Sodium in PDB 6rg1: Photorhabdus Laumondii Lectin PLL2 in Complex with L-Rhamnose

The structure of Photorhabdus Laumondii Lectin PLL2 in Complex with L-Rhamnose, PDB code: 6rg1 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)	45.05 / 1.70
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	65.066, 71.003, 85.764, 90.00, 104.58, 90.00
R / Rfree (%)	18.1 / 20.9

The binding sites of Sodium atom in the Photorhabdus Laumondii Lectin PLL2 in Complex with L-Rhamnose (pdb code 6rg1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Photorhabdus Laumondii Lectin PLL2 in Complex with L-Rhamnose, PDB code: 6rg1:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Photorhabdus Laumondii Lectin PLL2 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 Laumondii Lectin PLL2 in Complex with L-Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na409 b:24.0 occ:1.00 O A:GLY139 2.6 15.3 1.0 OD1 A:ASN89 2.9 15.8 1.0 N A:THR90 3.0 15.9 1.0 CA A:ASN89 3.3 15.6 1.0 CB A:ASN89 3.5 15.5 1.0 CB A:HIS161 3.5 19.2 1.0 CG A:ASN89 3.6 15.8 1.0 CG2 A:VAL135 3.6 17.9 1.0 OG1 A:THR90 3.6 15.7 1.0 C A:ASN89 3.6 15.7 1.0 C A:GLY139 3.7 15.9 1.0 CA A:HIS161 3.7 18.9 1.0 N A:HIS161 3.8 17.7 1.0 CG2 A:THR90 3.9 16.1 1.0 CG1 A:ILE141 3.9 18.6 1.0 OE1 A:GLN157 4.0 20.0 1.0 CB A:THR90 4.1 15.9 1.0 CA A:THR90 4.1 16.2 1.0 CA A:GLY139 4.2 15.7 1.0 CG A:HIS161 4.4 18.7 1.0 CD1 A:ILE141 4.5 18.9 1.0 CB A:VAL135 4.6 17.5 1.0 CD2 A:HIS161 4.6 18.3 1.0 N A:ASN89 4.6 15.7 1.0 N A:ILE141 4.7 17.1 1.0 N A:ARG140 4.7 15.9 0.3 N A:ARG140 4.7 16.6 0.7 ND2 A:ASN89 4.8 15.5 1.0 O A:ASN89 4.9 15.8 1.0 O A:ILE88 4.9 16.6 1.0 C A:ALA160 4.9 17.5 1.0

Sodium binding site 2 out of 6 in the Photorhabdus Laumondii Lectin PLL2 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 Laumondii Lectin PLL2 in Complex with L-Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na410 b:24.5 occ:1.00 O A:GLY187 2.6 15.3 1.0 OD1 A:ASN136 2.8 19.2 1.0 N A:ASP209 3.1 19.4 1.0 N A:THR137 3.3 16.8 1.0 OE1 A:GLN205 3.3 16.9 1.0 CA A:ASN136 3.4 16.9 1.0 OD1 A:ASP209 3.4 19.1 1.0 CB A:ASN136 3.4 17.1 1.0 CG A:ASN136 3.5 17.7 1.0 CA A:PRO208 3.7 18.7 1.0 CG2 A:THR137 3.7 17.5 1.0 C A:ASN136 3.8 16.3 1.0 CB A:PRO208 3.8 18.4 1.0 C A:PRO208 3.9 18.9 1.0 C A:GLY187 3.9 15.2 1.0 CA A:ASP209 3.9 20.5 1.0 CD1 A:ILE183 4.0 16.1 1.0 OG1 A:THR137 4.1 16.6 1.0 CD A:GLN205 4.2 17.8 1.0 CB A:THR137 4.2 17.1 1.0 CG A:ASP209 4.3 19.8 1.0 NE2 A:GLN205 4.3 18.0 1.0 CG A:LEU189 4.3 15.6 1.0 CA A:THR137 4.3 16.6 1.0 N A:LEU189 4.6 16.1 1.0 N A:ASN136 4.7 16.7 1.0 CB A:ASP209 4.7 19.8 1.0 CA A:GLY187 4.8 15.1 1.0 CG1 A:ILE183 4.8 16.4 1.0 N A:ARG188 4.8 15.2 1.0 ND2 A:ASN136 4.8 17.3 1.0 CA A:ARG188 4.8 15.8 1.0 CD2 A:LEU189 4.8 15.7 1.0 CD1 A:LEU189 4.9 15.9 1.0

