Chlorine in PDB 6rgr: Photorhabdus Asymbiotica Lectin Phl in Complex with L-Rhamnose

Protein crystallography data

The structure of Photorhabdus Asymbiotica Lectin Phl in Complex with L-Rhamnose, PDB code: 6rgr was solved by J.Houser, E.Fujdiarova, G.Jancarikova, M.Wimmerova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.99 / 1.89
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.499, 80.499, 113.413, 90.00, 90.00, 120.00
R / Rfree (%) 20 / 22.9

Other elements in 6rgr:

The structure of Photorhabdus Asymbiotica Lectin Phl in Complex with L-Rhamnose also contains other interesting chemical elements:

Sodium (Na) 4 atoms

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 3 in 6rgr

Go back to Chlorine Binding Sites List in 6rgr
Chlorine binding site 1 out of 3 in the Photorhabdus Asymbiotica Lectin Phl in Complex with L-Rhamnose


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 L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl409

b:51.5
occ:1.00
N A:TRP214 3.1 33.4 1.0
O A:HOH506 3.6 45.8 1.0
CA A:SER213 3.7 33.4 1.0
CD1 A:TRP214 3.7 30.7 1.0
CB A:SER213 3.9 32.4 1.0
C A:SER213 3.9 31.2 1.0
CB A:TRP214 3.9 33.0 1.0
CA A:TRP214 4.1 32.9 1.0
CG A:TRP214 4.2 31.4 1.0
OG A:SER213 4.5 38.3 1.0
O A:TRP214 4.8 34.9 1.0
NE1 A:TRP214 4.9 30.2 1.0
O A:HOH541 5.0 40.6 1.0
N A:SER213 5.0 30.9 1.0

Chlorine binding site 2 out of 3 in 6rgr

Go back to Chlorine Binding Sites List in 6rgr
Chlorine binding site 2 out of 3 in the Photorhabdus Asymbiotica Lectin Phl in Complex with L-Rhamnose


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 L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl410

b:47.2
occ:1.00
CB A:PRO67 3.6 30.8 1.0
CG A:PRO67 3.7 30.6 1.0
CD A:PRO67 4.3 31.4 1.0
CA A:PRO67 4.7 30.5 1.0
N A:PRO67 4.9 30.9 1.0

Chlorine binding site 3 out of 3 in 6rgr

Go back to Chlorine Binding Sites List in 6rgr
Chlorine binding site 3 out of 3 in the Photorhabdus Asymbiotica Lectin Phl in Complex with L-Rhamnose


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 L-Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl411

b:60.7
occ:1.00
NH1 A:ARG240 3.2 37.0 1.0
O A:HOH504 3.6 30.4 1.0
CA A:THR270 3.6 37.0 1.0
CB A:THR270 3.9 38.1 1.0
O A:THR270 4.0 36.3 1.0
CG2 A:THR270 4.0 39.1 1.0
C A:THR270 4.2 37.7 1.0
CZ A:ARG240 4.3 37.5 1.0
NH2 A:ARG240 4.7 38.6 1.0
O A:ILE269 4.7 39.6 1.0
N A:THR270 4.8 35.3 1.0
ND2 A:ASN244 5.0 50.5 1.0

Reference:

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
Page generated: Sat Dec 12 13:36:10 2020

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