Chlorine in PDB 6rgj: Photorhabdus Asymbiotica Lectin Phl in Complex with D-Glucose

Protein crystallography data

The structure of Photorhabdus Asymbiotica Lectin Phl in Complex with D-Glucose, PDB code: 6rgj 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) 44.03 / 1.80
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.638, 80.638, 113.437, 90.00, 90.00, 120.00
R / Rfree (%) 17 / 19.7

Other elements in 6rgj:

The structure of Photorhabdus Asymbiotica Lectin Phl in Complex with D-Glucose 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 D-Glucose (pdb code 6rgj). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Photorhabdus Asymbiotica Lectin Phl in Complex with D-Glucose, PDB code: 6rgj:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 6rgj

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Chlorine binding site 1 out of 7 in the Photorhabdus Asymbiotica Lectin Phl in Complex with D-Glucose


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 D-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl412

b:25.4
occ:1.00
 O A:HOH814 2.7 30.7 1.0
N A:ASP51 3.2 25.0 1.0
NE1 A:TRP55 3.2 19.3 1.0
N A:ALA53 3.4 16.3 1.0
C A:ASP51 3.4 23.6 1.0
N A:LYS52 3.5 21.9 1.0
CA A:ASP51 3.5 26.7 1.0
CB A:ASP51 3.5 31.4 1.0
CA A:GLY49 3.5 18.5 1.0
C A:GLY49 3.5 19.8 1.0
CB A:ALA53 3.6 14.9 1.0
O A:GLY49 3.9 20.6 1.0
N A:THR50 3.9 21.9 1.0
CA A:ALA53 4.0 15.0 1.0
N A:GLY49 4.0 16.9 1.0
O A:ASP51 4.1 23.5 1.0
CE2 A:TRP55 4.1 19.0 1.0
CD1 A:TRP55 4.2 18.8 1.0
O A:ALA53 4.2 12.8 1.0
C A:THR50 4.3 24.4 1.0
CZ2 A:TRP55 4.4 19.0 1.0
C A:LYS52 4.4 18.5 1.0
C A:ALA53 4.5 13.6 1.0
CA A:LYS52 4.5 20.3 1.0
CG A:ASP51 4.5 37.2 1.0
O A:HOH677 4.6 39.4 1.0
O A:HOH624 4.7 23.2 1.0
CA A:THR50 4.8 23.9 1.0
O A:HOH534 4.9 21.5 1.0
OD2 A:ASP51 4.9 41.6 1.0

Chlorine binding site 2 out of 7 in 6rgj

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Chlorine binding site 2 out of 7 in the Photorhabdus Asymbiotica Lectin Phl in Complex with D-Glucose


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 D-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl413

b:30.2
occ:1.00
 N A:TRP214 3.2 16.4 1.0
O A:HOH532 3.3 27.5 1.0
CD1 A:TRP214 3.7 15.6 1.0
CA A:SER213 3.8 16.3 1.0
O A:HOH721 3.8 37.4 1.0
CB A:TRP214 3.9 16.0 1.0
CB A:SER213 4.0 16.9 1.0
C A:SER213 4.0 15.7 1.0
CA A:TRP214 4.2 15.9 1.0
CG A:TRP214 4.2 15.8 1.0
OG A:SER213 4.4 20.1 1.0
O A:TRP214 4.8 16.6 1.0
NE1 A:TRP214 4.8 15.6 1.0
O A:HOH627 4.8 31.0 1.0
CB A:ASN170 4.9 15.1 1.0

Chlorine binding site 3 out of 7 in 6rgj

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Chlorine binding site 3 out of 7 in the Photorhabdus Asymbiotica Lectin Phl in Complex with D-Glucose


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 D-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl414

b:29.3
occ:1.00
 O A:HOH755 3.2 33.4 1.0
N A:TRP118 3.3 15.0 1.0
O A:HOH595 3.4 28.6 1.0
O A:HOH521 3.6 31.5 1.0
CD1 A:TRP118 3.7 13.1 1.0
CB A:ASN117 3.7 18.1 1.0
CA A:ASN117 3.8 16.2 1.0
OD1 A:ASN117 3.8 24.1 1.0
CB A:TRP118 4.0 13.9 1.0
C A:ASN117 4.0 15.7 1.0
CG A:ASN117 4.1 20.2 1.0
CG A:TRP118 4.2 13.5 1.0
CA A:TRP118 4.2 14.5 1.0
O A:TRP118 4.8 14.2 1.0
O A:HOH530 4.8 33.3 1.0
CB A:LYS75 4.8 18.4 1.0
NE1 A:TRP118 4.9 13.6 1.0

