Sodium in PDB 6rg2: Photorhabdus Laumondii Lectin PLL2 in Complex with 3-O-Methyl-D- Glucose

The structure of Photorhabdus Laumondii Lectin PLL2 in Complex with 3-O-Methyl-D- Glucose, PDB code: 6rg2 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)	44.84 / 1.12
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.646, 56.708, 108.477, 90.00, 95.33, 90.00
R / Rfree (%)	13.6 / 16.1

The binding sites of Sodium atom in the Photorhabdus Laumondii Lectin PLL2 in Complex with 3-O-Methyl-D- Glucose (pdb code 6rg2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Photorhabdus Laumondii Lectin PLL2 in Complex with 3-O-Methyl-D- Glucose, PDB code: 6rg2:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Photorhabdus Laumondii Lectin PLL2 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 Laumondii Lectin PLL2 in Complex with 3-O-Methyl-D- Glucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na413 b:39.1 occ:1.00 O A:HOH738 2.1 30.5 1.0 O A:HOH904 2.5 30.7 1.0 O A:HOH916 2.6 22.7 1.0 OD2 A:ASP186 2.7 12.8 1.0 O A:HOH853 3.1 36.2 1.0 NE A:ARG188 3.7 9.7 1.0 CG A:ASP186 3.7 10.7 1.0 O B:HOH866 4.1 26.6 1.0 CD A:ARG188 4.1 10.0 1.0 O A:HOH600 4.2 16.4 1.0 CB A:ASP186 4.2 11.7 1.0 ND1 A:HIS257 4.6 15.2 1.0 CZ A:ARG188 4.7 9.7 1.0 OD1 A:ASP186 4.7 10.8 1.0 O A:HOH773 4.8 25.4 1.0 CE1 A:HIS257 4.8 17.4 1.0 NH2 A:ARG188 4.9 11.1 1.0 CG A:ARG188 4.9 10.1 1.0

Sodium binding site 2 out of 2 in the Photorhabdus Laumondii Lectin PLL2 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 Laumondii Lectin PLL2 in Complex with 3-O-Methyl-D- Glucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na414 b:36.1 occ:1.00 O A:HOH736 2.1 31.5 1.0 O A:GLY269 2.8 11.6 1.0 O A:ASN245 2.8 14.8 1.0 N A:ALA247 3.6 10.6 1.0 CG2 A:VAL270 3.7 14.9 1.0 CB A:ALA247 3.7 12.2 1.0 C A:ASN245 3.8 13.2 1.0 CA A:ALA247 3.9 11.1 1.0 C A:GLY269 3.9 11.2 1.0 CG A:ASN245 4.0 15.4 1.0 C A:ASN246 4.1 12.0 1.0 ND2 A:ASN245 4.1 18.5 1.0 O A:HOH717 4.2 25.1 1.0 CB A:ASN245 4.2 15.7 1.0 OD1 A:ASN245 4.2 15.7 1.0 CA A:VAL270 4.4 10.9 1.0 O A:ASN246 4.5 12.1 1.0 N A:VAL270 4.6 10.8 1.0 CB A:VAL270 4.6 12.7 1.0 N A:ASN246 4.6 12.9 1.0 CA A:ASN245 4.7 14.7 1.0 CA A:ASN246 4.8 12.6 1.0 CB A:ASN246 5.0 14.5 1.0 N A:GLY269 5.0 11.9 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