Sodium in PDB 6rfz: Photorhabdus Laumondii Lectin PLL2 in Complex with D-Glucose

The structure of Photorhabdus Laumondii Lectin PLL2 in Complex with D-Glucose, PDB code: 6rfz was solved by J.Houser, E.Fujdiarova, M.Wimmerova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.64 / 1.80
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	65.498, 71.099, 86.221, 90.00, 103.95, 90.00
R / Rfree (%)	21 / 23.5

The binding sites of Sodium atom in the Photorhabdus Laumondii Lectin PLL2 in Complex with D-Glucose (pdb code 6rfz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Photorhabdus Laumondii Lectin PLL2 in Complex with D-Glucose, PDB code: 6rfz:

Sodium binding site 1 out of 1 in the Photorhabdus Laumondii Lectin PLL2 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 Laumondii Lectin PLL2 in Complex with D-Glucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na412 b:36.0 occ:1.00 OG A:SER36 2.5 15.8 1.0 O A:HOH757 2.7 13.6 1.0 O A:HOH657 2.9 22.5 1.0 O A:HOH582 3.2 18.2 1.0 CB A:SER36 3.6 15.3 1.0 O A:HOH592 3.8 18.5 1.0 CA A:SER36 3.9 15.3 1.0 CG1 A:VAL85 3.9 13.9 1.0 O A:HOH818 4.1 33.5 1.0 O A:HOH858 4.2 29.0 1.0 NZ A:LYS83 4.3 17.8 1.0 CE A:LYS83 4.4 17.8 1.0 O A:VAL86 4.5 14.8 1.0 N A:VAL37 4.5 15.1 1.0 O A:HOH619 4.5 19.7 1.0 C A:SER36 4.7 15.1 1.0 CA A:VAL85 4.7 13.9 1.0 CB A:VAL85 4.7 13.9 1.0 N A:VAL86 4.8 14.3 1.0 CG2 A:VAL85 4.9 14.1 1.0 O A:VAL37 5.0 15.6 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