Sodium in PDB 6rgg: Photorhabdus Laumondii Lectin PLL2 in Complex with O-Methylated Pgl-1- Derived Disaccharide

The structure of Photorhabdus Laumondii Lectin PLL2 in Complex with O-Methylated Pgl-1- Derived Disaccharide, PDB code: 6rgg 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)	67.03 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.304, 89.347, 68.401, 90.00, 101.35, 90.00
R / Rfree (%)	19.9 / 22.4

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

Sodium binding site 1 out of 5 in the Photorhabdus Laumondii Lectin PLL2 in Complex with O-Methylated Pgl-1- Derived Disaccharide


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 O-Methylated Pgl-1- Derived Disaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:70.3 occ:1.00 O A:GLY139 2.6 53.2 1.0 OD1 A:ASN89 3.1 62.9 1.0 N A:THR90 3.2 63.8 1.0 CB A:HIS161 3.4 73.8 1.0 OG1 A:THR90 3.4 75.8 1.0 CA A:ASN89 3.5 57.9 1.0 CA A:HIS161 3.6 75.1 1.0 C A:GLY139 3.6 55.8 1.0 CG2 A:VAL135 3.6 71.8 1.0 CB A:ASN89 3.6 58.5 1.0 N A:HIS161 3.7 75.5 1.0 CG A:ASN89 3.8 62.9 1.0 C A:ASN89 3.8 59.6 1.0 CG2 A:THR90 3.9 71.5 1.0 CA A:GLY139 4.0 56.4 1.0 CB A:THR90 4.0 72.8 1.0 OE1 A:GLN157 4.0 67.3 1.0 CG1 A:ILE141 4.1 60.2 1.0 CA A:THR90 4.2 68.6 1.0 CG A:HIS161 4.5 74.0 1.0 CD1 A:ILE141 4.5 65.8 1.0 N A:ARG140 4.6 55.4 1.0 N A:ILE141 4.7 57.1 1.0 CB A:VAL135 4.7 66.8 1.0 CD2 A:HIS161 4.7 76.9 1.0 N A:ASN89 4.8 54.1 1.0 C A:ALA160 4.9 74.6 1.0 CA A:ARG140 5.0 55.5 1.0 CD A:GLN157 5.0 66.7 1.0

Sodium binding site 2 out of 5 in the Photorhabdus Laumondii Lectin PLL2 in Complex with O-Methylated Pgl-1- Derived Disaccharide


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 O-Methylated Pgl-1- Derived Disaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:89.3 occ:1.00 O A:ALA30 2.6 78.8 1.0 OG A:SER32 2.9 97.8 1.0 N A:ASP226 3.4 68.9 1.0 CG2 A:ILE29 3.4 92.7 1.0 CB A:ALA274 3.4 59.8 1.0 OD2 A:ASP226 3.6 99.4 1.0 C A:ALA30 3.6 81.0 1.0 CG A:ASP226 3.7 95.4 1.0 CB A:ASP226 3.9 80.7 1.0 N A:ALA30 4.0 93.5 1.0 CB A:SER32 4.0 90.3 1.0 CA A:SER225 4.1 74.1 1.0 CA A:SER32 4.1 86.5 1.0 O A:LEU31 4.1 73.5 1.0 CB A:SER225 4.1 74.2 1.0 CA A:ALA30 4.2 84.5 1.0 C A:SER225 4.2 70.1 1.0 C A:LEU31 4.2 76.4 1.0 CA A:ASP226 4.2 75.1 1.0 CB A:ALA30 4.2 76.2 1.0 N A:SER32 4.2 79.0 1.0 CA A:ALA274 4.2 61.0 1.0 OD1 A:ASP226 4.3 0.0 1.0 N A:ALA274 4.4 62.2 1.0 N A:LEU31 4.6 73.4 1.0 C A:ILE29 4.6 96.1 1.0 CB A:ILE29 4.7 98.1 1.0 CD1 A:ILE29 4.9 0.5 1.0 OG A:SER225 4.9 69.8 1.0 CA A:ILE29 5.0 0.5 1.0 O A:ASP226 5.0 62.1 1.0 CA A:LEU31 5.0 75.6 1.0

Sodium binding site 3 out of 5 in the Photorhabdus Laumondii Lectin PLL2 in Complex with O-Methylated Pgl-1- Derived Disaccharide