Chlorine binding site 4 out of 7 in 6rgj

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Chlorine binding site 4 out of 7 in the Photorhabdus Asymbiotica Lectin Phl in Complex with D-Glucose


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 D-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl415

b:27.5
occ:1.00
 O A:HOH539 3.2 24.6 1.0
ND2 A:ASN281 3.2 15.1 1.0
O A:HOH810 3.9 25.4 1.0
CG A:ASN281 4.3 14.9 1.0
O A:HOH631 4.4 22.1 1.0
OD1 A:ASN281 4.5 16.5 1.0

Chlorine binding site 5 out of 7 in 6rgj

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Chlorine binding site 5 out of 7 in the Photorhabdus Asymbiotica Lectin Phl in Complex with D-Glucose


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 D-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl416

b:35.0
occ:1.00
 O A:HOH772 3.0 37.0 1.0
NH1 A:ARG240 3.2 19.4 1.0
O A:HOH696 3.2 25.1 1.0
CA A:THR270 3.5 20.0 1.0
O A:HOH542 3.6 20.5 1.0
CB A:THR270 3.7 19.9 1.0
CG2 A:THR270 4.0 20.8 1.0
O A:THR270 4.0 19.2 1.0
C A:THR270 4.1 19.2 1.0
CZ A:ARG240 4.3 19.0 1.0
O A:ILE269 4.4 21.3 1.0
NH2 A:ARG240 4.6 19.2 1.0
N A:THR270 4.6 19.3 1.0
O A:HOH852 4.9 39.4 1.0
C A:ILE269 4.9 19.7 1.0

Chlorine binding site 6 out of 7 in 6rgj

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Chlorine binding site 6 out of 7 in the Photorhabdus Asymbiotica Lectin Phl in Complex with D-Glucose


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 D-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl417

b:35.3
occ:1.00
 N A:ASN117 3.1 15.0 1.0
NE2 A:GLN119 3.7 20.3 0.5
CB A:SER116 3.7 13.8 1.0
CB A:ASN117 3.8 18.1 1.0
ND2 A:ASN117 3.9 22.7 1.0
CA A:SER116 3.9 14.0 1.0
NE2 A:GLN119 3.9 18.4 0.5
CA A:ASN117 4.0 16.2 1.0
C A:SER116 4.0 14.5 1.0
CG A:ASN117 4.1 20.2 1.0
O A:ASN117 4.1 16.7 1.0
C A:ASN117 4.5 15.7 1.0
OG A:SER116 4.6 12.8 1.0
O A:HOH562 4.6 41.4 1.0
CD A:GLN119 4.6 19.1 0.5
CG A:GLN119 4.6 17.9 0.5
CZ2 A:TRP107 4.7 15.5 1.0
CD A:GLN119 4.9 17.3 0.5
CH2 A:TRP107 5.0 15.1 1.0

Chlorine binding site 7 out of 7 in 6rgj

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Chlorine binding site 7 out of 7 in the Photorhabdus Asymbiotica Lectin Phl in Complex with D-Glucose


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 D-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl418

b:28.5
occ:1.00
 N A:ASP364 3.2 19.4 1.0
NH1 A:ARG336 3.3 22.3 1.0
O A:HOH695 3.3 32.2 1.0
O A:HOH689 3.7 36.0 1.0
CA A:ILE363 3.7 20.9 1.0
CB A:ILE363 3.9 22.1 1.0
C A:ILE363 3.9 20.5 1.0
O A:HOH686 4.0 33.3 1.0
NH2 A:ARG336 4.0 24.4 1.0
CB A:ASP364 4.1 18.9 1.0
CZ A:ARG336 4.1 22.5 1.0
CA A:ASP364 4.1 18.2 1.0
O A:ASP364 4.3 19.2 1.0
CG2 A:ILE363 4.5 24.3 1.0
C A:ASP364 4.7 18.7 1.0
O A:HOH529 4.9 24.5 1.0
O A:LEU362 5.0 20.7 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 13:36:09 2020

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