Chlorine in PDB 5mxe: Photorhabdus Asymbiotica Lectin (Phl) in Free Form

The structure of Photorhabdus Asymbiotica Lectin (Phl) in Free Form, PDB code: 5mxe 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)	44.16 / 1.90
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	81.235, 81.235, 113.441, 90.00, 90.00, 120.00
R / Rfree (%)	16.6 / 19.1

The structure of Photorhabdus Asymbiotica Lectin (Phl) in Free Form also contains other interesting chemical elements:

Sodium

(Na)

4 atoms

The binding sites of Chlorine atom in the Photorhabdus Asymbiotica Lectin (Phl) in Free Form (pdb code 5mxe). 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 Free Form, PDB code: 5mxe:
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 Free Form


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 Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl405 b:14.4 occ:1.00 O A:HOH853 3.0 21.4 1.0 OG1 A:THR178 3.1 8.4 1.0 O A:HOH818 3.2 16.2 1.0 O A:HOH814 3.3 12.9 1.0 N A:VAL227 3.3 9.5 1.0 O A:HOH610 3.5 13.0 1.0 CA A:VAL226 3.6 10.1 1.0 O A:VAL227 3.7 9.8 1.0 C A:VAL226 3.9 9.7 1.0 CG1 A:VAL226 3.9 11.1 1.0 CB A:THR178 4.0 8.1 1.0 NA A:NA401 4.1 14.3 1.0 CB A:VAL226 4.1 10.6 1.0 CG1 A:VAL227 4.2 9.6 1.0 CG2 A:VAL226 4.3 11.0 1.0 CA A:VAL227 4.3 9.5 1.0 CG2 A:THR178 4.3 8.3 1.0 C A:VAL227 4.4 9.6 1.0 O A:PRO225 4.4 9.8 1.0 O A:HOH546 4.6 17.7 1.0 O A:HOH855 4.7 22.4 1.0 O A:HOH861 4.7 23.8 1.0 O A:HOH777 4.8 15.8 1.0 N A:VAL226 4.8 9.8 1.0 O A:HOH828 4.9 12.6 1.0 CB A:VAL227 4.9 9.4 1.0 O A:HOH584 4.9 22.0 1.0 O A:HOH577 5.0 12.1 1.0

Chlorine binding site 2 out of 8 in the Photorhabdus Asymbiotica Lectin (Phl) in Free Form


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 Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl406 b:16.7 occ:1.00 N A:ASP364 3.2 11.7 1.0 O A:HOH656 3.3 31.2 1.0 NH1 A:ARG336 3.3 13.9 1.0 O A:HOH682 3.4 23.8 1.0 CA A:ILE363 3.7 11.6 1.0 CB A:ILE363 3.8 11.8 1.0 O A:HOH632 3.9 21.3 1.0 C A:ILE363 4.0 11.6 1.0 CB A:ASP364 4.0 12.0 1.0 CA A:ASP364 4.1 11.6 1.0 NH2 A:ARG336 4.2 13.8 1.0 CZ A:ARG336 4.2 13.4 1.0 O A:ASP364 4.3 11.3 1.0 CG2 A:ILE363 4.4 11.8 1.0 C A:ASP364 4.6 11.5 1.0 O A:HOH510 4.9 11.6 1.0 O A:LEU362 5.0 11.3 1.0 O A:HOH640 5.0 17.4 1.0

Chlorine binding site 3 out of 8 in the Photorhabdus Asymbiotica Lectin (Phl) in Free Form


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 Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl407 b:16.1 occ:1.00 O A:HOH630 3.1 16.9 1.0 ND2 A:ASN281 3.2 10.5 1.0 O A:HOH830 4.2 14.5 1.0 CG A:ASN281 4.2 10.5 1.0 OD1 A:ASN281 4.4 10.8 1.0 O A:HOH569 4.4 17.9 1.0 CB A:ALA231 4.8 11.6 1.0

Chlorine binding site 4 out of 8 in the Photorhabdus Asymbiotica Lectin (Phl) in Free Form


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 Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl408 b:22.1 occ:1.00 O A:HOH515 3.1 26.1 1.0 N A:TRP166 3.3 10.9 1.0 O A:HOH774 3.5 25.5 1.0 CA A:SER165 3.6 11.5 0.5 CA A:SER165 3.6 11.5 0.5 CD1 A:TRP166 3.8 10.1 1.0 CB A:SER165 3.8 11.8 0.5 C A:SER165 3.9 11.3 0.5 C A:SER165 3.9 11.3 0.5 CB A:SER165 3.9 11.9 0.5 CB A:TRP166 4.1 10.4 1.0 O A:HOH619 4.2 24.3 1.0 CA A:TRP166 4.3 10.7 1.0 CG A:TRP166 4.3 10.3 1.0 OG A:SER165 4.4 11.8 0.5 O A:SER164 4.7 10.9 1.0 N A:SER165 4.8 11.5 0.5 N A:SER165 4.8 11.5 0.5 NE1 A:TRP166 4.9 10.1 1.0