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 O-Methylated Pgl-1- Derived Disaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:86.7 occ:1.00 O A:GLY187 2.5 53.1 1.0 OE1 A:GLN205 3.1 62.7 1.0 OD1 A:ASN136 3.1 59.1 1.0 N A:ASP209 3.4 78.8 1.0 N A:THR137 3.4 61.0 1.0 CA A:ASN136 3.7 64.2 1.0 C A:GLY187 3.7 50.5 1.0 CB A:ASN136 3.8 64.4 1.0 CG2 A:THR137 3.8 63.5 1.0 CG A:ASN136 3.8 67.4 1.0 CA A:PRO208 3.9 73.2 1.0 CD A:GLN205 3.9 65.4 1.0 OG1 A:THR137 3.9 67.7 1.0 OD1 A:ASP209 3.9 94.2 1.0 C A:ASN136 4.0 62.1 1.0 NE2 A:GLN205 4.0 54.6 1.0 CD1 A:ILE183 4.1 58.2 1.0 C A:PRO208 4.1 72.4 1.0 CG A:LEU189 4.2 64.8 1.0 CA A:ASP209 4.2 82.7 1.0 CB A:THR137 4.3 66.7 1.0 CB A:PRO208 4.3 75.1 1.0 N A:LEU189 4.3 58.9 1.0 CA A:THR137 4.4 67.2 1.0 CA A:ARG188 4.5 54.9 1.0 N A:ARG188 4.5 50.2 1.0 CA A:GLY187 4.7 52.7 1.0 CD2 A:LEU189 4.7 70.7 1.0 CD1 A:LEU189 4.7 69.4 1.0 CG A:ASP209 4.8 88.8 1.0 C A:ARG188 4.8 57.1 1.0 CG1 A:ILE183 4.9 56.9 1.0 N A:ASN136 5.0 64.2 1.0

Sodium binding site 4 out of 5 in the Photorhabdus Laumondii Lectin PLL2 in Complex with O-Methylated Pgl-1- Derived Disaccharide


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 O-Methylated Pgl-1- Derived Disaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na408 b:81.9 occ:1.00 O A:ALA322 2.5 56.8 1.0 OG1 A:THR324 2.8 74.5 1.0 O A:PHE336 3.5 53.5 1.0 N A:ILE34 3.5 76.0 1.0 N A:THR324 3.6 57.6 1.0 C A:PRO323 3.6 59.1 1.0 CG2 A:VAL35 3.6 70.1 1.0 C A:ALA322 3.7 59.8 1.0 CB A:THR324 3.7 65.2 1.0 OG A:SER321 3.7 64.1 1.0 CA A:GLU33 3.9 86.8 1.0 CG2 A:ILE34 3.9 84.6 1.0 N A:VAL35 3.9 62.0 1.0 O A:PRO323 4.0 59.2 1.0 CA A:PRO323 4.0 59.1 1.0 CB A:GLU33 4.0 87.7 1.0 C A:GLU33 4.2 80.1 1.0 CA A:THR324 4.2 60.0 1.0 CA A:ALA337 4.3 51.9 1.0 C A:PHE336 4.3 53.8 1.0 N A:PRO323 4.3 61.2 1.0 O A:VAL35 4.3 65.6 1.0 CG A:GLU33 4.5 95.7 1.0 CA A:ILE34 4.5 77.3 1.0 CB A:SER321 4.6 57.6 1.0 N A:ALA337 4.6 54.0 1.0 CB A:ILE34 4.7 81.6 1.0 C A:ILE34 4.7 66.2 1.0 CB A:VAL35 4.8 66.8 1.0 CA A:VAL35 4.8 65.0 1.0 CA A:ALA322 4.8 65.1 1.0 N A:ALA322 4.9 63.0 1.0 CG2 A:THR324 5.0 72.3 1.0

Sodium binding site 5 out of 5 in the Photorhabdus Laumondii Lectin PLL2 in Complex with O-Methylated Pgl-1- Derived Disaccharide


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 O-Methylated Pgl-1- Derived Disaccharide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na406 b:74.5 occ:1.00 O B:GLY187 2.7 48.9 1.0 OD1 B:ASN136 3.0 57.6 1.0 N B:THR137 3.2 58.4 1.0 N B:ASP209 3.3 73.6 1.0 OE1 B:GLN205 3.3 63.3 1.0 OD1 B:ASP209 3.3 90.0 1.0 CA B:ASN136 3.4 53.4 1.0 CB B:ASN136 3.5 56.8 1.0 CG2 B:THR137 3.5 64.0 1.0 CG B:ASN136 3.7 55.7 1.0 C B:ASN136 3.8 54.8 1.0 C B:GLY187 3.9 50.7 1.0 CA B:ASP209 3.9 78.1 1.0 CA B:PRO208 4.0 67.7 1.0 C B:PRO208 4.0 68.4 1.0 CD1 B:ILE183 4.1 55.8 1.0 OG1 B:THR137 4.1 65.1 1.0 CB B:THR137 4.2 63.0 1.0 CG B:LEU189 4.2 53.1 1.0 CD B:GLN205 4.2 65.9 1.0 CG B:ASP209 4.3 95.2 1.0 CA B:THR137 4.3 58.2 1.0 CB B:PRO208 4.4 66.7 1.0 NE2 B:GLN205 4.5 56.1 1.0 N B:LEU189 4.5 55.5 1.0 CD2 B:LEU189 4.6 51.6 1.0 N B:ASN136 4.7 53.7 1.0 CA B:GLY187 4.7 49.9 1.0 CB B:ASP209 4.7 83.8 1.0 CG1 B:ILE183 4.8 53.2 1.0 N B:ARG188 4.8 53.8 1.0 CA B:ARG188 4.8 52.1 1.0 CD1 B:LEU189 4.8 52.7 1.0 O B:VAL135 4.9 54.3 1.0 ND2 B:ASN136 5.0 54.1 1.0 O B:ASN136 5.0 55.0 1.0 C B:ARG188 5.0 52.2 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