Sodium binding site 3 out of 6 in the Photorhabdus Laumondii Lectin PLL2 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 Laumondii Lectin PLL2 in Complex with L-Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na411 b:27.2 occ:1.00 O A:GLY43 2.5 19.1 1.0 OE1 A:GLN61 2.7 18.1 1.0 N A:ALA329 3.1 17.8 1.0 CB A:ASP328 3.4 18.3 1.0 CB A:ALA329 3.6 18.2 1.0 CD A:GLN61 3.7 18.0 1.0 C A:GLY43 3.7 18.9 1.0 CA A:ASP328 3.7 18.6 1.0 C A:PRO64 3.9 19.8 1.0 CA A:PRO64 3.9 19.5 1.0 N A:HIS65 3.9 20.0 1.0 C A:ASP328 3.9 18.5 1.0 CA A:ALA329 4.0 17.7 1.0 NE2 A:GLN61 4.0 18.3 1.0 N A:ILE45 4.1 19.1 1.0 CG1 A:ILE45 4.1 20.1 1.0 CA A:ARG44 4.2 21.1 1.0 CD1 A:ILE45 4.3 20.7 1.0 OD1 A:ASN39 4.4 25.9 1.0 N A:ARG44 4.4 19.7 1.0 O A:PRO64 4.4 19.7 1.0 CG A:ASP328 4.5 18.4 1.0 C A:ARG44 4.5 19.8 1.0 CB A:PRO64 4.6 19.6 1.0 ND2 A:ASN39 4.6 25.8 1.0 O A:HIS65 4.6 20.2 1.0 CA A:HIS65 4.6 20.2 0.5 CA A:HIS65 4.7 19.9 0.5 C A:HIS65 4.7 19.9 1.0 O A:ALA63 4.7 18.8 1.0 CG A:ASN39 4.7 24.4 1.0 CA A:GLY43 4.8 18.7 1.0 CB A:ILE45 4.9 19.2 1.0

Sodium binding site 4 out of 6 in the Photorhabdus Laumondii Lectin PLL2 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 Laumondii Lectin PLL2 in Complex with L-Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na412 b:24.9 occ:1.00 O A:ALA322 2.7 16.2 1.0 OG1 A:THR324 2.7 18.0 1.0 N A:ILE34 3.0 22.4 1.0 CA A:GLU33 3.5 20.6 1.0 CG2 A:ILE34 3.5 27.3 1.0 N A:THR324 3.7 16.9 1.0 CB A:THR324 3.7 17.2 1.0 C A:PRO323 3.7 16.6 1.0 C A:ALA322 3.7 16.2 1.0 C A:GLU33 3.7 21.5 1.0 OG A:SER321 3.8 15.0 1.0 N A:VAL35 3.8 19.9 1.0 CB A:GLU33 3.8 20.6 1.0 O A:PHE336 3.8 17.1 1.0 CG2 A:VAL35 3.8 18.2 1.0 CA A:ILE34 4.0 23.6 1.0 CA A:PRO323 4.0 16.1 1.0 O A:PRO323 4.1 17.2 1.0 CB A:ILE34 4.1 25.6 1.0 CA A:THR324 4.3 17.0 1.0 CG A:GLU33 4.3 20.9 1.0 N A:PRO323 4.3 16.1 1.0 C A:ILE34 4.4 22.2 1.0 CB A:SER321 4.5 15.2 1.0 O A:VAL35 4.5 17.5 1.0 CA A:ALA337 4.5 16.1 1.0 C A:PHE336 4.6 16.5 1.0 CA A:VAL35 4.8 18.3 1.0 OE2 A:GLU33 4.8 21.5 1.0 CB A:VAL35 4.8 18.2 1.0 CA A:ALA322 4.8 15.9 1.0 N A:GLU33 4.9 19.8 1.0 N A:ALA322 4.9 15.9 1.0 N A:ALA337 5.0 16.5 1.0 CG2 A:THR324 5.0 17.5 1.0 O A:GLU33 5.0 22.8 1.0

