THR135 4.5 19.6 1.0 OG1 A:THR88 4.7 21.8 1.0 O A:ASP136 4.9 20.1 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