Chlorine 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:

Sodium

(Na)

4 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Alpha-Methyl Fucoside, PDB code: 5mxf:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Alpha-Methyl Fucoside


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl407 b:25.1 occ:1.00 OG1 A:THR178 3.0 19.1 1.0 N A:VAL227 3.2 19.6 1.0 O A:HOH768 3.2 26.8 1.0 O A:HOH765 3.2 23.9 1.0 O A:HOH632 3.4 22.4 1.0 CA A:VAL226 3.7 22.1 1.0 O A:VAL227 3.7 19.0 1.0 C A:VAL226 3.9 20.5 1.0 CB A:THR178 4.0 19.0 1.0 CG1 A:VAL226 4.0 25.2 1.0 NA A:NA403 4.1 24.6 1.0 CG1 A:VAL227 4.2 21.7 1.0 CB A:VAL226 4.3 23.4 1.0 CA A:VAL227 4.3 19.9 1.0 CG2 A:THR178 4.4 19.4 1.0 O A:PRO225 4.4 22.7 1.0 C A:VAL227 4.4 20.2 1.0 CG2 A:VAL226 4.5 25.4 1.0 O A:HOH740 4.8 27.1 1.0 CB A:VAL227 4.8 19.9 1.0 N A:VAL226 4.8 20.8 1.0 O A:HOH784 4.9 25.9 1.0 O A:HOH605 5.0 23.5 1.0

Chlorine binding site 2 out of 8 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Alpha-Methyl Fucoside


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl408 b:33.4 occ:1.00 CB A:PRO67 3.7 21.9 1.0 CG A:PRO67 3.8 21.9 1.0 CD A:PRO67 4.3 21.6 1.0 CA A:PRO67 4.9 21.5 1.0

Chlorine binding site 3 out of 8 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Alpha-Methyl Fucoside


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl409 b:25.6 occ:0.90 O A:HOH787 3.0 28.4 1.0 N A:ASP51 3.2 28.7 1.0 NE1 A:TRP55 3.2 24.7 1.0 C A:GLY49 3.5 25.7 1.0 N A:ALA53 3.5 24.6 1.0 CA A:GLY49 3.5 23.9 1.0 N A:LYS52 3.5 27.4 1.0 CA A:ASP51 3.6 30.9 1.0 C A:ASP51 3.6 28.4 1.0 CB A:ASP51 3.6 33.5 1.0 N A:THR50 3.8 28.0 1.0 CB A:ALA53 3.8 25.3 1.0 O A:GLY49 3.8 24.5 1.0 N A:GLY49 4.0 23.4 1.0 CA A:ALA53 4.1 23.6 1.0 O A:ALA53 4.1 20.9 1.0 CE2 A:TRP55 4.2 24.7 1.0 CD1 A:TRP55 4.2 24.2 1.0 O A:ASP51 4.3 25.1 1.0 C A:THR50 4.3 29.5 1.0 CZ2 A:TRP55 4.4 24.6 1.0 C A:LYS52 4.4 25.4 1.0 CA A:LYS52 4.5 29.0 1.0 C A:ALA53 4.5 22.2 1.0 O A:HOH600 4.6 30.2 1.0 CA A:THR50 4.6 28.8 0.5 CA A:THR50 4.6 28.1 0.5 CG A:ASP51 4.7 37.2 1.0

Chlorine binding site 4 out of 8 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Alpha-Methyl Fucoside


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl410 b:39.2 occ:1.00 N A:TRP118 3.3 24.2 1.0 O A:HOH591 3.3 30.3 1.0 O A:HOH620 3.6 40.4 1.0 CD1 A:TRP118 3.7 22.8 1.0 CA A:ASN117 3.8 25.7 1.0 CB A:ASN117 3.8 28.9 1.0 CB A:TRP118 3.9 23.8 1.0 OD1 A:ASN117 4.0 34.2 1.0 C A:ASN117 4.0 24.5 1.0 CA A:TRP118 4.2 23.8 1.0 CG A:TRP118 4.2 22.6 1.0 CG A:ASN117 4.2 32.4 1.0 O A:HOH553 4.6 31.2 1.0 O A:HOH572 4.7 48.1 1.0 O A:TRP118 4.8 24.2 1.0 NE1 A:TRP118 4.8 23.4 1.0 CB A:LYS75 5.0 30.6 1.0

