Sodium in PDB 6rgr: Photorhabdus Asymbiotica Lectin Phl in Complex with L-Rhamnose

The structure of Photorhabdus Asymbiotica Lectin Phl in Complex with L-Rhamnose, PDB code: 6rgr 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)	43.99 / 1.89
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	80.499, 80.499, 113.413, 90.00, 90.00, 120.00
R / Rfree (%)	20 / 22.9

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

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Photorhabdus Asymbiotica Lectin Phl in Complex with L-Rhamnose (pdb code 6rgr). 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 L-Rhamnose, PDB code: 6rgr:
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 L-Rhamnose


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 L-Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:29.1 occ:1.00 O A:GLY185 2.6 22.8 1.0 OD1 A:ASN134 2.9 21.8 1.0 N A:ASP207 3.0 24.1 1.0 N A:THR135 3.2 21.6 1.0 OD1 A:ASP207 3.4 24.6 1.0 CA A:ASN134 3.4 20.9 1.0 OE1 A:GLN203 3.4 24.1 1.0 CB A:ASN134 3.5 20.9 1.0 CG A:ASN134 3.6 20.8 1.0 CA A:PRO206 3.7 24.4 1.0 CG2 A:THR135 3.7 24.6 1.0 C A:GLY185 3.8 22.9 1.0 C A:ASN134 3.8 22.1 1.0 C A:PRO206 3.8 24.3 1.0 CA A:ASP207 3.8 25.6 1.0 CB A:PRO206 3.9 24.8 1.0 OG1 A:THR135 4.2 23.6 1.0 CG A:ASP207 4.2 26.5 1.0 CG A:LEU187 4.2 23.4 1.0 CD1 A:ILE181 4.2 24.0 1.0 CB A:THR135 4.3 22.6 1.0 CD A:GLN203 4.3 25.5 1.0 CA A:THR135 4.3 21.6 1.0 NE2 A:GLN203 4.4 25.3 1.0 N A:LEU187 4.5 23.0 1.0 CD2 A:LEU187 4.6 23.1 1.0 CB A:ASP207 4.6 26.2 1.0 CA A:GLY185 4.6 23.5 1.0 N A:ASN134 4.7 20.2 1.0 N A:ARG186 4.7 23.2 1.0 CA A:ARG186 4.7 21.9 1.0 ND2 A:ASN134 4.9 19.1 1.0 CD1 A:LEU187 4.9 24.0 1.0 CG1 A:ILE181 4.9 24.4 1.0 O A:PRO206 5.0 23.8 1.0

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


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 L-Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:35.5 occ:1.00 O A:GLY233 2.7 36.2 1.0 OD1 A:ASN182 2.9 25.6 1.0 O A:HOH628 2.9 43.0 1.0 OE1 A:GLN251 3.0 26.4 1.0 N A:SER183 3.2 24.6 1.0 CA A:ASN182 3.5 23.4 1.0 CB A:ASN182 3.6 23.9 1.0 CG A:ASN182 3.6 25.1 1.0 OG A:SER183 3.6 26.0 1.0 C A:GLY233 3.7 31.3 1.0 C A:ASN182 3.8 24.6 1.0 CB A:SER183 3.9 24.7 1.0 CD A:GLN251 4.0 29.7 1.0 CA A:ARG234 4.1 29.8 1.0 N A:LEU235 4.1 26.6 1.0 CA A:SER183 4.2 25.3 1.0 CG A:LEU235 4.3 24.3 1.0 NE2 A:GLN251 4.3 26.9 1.0 N A:ARG234 4.3 29.7 1.0 C A:ARG234 4.3 28.1 1.0 CD2 A:LEU235 4.7 24.7 1.0 N A:ASN182 4.8 22.8 1.0 CA A:GLY233 4.8 32.1 1.0 ND2 A:ASN182 4.9 24.1 1.0 O A:ILE181 5.0 22.9 1.0

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


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 L-Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:55.5 occ:1.00 OG A:SER357 2.7 39.4 1.0 OD2 A:ASP339 2.7 46.1 1.0 CB A:SER357 3.4 40.8 1.0 CB A:ALA341 3.6 34.1 1.0 CZ2 A:TRP343 3.7 45.2 1.0 CG A:ASP339 3.8 49.1 1.0 CE2 A:TRP343 4.1 42.5 1.0 NE1 A:TRP343 4.2 42.7 1.0 OD1 A:ASP339 4.4 46.4 1.0 CH2 A:TRP343 4.5 41.6 1.0 CA A:GLY359 4.7 33.9 1.0 CA A:SER357 4.8 39.6 1.0 CB A:ASP339 4.9 45.7 1.0 O A:HOH507 4.9 44.6 1.0 N A:GLY359 4.9 36.3 1.0

Sodium binding site 4 out of 4 in the Photorhabdus Asymbiotica Lectin Phl in Complex with L-Rhamnose


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 L-Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na408 b:49.6 occ:1.00 O A:VAL179 2.4 24.0 1.0 O A:HOH607 2.6 27.5 1.0 O A:HOH550 2.7 30.7 1.0 OG1 A:THR178 3.4 32.7 1.0 C A:VAL179 3.6 27.0 1.0 N A:VAL179 4.0 26.6 1.0 O A:HOH606 4.0 22.5 1.0 ND1 A:HIS180 4.2 30.1 1.0 O A:HOH631 4.2 24.9 1.0 CA A:VAL179 4.4 25.8 1.0 CD1 A:TYR132 4.4 24.2 1.0 CG1 A:VAL227 4.5 29.2 1.0 CG1 A:VAL179 4.6 26.5 1.0 CE1 A:TYR132 4.6 26.0 1.0 N A:HIS180 4.6 25.2 1.0 O A:ILE131 4.7 22.0 1.0 CB A:THR178 4.7 31.3 1.0 CA A:HIS180 4.8 25.5 1.0 C A:THR178 4.8 28.9 1.0 CB A:HIS180 4.9 25.9 1.0 CG A:HIS180 5.0 26.9 1.0 CA A:THR178 5.0 28.8 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