Sodium in PDB 5mxf: Photorhabdus Asymbiotica Lectin (Phl) in Complex with Alpha-Methyl Fucoside

The structure of Photorhabdus Asymbiotica Lectin (Phl) in Complex with Alpha-Methyl Fucoside, PDB code: 5mxf was solved by G.Jancarikova, J.Houser, G.Demo, M.Wimmerova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.11 / 1.90
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	81.249, 81.249, 113.231, 90.00, 90.00, 120.00
R / Rfree (%)	16.7 / 19.6

The structure of Photorhabdus Asymbiotica Lectin (Phl) in Complex with Alpha-Methyl Fucoside also contains other interesting chemical elements:

Chlorine

(Cl)

8 atoms

The binding sites of Sodium atom in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Alpha-Methyl Fucoside (pdb code 5mxf). 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 Alpha-Methyl Fucoside, PDB code: 5mxf:
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 Alpha-Methyl Fucoside


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 Alpha-Methyl Fucoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:24.6 occ:1.00 O A:HOH710 2.2 18.0 1.0 O A:HOH632 2.4 22.4 1.0 O A:VAL179 2.4 17.5 1.0 O A:HOH768 2.4 26.8 1.0 O A:HOH578 2.5 19.4 1.0 OG1 A:THR178 3.1 19.1 1.0 C A:VAL179 3.5 17.9 1.0 N A:VAL179 3.7 17.0 1.0 O A:HOH680 4.1 15.7 1.0 CL A:CL407 4.1 25.1 1.0 CA A:VAL179 4.1 16.8 1.0 O A:HOH791 4.2 29.1 1.0 CG1 A:VAL179 4.3 16.6 1.0 CB A:THR178 4.4 19.0 1.0 ND1 A:HIS180 4.5 21.0 1.0 CG1 A:VAL227 4.5 21.7 1.0 C A:THR178 4.5 17.4 1.0 N A:HIS180 4.6 17.5 1.0 O A:ILE131 4.6 14.7 1.0 CD2 A:TYR132 4.6 19.2 1.0 CA A:THR178 4.7 17.9 1.0 O A:HOH605 4.7 23.5 1.0 CE2 A:TYR132 4.8 19.9 1.0 CA A:HIS180 4.9 18.5 1.0 CB A:VAL179 4.9 16.4 1.0

Sodium binding site 2 out of 4 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Alpha-Methyl Fucoside


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 Alpha-Methyl Fucoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:33.1 occ:1.00 O A:HOH637 2.3 24.7 1.0 O A:HOH599 2.4 31.9 1.0 O A:HOH765 2.4 23.9 1.0 O A:HOH740 2.4 27.1 1.0 O A:HOH662 2.6 23.1 1.0 O A:HOH595 2.8 32.2 1.0 O A:HOH690 3.6 21.6 1.0 NZ A:LYS81 3.7 25.2 1.0 O A:HOH651 3.9 18.1 1.0 O A:HOH562 4.1 24.4 1.0 O A:HOH605 4.1 23.5 1.0 O A:HOH664 4.3 23.9 1.0 O A:HOH784 4.3 25.9 1.0 OE2 A:GLU31 4.5 21.3 1.0 OD2 A:ASP224 4.7 21.5 1.0

Sodium binding site 3 out of 4 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Alpha-Methyl Fucoside


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 Alpha-Methyl Fucoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:35.2 occ:1.00 O A:HOH675 2.2 23.3 1.0 O A:HOH583 2.5 20.7 1.0 OD1 A:ASP40 2.5 24.5 1.0 O A:HOH676 2.6 32.5 1.0 O A:HOH732 2.6 26.8 1.0 OG1 A:THR38 2.7 19.1 1.0 CG A:ASP40 3.4 23.8 1.0 CB A:THR38 3.4 21.1 1.0 O A:HOH695 3.4 28.5 1.0 OD2 A:ASP40 3.5 25.6 1.0 CG2 A:THR38 3.7 22.8 1.0 O A:HOH649 4.0 29.1 1.0 OE1 A:GLU44 4.1 18.8 1.0 CB A:ARG42 4.2 22.6 1.0 CD A:ARG42 4.4 27.2 1.0 O A:ARG42 4.5 22.0 1.0 NE A:ARG58 4.6 31.0 1.0 CB A:ASP40 4.7 22.9 1.0 N A:ASP40 4.8 20.1 1.0 CD A:ARG58 4.8 29.9 1.0 CA A:THR38 4.8 20.2 1.0 CG A:ARG42 4.9 24.6 1.0 N A:ARG42 4.9 20.9 1.0 CA A:ARG42 5.0 21.3 1.0

Sodium binding site 4 out of 4 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Alpha-Methyl Fucoside


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 Alpha-Methyl Fucoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:22.7 occ:1.00 O A:HOH745 2.3 27.7 1.0 O A:HOH753 2.3 29.3 1.0 OD1 A:ASN37 2.5 24.4 1.0 O A:THR38 2.5 18.4 1.0 O A:ASN37 3.3 22.4 1.0 CG A:ASN37 3.4 23.2 1.0 O A:HOH803 3.5 28.7 1.0 C A:THR38 3.5 18.8 1.0 C A:ASN37 3.7 21.8 1.0 N A:THR38 4.1 20.2 1.0 ND2 A:ASN37 4.1 24.3 1.0 N A:GLY41 4.2 19.8 1.0 CB A:ASN37 4.2 21.9 1.0 CA A:GLY41 4.2 19.9 1.0 CA A:THR38 4.4 20.2 1.0 N A:SER39 4.4 18.3 1.0 CA A:SER39 4.4 19.5 1.0 O A:HOH789 4.5 40.6 1.0 CA A:ASN37 4.5 21.8 1.0 C A:SER39 4.6 19.7 1.0 O A:HOH773 4.7 18.2 1.0 O A:HOH537 4.7 24.4 1.0 O A:SER39 4.9 19.1 1.0

G.Jancarikova, J.Houser, P.Dobes, G.Demo, P.Hyrsl, M.Wimmerova. Characterization of Novel Bangle Lectin From Photorhabdus Asymbiotica with Dual Sugar-Binding Specificity and Its Effect on Host Immunity. Plos Pathog. V. 13 06564 2017.
ISSN: ESSN 1553-7374
PubMed: 28806750
DOI: 10.1371/JOURNAL.PPAT.1006564