Chlorine binding site 5 out of 8 in the Photorhabdus Asymbiotica Lectin (Phl) in Free Form


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 Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl409 b:25.1 occ:1.00 N A:TRP118 3.2 14.3 1.0 O A:HOH586 3.2 17.5 1.0 O A:HOH744 3.4 21.0 1.0 CD1 A:TRP118 3.7 13.5 1.0 CB A:ASN117 3.7 18.4 1.0 CA A:ASN117 3.7 16.3 1.0 C A:ASN117 4.0 14.9 1.0 OD1 A:ASN117 4.0 23.3 1.0 CB A:TRP118 4.0 13.8 1.0 CG A:ASN117 4.1 20.9 1.0 CA A:TRP118 4.2 14.2 1.0 CG A:TRP118 4.2 13.6 1.0 CE A:LYS75 4.3 27.3 1.0 O A:HOH556 4.7 19.4 1.0 O A:TRP118 4.8 13.7 1.0 NZ A:LYS75 4.8 29.3 1.0 O A:HOH678 4.8 38.1 1.0 NE1 A:TRP118 4.8 13.8 1.0

Chlorine binding site 6 out of 8 in the Photorhabdus Asymbiotica Lectin (Phl) in Free Form


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 Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl410 b:25.2 occ:1.00 O A:HOH783 3.2 19.2 1.0 O A:HOH673 3.2 21.8 1.0 N A:TRP310 3.2 13.6 1.0 O A:HOH684 3.3 15.9 1.0 CB A:SER309 3.6 16.2 1.0 CA A:SER309 3.7 15.1 1.0 CD1 A:TRP310 3.8 13.1 1.0 C A:SER309 4.0 14.4 1.0 CB A:TRP310 4.1 13.3 1.0 CA A:TRP310 4.2 13.5 1.0 CG A:TRP310 4.3 12.9 1.0 O A:HOH816 4.6 24.6 1.0 O A:TRP310 4.6 14.2 1.0 CB A:ASN266 4.7 13.1 1.0 OG A:SER309 4.8 17.0 1.0 NE1 A:TRP310 4.9 13.1 1.0 C A:TRP310 4.9 14.2 1.0 N A:GLY267 5.0 11.9 1.0

Chlorine binding site 7 out of 8 in the Photorhabdus Asymbiotica Lectin (Phl) in Free Form


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 Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl411 b:21.9 occ:1.00 O A:HOH797 3.1 27.6 1.0 N A:TRP355 3.3 13.2 1.0 O A:HOH618 3.3 29.3 1.0 CD1 A:TRP355 3.6 13.3 1.0 CA A:PRO354 3.7 13.6 1.0 O A:HOH731 3.8 32.5 1.0 CB A:PRO354 3.9 13.7 1.0 C A:PRO354 4.0 13.7 1.0 CB A:TRP355 4.2 12.9 1.0 CG A:TRP355 4.3 13.1 1.0 CA A:TRP355 4.3 12.8 1.0 NE1 A:TRP355 4.8 13.2 1.0 O A:TRP355 4.8 12.7 1.0

Chlorine binding site 8 out of 8 in the Photorhabdus Asymbiotica Lectin (Phl) in Free Form


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 Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl412 b:16.3 occ:1.00 O A:HOH842 2.9 20.8 1.0 NE1 A:TRP55 3.2 11.8 1.0 N A:ASP51 3.2 19.8 1.0 N A:ALA53 3.4 14.1 1.0 C A:GLY49 3.5 14.6 1.0 CA A:GLY49 3.5 13.4 1.0 C A:ASP51 3.6 19.2 1.0 CA A:ASP51 3.6 20.7 1.0 N A:LYS52 3.6 17.7 1.0 CB A:ALA53 3.7 13.3 1.0 CB A:ASP51 3.7 23.1 1.0 N A:THR50 3.8 16.3 1.0 O A:GLY49 3.8 13.7 1.0 CA A:ALA53 4.0 13.4 1.0 N A:GLY49 4.0 12.4 1.0 CE2 A:TRP55 4.1 12.2 1.0 O A:ALA53 4.1 12.0 1.0 CD1 A:TRP55 4.2 11.8 1.0 O A:ASP51 4.2 17.2 1.0 C A:THR50 4.3 19.1 1.0 CZ2 A:TRP55 4.3 12.3 1.0 C A:LYS52 4.4 15.7 1.0 C A:ALA53 4.5 12.6 1.0 CA A:LYS52 4.6 17.8 1.0 O A:HOH652 4.6 25.8 1.0 CA A:THR50 4.6 18.3 1.0 O A:HOH745 4.7 32.5 1.0 CG A:ASP51 4.8 25.4 1.0 O A:HOH517 5.0 16.8 1.0 OD2 A:ASP51 5.0 29.5 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