Chlorine binding site 5 out of 8 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Alpha-Methyl Fucoside


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Photorhabdus Asymbiotica Lectin (Phl) in Complex with Alpha-Methyl Fucoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl411 b:38.8 occ:1.00 O A:HOH699 3.1 35.1 1.0 O A:HOH737 3.2 33.0 1.0 N A:TRP310 3.2 26.8 1.0 CB A:SER309 3.7 32.0 1.0 CA A:SER309 3.7 29.4 1.0 CD1 A:TRP310 3.8 25.6 1.0 C A:SER309 4.0 29.1 1.0 CB A:TRP310 4.0 26.7 1.0 CA A:TRP310 4.2 27.3 1.0 CG A:TRP310 4.3 25.9 1.0 O A:TRP310 4.6 27.3 1.0 OG A:SER309 4.8 35.7 1.0 CB A:ASN266 4.9 27.3 1.0 NE1 A:TRP310 4.9 26.1 1.0 C A:TRP310 5.0 28.7 1.0

Chlorine binding site 6 out of 8 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Alpha-Methyl Fucoside


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Photorhabdus Asymbiotica Lectin (Phl) in Complex with Alpha-Methyl Fucoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl412 b:30.6 occ:1.00 N A:ASP364 3.2 23.7 1.0 NH1 A:ARG336 3.4 30.6 1.0 CA A:ILE363 3.7 25.3 1.0 CB A:ILE363 3.8 27.0 1.0 C A:ILE363 4.0 26.0 1.0 CB A:ASP364 4.0 23.7 1.0 NH2 A:ARG336 4.1 31.2 1.0 CA A:ASP364 4.1 24.0 1.0 CZ A:ARG336 4.2 29.1 1.0 O A:ASP364 4.4 22.0 1.0 CG2 A:ILE363 4.4 28.7 1.0 C A:ASP364 4.7 23.5 1.0 O A:LEU362 5.0 25.0 1.0 O A:HOH517 5.0 25.0 1.0

Chlorine binding site 7 out of 8 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Alpha-Methyl Fucoside


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Photorhabdus Asymbiotica Lectin (Phl) in Complex with Alpha-Methyl Fucoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl413 b:37.5 occ:1.00 N A:SER216 3.2 22.6 1.0 CA A:GLU215 3.7 23.6 1.0 C A:GLU215 3.9 23.6 1.0 CB A:SER216 4.0 22.6 1.0 CB A:GLU215 4.1 26.6 1.0 CA A:SER216 4.1 22.3 1.0 O A:SER216 4.4 22.2 1.0 CZ3 A:TRP199 4.4 24.4 1.0 CG A:GLU215 4.5 29.0 1.0 CH2 A:TRP199 4.7 24.6 1.0 O A:TRP214 4.7 24.2 1.0 C A:SER216 4.8 21.8 1.0 N A:GLU215 5.0 22.4 1.0

Chlorine binding site 8 out of 8 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Alpha-Methyl Fucoside


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Photorhabdus Asymbiotica Lectin (Phl) in Complex with Alpha-Methyl Fucoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl414 b:25.9 occ:1.00 O A:HOH614 3.1 29.4 1.0 ND2 A:ASN281 3.2 20.8 1.0 O A:HOH780 4.1 23.7 1.0 CG A:ASN281 4.3 20.7 1.0 O A:HOH590 4.4 26.7 1.0 OD1 A:ASN281 4.5 22.9 1.0 CB A:ALA231 5.0 19.7 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