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Chlorine in PDB 6flu: Photorhabdus Asymbiotica Lectin (Phl) in Complex with Synthetic C- Fucoside

Protein crystallography data

The structure of Photorhabdus Asymbiotica Lectin (Phl) in Complex with Synthetic C- Fucoside, PDB code: 6flu was solved by J.Houser, G.Jancarikova, M.Wimmerova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.93 / 1.78
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.940, 81.940, 224.645, 90.00, 90.00, 120.00
R / Rfree (%) 18.4 / 22.2

Other elements in 6flu:

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

Chlorine binding site 1 out of 6 in 6flu

Go back to Chlorine Binding Sites List in 6flu
Chlorine binding site 1 out of 6 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Synthetic C- Fucoside


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 Synthetic C- Fucoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:14.6
occ:0.50
 O A:HOH748 2.9 24.4 1.0
N A:SER312 3.3 11.9 1.0
CA A:GLN311 3.9 12.4 1.0
O A:HOH548 3.9 14.4 1.0
CB A:SER312 4.0 11.6 1.0
CZ3 A:TRP295 4.0 10.2 1.0
C A:GLN311 4.1 12.5 1.0
CG A:GLN311 4.2 14.0 1.0
CA A:SER312 4.2 11.3 1.0
CH2 A:TRP295 4.3 10.1 1.0
CB A:GLN311 4.5 13.9 1.0
O A:TRP310 4.8 11.8 1.0
CE3 A:TRP295 4.8 9.4 1.0
O A:SER312 4.9 11.6 1.0

Chlorine binding site 2 out of 6 in 6flu

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Chlorine binding site 2 out of 6 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Synthetic C- Fucoside


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 Synthetic C- Fucoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl409

b:15.9
occ:1.00
 O A:HOH620 3.0 28.6 1.0
N A:ASP364 3.2 10.3 1.0
NH1 A:ARG336 3.4 11.3 1.0
O A:HOH777 3.6 23.9 1.0
CA A:ILE363 3.8 10.8 1.0
CB A:ILE363 3.8 11.9 1.0
C A:ILE363 4.0 10.6 1.0
CB A:ASP364 4.0 9.9 1.0
CG2 A:ILE363 4.2 12.9 1.0
CA A:ASP364 4.2 9.8 1.0
NH2 A:ARG336 4.2 13.4 1.0
CZ A:ARG336 4.2 12.4 1.0
O A:HOH845 4.3 31.2 1.0
O A:ASP364 4.4 8.9 1.0
C A:ASP364 4.7 9.6 1.0
O A:LEU362 4.8 9.3 1.0
O A:HOH632 5.0 11.6 1.0

Chlorine binding site 3 out of 6 in 6flu

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Chlorine binding site 3 out of 6 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Synthetic C- Fucoside


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 Synthetic C- Fucoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl410

b:30.3
occ:1.00
 N A:TRP307 3.1 11.2 1.0
CA A:PRO306 3.5 12.7 1.0
CB A:PRO306 3.7 13.1 1.0
CD1 A:TRP307 3.8 11.4 1.0
C A:PRO306 3.8 11.9 1.0
O A:HOH807 3.9 21.8 1.0
CB A:TRP307 4.1 11.0 1.0
CA A:TRP307 4.1 11.5 1.0
O A:HOH596 4.2 22.7 1.0
CG A:TRP307 4.3 11.2 1.0
O A:HOH760 4.4 27.1 1.0
O A:TRP307 4.7 14.4 1.0
N A:PRO306 4.8 12.8 1.0
C A:TRP307 4.9 13.5 1.0
NE1 A:TRP307 4.9 11.3 1.0
O A:GLY305 5.0 12.8 1.0

Chlorine binding site 4 out of 6 in 6flu

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Chlorine binding site 4 out of 6 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Synthetic C- Fucoside