Sodium binding site 5 out of 6 in the Photorhabdus Laumondii Lectin PLL2 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 5 of Photorhabdus Laumondii Lectin PLL2 in Complex with L-Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na413 b:29.9 occ:1.00 O A:GLY92 2.5 16.5 1.0 OD1 A:ASN114 2.5 39.9 1.0 OG A:SER41 3.0 19.3 1.0 N A:SER41 3.1 18.9 1.0 CG A:ASN114 3.3 39.7 1.0 CD1 A:ILE88 3.4 21.5 1.0 CB A:SER41 3.5 19.3 1.0 ND2 A:ASN114 3.6 39.0 1.0 CB A:THR40 3.6 18.7 1.0 C A:GLY92 3.6 16.8 1.0 CA A:THR40 3.9 19.0 1.0 CA A:SER41 3.9 19.3 1.0 C A:THR40 4.0 19.1 1.0 CG2 A:THR113 4.0 27.5 1.0 CD2 A:LEU94 4.1 18.9 1.0 CA A:GLY92 4.1 16.6 1.0 CG1 A:ILE88 4.3 19.7 1.0 CG2 A:THR40 4.3 18.8 1.0 CG A:LEU94 4.3 18.6 1.0 N A:ASN114 4.5 31.5 1.0 OG1 A:THR40 4.5 18.8 1.0 OE1 A:GLN110 4.6 20.6 1.0 CB A:ASN114 4.6 36.6 1.0 N A:ARG93 4.8 16.9 1.0 O A:HOH624 4.8 36.1 1.0 CA A:ASN114 4.8 33.5 1.0 C A:SER41 4.9 19.0 1.0 O A:HOH544 4.9 20.2 1.0 N A:LEU94 4.9 16.9 1.0 N A:ASP42 5.0 19.0 1.0

Sodium binding site 6 out of 6 in the Photorhabdus Laumondii Lectin PLL2 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 6 of Photorhabdus Laumondii Lectin PLL2 in Complex with L-Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na414 b:38.4 occ:1.00 O A:HOH686 2.3 24.9 1.0 OE2 A:GLU334 2.6 20.9 1.0 O A:HOH668 3.0 38.3 1.0 N A:GLY67 3.1 21.4 1.0 OE1 A:GLU334 3.2 21.5 1.0 OD1 A:ASN346 3.2 21.9 1.0 CD A:GLU334 3.2 20.4 1.0 CA A:GLY67 3.5 21.8 1.0 CD1 A:TRP348 3.7 21.4 1.0 CG A:ASN346 3.9 20.6 1.0 NE2 A:GLN61 4.1 18.3 1.0 ND2 A:ASN346 4.1 19.8 1.0 C A:SER66 4.2 21.2 1.0 N A:SER68 4.2 21.7 1.0 NE1 A:TRP348 4.2 22.3 1.0 C A:GLY67 4.2 21.8 1.0 CG A:TRP348 4.3 20.6 1.0 O A:HOH657 4.4 36.2 1.0 CA A:SER66 4.5 20.5 1.0 CB A:TRP348 4.6 19.6 1.0 NE1 A:TRP70 4.7 19.2 1.0 O A:SER68 4.7 18.9 1.0 CZ2 A:TRP70 4.7 18.6 1.0 CG A:GLU334 4.7 18.9 1.0 O A:HOH757 4.9 29.1 1.0 O A:HIS65 5.0 20.2 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