Chlorine in PDB 6rgu: Photorhabdus Asymbiotica Lectin Phl in Complex with 3-O-Methyl-D- Glucose

Protein crystallography data

The structure of Photorhabdus Asymbiotica Lectin Phl in Complex with 3-O-Methyl-D- Glucose, PDB code: 6rgu 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) 40.45 / 1.75
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.828, 80.828, 113.243, 90.00, 90.00, 120.00
R / Rfree (%) 16.9 / 19.7

Other elements in 6rgu:

The structure of Photorhabdus Asymbiotica Lectin Phl in Complex with 3-O-Methyl-D- Glucose also contains other interesting chemical elements:

Sodium (Na) 3 atoms

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 5 in 6rgu

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Chlorine binding site 1 out of 5 in the Photorhabdus Asymbiotica Lectin Phl in Complex with 3-O-Methyl-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 3-O-Methyl-D- Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl409

b:32.9
occ:1.00
O A:HOH744 3.1 30.3 1.0
ND2 A:ASN37 3.3 27.4 1.0
CA A:ALA327 3.7 24.6 1.0
O A:ASP326 4.1 26.4 1.0
CG A:ASN37 4.1 26.8 1.0
OD1 A:ASN37 4.1 27.3 1.0
CB A:ALA327 4.3 25.1 1.0
NA A:NA414 4.3 28.0 1.0
N A:ALA327 4.4 25.8 1.0
C A:ASP326 4.5 25.8 1.0
C A:ALA327 4.6 25.1 1.0
O A:ALA327 4.6 26.9 1.0
O A:HOH781 4.8 28.1 1.0

Chlorine binding site 2 out of 5 in 6rgu

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Chlorine binding site 2 out of 5 in the Photorhabdus Asymbiotica Lectin Phl in Complex with 3-O-Methyl-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 3-O-Methyl-D- Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl410

b:41.6
occ:1.00
O A:HOH567 3.1 40.5 1.0
N A:TRP166 3.2 26.2 1.0
CA A:SER165 3.5 27.3 0.5
CA A:SER165 3.6 27.5 0.5
CD1 A:TRP166 3.6 23.6 1.0
CB A:SER165 3.8 27.3 0.5
C A:SER165 3.9 26.4 1.0
O A:HOH596 4.0 36.8 1.0
CB A:SER165 4.0 27.4 0.5
CB A:TRP166 4.1 25.9 1.0
CG A:TRP166 4.2 24.1 1.0
CA A:TRP166 4.3 25.4 1.0
OG A:SER165 4.5 28.4 0.5
O A:HOH747 4.6 41.1 1.0
O A:SER164 4.6 22.5 1.0
NE1 A:TRP166 4.7 24.8 1.0
N A:SER165 4.8 26.6 1.0
CD1 A:ILE153 4.9 23.6 1.0

Chlorine binding site 3 out of 5 in 6rgu

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Chlorine binding site 3 out of 5 in the Photorhabdus Asymbiotica Lectin Phl in Complex with 3-O-Methyl-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 3-O-Methyl-D- Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl411

b:50.5
occ:1.00
O A:HOH550 2.7 32.7 1.0
O A:HOH641 2.7 28.1 1.0
O A:HIS303 2.9 28.0 1.0
OE1 A:GLN299 3.0 30.1 1.0
O A:HOH608 3.0 34.1 1.0
CD1 A:LEU283 3.4 32.5 1.0
CG A:LEU283 3.6 29.6 1.0
CD A:GLN299 3.7 30.9 1.0
NE2 A:GLN299 3.7 32.0 1.0
CG2 A:THR230 3.9 25.1 1.0
C A:HIS303 3.9 31.2 1.0
CB A:HIS303 3.9 28.2 1.0
CB A:THR230 4.0 23.6 1.0
CA A:HIS303 4.1 29.3 1.0
O A:ASN281 4.2 27.6 1.0
ND1 A:HIS303 4.4 28.6 1.0
CB A:LEU283 4.5 27.5 1.0
CD2 A:LEU283 4.6 29.2 1.0
CG A:HIS303 4.6 26.6 1.0
OE1 A:GLU236 4.6 29.2 1.0
CA A:THR230 4.7 24.9 1.0
N A:LEU283 4.8 25.8 1.0
N A:ALA231 5.0 26.2 1.0

Chlorine binding site 4 out of 5 in 6rgu

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Chlorine binding site 4 out of 5 in the Photorhabdus Asymbiotica Lectin Phl in Complex with 3-O-Methyl-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 3-O-Methyl-D- Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl412

b:37.5
occ:1.00
N A:ASP364 3.1 30.5 1.0
NH1 A:ARG336 3.3 32.2 1.0
CA A:ILE363 3.7 31.0 1.0
C A:ILE363 3.9 31.2 1.0
CB A:ILE363 3.9 32.0 1.0
CB A:ASP364 4.1 31.5 1.0
CA A:ASP364 4.1 28.1 1.0
NH2 A:ARG336 4.2 35.3 1.0
CZ A:ARG336 4.2 32.2 1.0
O A:ASP364 4.4 30.6 1.0
O A:HOH693 4.5 46.0 1.0
CG2 A:ILE363 4.5 34.3 1.0
C A:ASP364 4.7 31.0 1.0
O A:HOH579 5.0 35.6 1.0
O A:LEU362 5.0 29.6 1.0

Chlorine binding site 5 out of 5 in 6rgu

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Chlorine binding site 5 out of 5 in the Photorhabdus Asymbiotica Lectin Phl in Complex with 3-O-Methyl-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 3-O-Methyl-D- Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl413

b:39.3
occ:1.00
O A:HOH536 2.9 34.3 1.0
O A:HOH732 3.0 38.5 1.0
O A:HOH756 3.2 33.0 1.0
CA A:SER39 3.7 25.0 1.0
CB A:SER39 3.9 26.4 1.0
N A:SER39 4.1 24.3 1.0
CG2 A:ILE86 4.1 26.8 1.0
CD1 A:ILE86 4.1 31.0 1.0
C A:THR38 4.5 23.4 1.0
O A:HOH764 4.5 43.7 1.0
O A:HOH516 4.6 26.9 1.0
NA A:NA414 4.6 28.0 1.0
O A:THR38 4.6 22.7 1.0
CB A:ILE86 4.8 26.6 1.0
O A:ASN37 5.0 26.2 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 13:36:11 2020

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