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 Synthetic C- Fucoside within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl411

b:21.0
occ:1.00
 OG1 A:THR26 3.0 20.7 1.0
O A:HOH796 3.1 20.8 1.0
O A:HOH518 3.3 11.2 1.0
NH2 A:ARG240 3.4 8.2 1.0
C A:ILE27 3.4 12.1 1.0
O A:HOH544 3.4 27.3 1.0
C A:THR26 3.4 15.2 1.0
N A:ILE27 3.4 14.1 1.0
CA A:ILE27 3.5 12.5 1.0
O A:THR26 3.6 15.0 1.0
O A:THR222 3.6 10.9 1.0
CB A:THR26 3.7 19.5 1.0
N A:ALA28 3.7 10.1 1.0
O A:ILE27 3.8 10.7 1.0
O A:HOH737 4.0 15.6 1.0
O A:HOH828 4.2 36.4 1.0
CA A:THR26 4.2 17.7 1.0
CB A:THR222 4.4 10.3 1.0
C A:THR222 4.5 10.5 1.0
CA A:ALA28 4.6 10.4 1.0
CZ A:ARG240 4.7 9.0 1.0
CA A:THR222 4.7 10.2 1.0
OG A:SER24 4.8 25.1 1.0
O A:HOH540 4.8 23.7 1.0
CB A:ILE27 5.0 12.9 1.0

Chlorine binding site 5 out of 6 in 6flu

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Chlorine binding site 5 out of 6 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Synthetic C- Fucoside


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 Synthetic C- Fucoside within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl409

b:22.4
occ:1.00
 OG1 B:THR26 2.9 23.8 1.0
O B:HOH717 3.1 34.9 1.0
O B:HOH769 3.2 17.3 1.0
NH2 B:ARG240 3.2 11.6 1.0
C B:ILE27 3.5 13.2 1.0
O B:THR222 3.6 11.3 1.0
CA B:ILE27 3.6 15.0 1.0
N B:ALA28 3.7 11.6 1.0
N B:ILE27 3.7 15.6 1.0
O B:HOH719 3.8 15.2 1.0
C B:THR26 3.8 16.7 1.0
O B:THR26 3.8 16.3 1.0
O B:ILE27 3.9 13.4 1.0
CB B:THR26 4.0 22.4 1.0
CB B:THR222 4.3 11.4 1.0
CZ B:ARG240 4.5 12.4 1.0
C B:THR222 4.5 11.6 1.0
CA B:THR26 4.5 20.6 1.0
CA B:ALA28 4.5 11.3 1.0
CA B:THR222 4.7 11.2 1.0

Chlorine binding site 6 out of 6 in 6flu

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Chlorine binding site 6 out of 6 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Synthetic C- Fucoside


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 Synthetic C- Fucoside within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl410

b:36.6
occ:1.00
 N B:ILE86 3.1 9.3 1.0
CD1 B:TYR85 3.6 8.7 1.0
CE1 B:TYR85 3.6 9.0 1.0
O B:HOH585 3.7 29.4 1.0
CG1 B:ILE86 3.7 10.3 1.0
CZ B:TYR85 3.8 8.4 1.0
CB B:ILE86 3.8 9.8 1.0
CG B:TYR85 3.8 8.1 1.0
CE2 B:TYR85 3.9 8.8 1.0
CA B:TYR85 3.9 8.0 1.0
CD2 B:TYR85 3.9 8.3 1.0
CA B:ILE86 4.0 9.1 1.0
C B:TYR85 4.0 8.1 1.0
CD1 B:ILE86 4.1 11.1 1.0
O B:ILE86 4.3 9.3 1.0
CG1 B:VAL36 4.3 12.2 1.0
O B:HOH520 4.4 14.5 1.0
O B:HOH838 4.4 25.4 1.0
OH B:TYR85 4.5 9.2 1.0
O B:HOH840 4.5 26.7 1.0
CB B:TYR85 4.5 8.0 1.0
C B:ILE86 4.6 9.1 1.0

Reference:

G.Paulikova, J.Houser, M.Kasakova, B.Oroszova, B.Bertolotti, K.Parkan, J.Moravcova, M.Wimmerova. Fucosylated Inhibitors of Recently Identified Bangle Lectin From Photorhabdus Asymbiotica. Sci Rep V. 9 14904 2019.
ISSN: ESSN 2045-2322
PubMed: 31624296
DOI: 10.1038/S41598-019-51357-9
Page generated: Sat Jul 27 23:21:05 2024

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