Atomistry » Chlorine » PDB 6r66-6ri0 » 6rgj
Atomistry »
  Chlorine »
    PDB 6r66-6ri0 »
      6rgj »

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

Go back to Chlorine Binding Sites List in 6rgj
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

Go back to Chlorine Binding Sites List in 6rgj
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

Go back to Chlorine Binding Sites List in 6rgj
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

Go back to Chlorine Binding Sites List in 6rgj
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

Go back to Chlorine Binding Sites List in 6rgj
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

Go back to Chlorine Binding Sites List in 6rgj
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

Go back to Chlorine Binding Sites List in 6rgj
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: Mon Jul 29 14:27:45 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy