Chlorine in PDB 6f5w: Photorhabdus Asymbiotica Lectin (Phl) in Complex with Propargyl- Fucoside

The structure of Photorhabdus Asymbiotica Lectin (Phl) in Complex with Propargyl- Fucoside, PDB code: 6f5w was solved by J.Houser, G.Jancarikova, M.Wimmerova, M.Csavas, A.Borbas, M.Herczeg, E.Fujdiarova, E.K.Kover, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.96 / 1.91
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	80.571, 80.571, 224.799, 90.00, 90.00, 120.00
R / Rfree (%)	17.3 / 21.3

The structure of Photorhabdus Asymbiotica Lectin (Phl) in Complex with Propargyl- Fucoside also contains other interesting chemical elements:

Sodium

(Na)

9 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Chlorine atom in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Propargyl- Fucoside (pdb code 6f5w). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 11 binding sites of Chlorine where determined in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Propargyl- Fucoside, PDB code: 6f5w:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 11 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Propargyl- 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 Propargyl- Fucoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl405 b:45.3 occ:1.00 N A:TRP307 3.0 25.7 1.0 CA A:PRO306 3.7 29.5 1.0 CD1 A:TRP307 3.7 24.5 1.0 CB A:TRP307 3.8 27.0 1.0 C A:PRO306 3.8 26.5 1.0 CA A:TRP307 4.0 27.0 1.0 CB A:PRO306 4.0 30.1 1.0 CG A:TRP307 4.2 25.9 1.0 O A:TRP307 4.4 28.1 1.0 NE2 A:GLN263 4.6 42.5 1.0 C A:TRP307 4.7 28.6 1.0 CD2 A:LEU265 4.8 26.1 1.0 NE1 A:TRP307 4.9 24.6 1.0 N A:PRO306 5.0 30.7 1.0

Chlorine binding site 2 out of 11 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Propargyl- 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 Propargyl- Fucoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl406 b:45.8 occ:1.00 N A:TRP118 3.2 23.6 1.0 C8 A:KG1413 3.5 42.9 1.0 CB A:ASN117 3.6 27.9 1.0 CA A:ASN117 3.6 24.9 1.0 OD1 A:ASN117 3.7 33.4 1.0 C7 A:KG1413 3.9 40.3 1.0 C A:ASN117 3.9 24.1 1.0 CB A:TRP118 4.0 22.7 1.0 CD1 A:TRP118 4.0 21.5 1.0 CG A:ASN117 4.0 31.4 1.0 CA A:TRP118 4.1 23.2 1.0 O A:HOH539 4.2 42.9 1.0 O A:HOH579 4.3 31.8 1.0 CG A:TRP118 4.4 22.3 1.0 CM A:KG1413 4.6 34.4 1.0 O A:TRP118 4.6 24.9 1.0 C A:TRP118 4.9 24.8 1.0 N A:ASN117 5.0 23.3 1.0

Chlorine binding site 3 out of 11 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Propargyl- 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 Propargyl- Fucoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl407 b:27.5 occ:1.00 OG1 A:THR178 3.2 25.8 1.0 N A:VAL227 3.3 19.8 1.0 O A:HOH726 3.4 27.2 1.0 O A:HOH616 3.5 40.6 1.0 O A:HOH568 3.6 24.1 1.0 CA A:VAL226 3.7 20.9 1.0 O A:HOH601 3.7 40.9 1.0 O A:VAL227 3.7 19.3 1.0 CG1 A:VAL226 3.9 23.0 1.0 C A:VAL226 4.0 21.0 1.0 CG1 A:VAL227 4.1 22.7 1.0 CB A:THR178 4.1 24.2 1.0 CB A:VAL226 4.2 22.0 1.0 NA A:NA401 4.3 24.6 1.0 CA A:VAL227 4.3 20.1 1.0 C A:VAL227 4.5 19.8 1.0 O A:PRO225 4.5 19.5 1.0 CG2 A:THR178 4.6 25.1 1.0 CG2 A:VAL226 4.7 23.3 1.0 N A:VAL226 4.8 20.6 1.0 CB A:VAL227 4.8 20.2 1.0 O A:HOH676 4.9 21.1 1.0 O A:HOH606 5.0 23.3 1.0

Chlorine binding site 4 out of 11 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Propargyl- 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 Propargyl- Fucoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl408 b:30.6 occ:1.00 O B:HOH574 3.1 27.1 1.0 O A:HOH592 3.1 19.9 0.5 ND2 B:ASN281 3.4 24.5 1.0 ND2 A:ASN37 3.4 30.0 1.0 CA A:ALA327 3.7 20.6 1.0 OD1 A:ASN37 4.0 27.8 1.0 CB A:ALA327 4.1 19.9 1.0 CG A:ASN37 4.1 27.4 1.0 O A:ASP326 4.2 19.9 1.0 NA A:NA402 4.3 30.8 1.0 CG B:ASN281 4.4 26.6 1.0 N A:ALA327 4.4 20.0 1.0 O B:HOH702 4.5 38.0 1.0 O B:HOH696 4.5 46.1 1.0 C A:ASP326 4.6 19.7 1.0 O A:HOH592 4.6 22.1 0.5 OD1 B:ASN281 4.6 26.2 1.0 O B:HOH537 4.7 36.6 1.0 C A:ALA327 4.7 21.4 1.0 O A:ALA327 4.8 23.7 1.0

Chlorine binding site 5 out of 11 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Propargyl- 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 Propargyl- Fucoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl409 b:37.8 occ:1.00 O A:HOH614 3.2 28.9 1.0 N A:TRP71 3.2 21.0 1.0 CD1 A:TRP71 3.7 21.6 1.0 CA A:GLY70 3.7 20.0 1.0 C8 A:KG1417 3.7 46.4 1.0 C7 A:KG1417 3.8 44.5 1.0 C A:GLY70 3.9 19.8 1.0 CB A:TRP71 4.1 20.2 1.0 CA A:TRP71 4.2 20.2 1.0 CM A:KG1417 4.2 40.0 1.0 CG A:TRP71 4.3 20.8 1.0 O A:HOH739 4.3 30.3 1.0 O A:LEU358 4.4 22.7 1.0 O A:HOH603 4.4 21.9 1.0 O A:TRP71 4.7 22.2 1.0 N A:GLY360 4.8 22.3 1.0 NE1 A:TRP71 4.8 21.6 1.0 C A:TRP71 5.0 22.2 1.0

Chlorine binding site 6 out of 11 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Propargyl- 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 Propargyl- Fucoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl419 b:26.3 occ:1.00 O A:HOH543 3.1 37.2 1.0 O B:HOH679 3.2 28.5 1.0 ND2 A:ASN281 3.4 22.0 1.0 O B:HOH564 3.4 37.5 1.0 ND2 B:ASN37 3.5 26.1 1.0 CA B:ALA327 3.7 18.2 1.0 CB B:ALA327 4.0 17.2 1.0 OD1 B:ASN37 4.1 22.6 1.0 CG B:ASN37 4.2 24.3 1.0 O B:ASP326 4.2 18.6 1.0 N B:ALA327 4.4 18.9 1.0 CG A:ASN281 4.5 24.3 1.0 C B:ASP326 4.5 18.5 1.0 NA B:NA403 4.6 31.6 1.0 O A:HOH705 4.7 34.6 1.0 C B:ALA327 4.7 18.9 1.0 O B:ALA327 4.8 18.0 1.0 OD1 A:ASN281 4.8 25.7 1.0 O B:HOH698 4.9 42.4 1.0

Chlorine binding site 7 out of 11 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Propargyl- Fucoside


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 Propargyl- Fucoside within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl406 b:35.0 occ:1.00 O B:HOH708 3.2 40.9 1.0 N B:TRP166 3.3 21.9 1.0 CA B:SER165 3.4 24.8 1.0 CB B:SER165 3.5 27.8 1.0 C B:SER165 3.9 23.6 1.0 CD1 B:TRP166 4.0 20.1 1.0 CB B:TRP166 4.3 21.0 1.0 CA B:TRP166 4.4 21.9 1.0 CG B:TRP166 4.6 19.9 1.0 O B:SER164 4.7 19.1 1.0 N B:SER165 4.7 24.1 1.0 OG B:SER165 4.9 31.8 1.0 O B:TRP166 4.9 22.3 1.0

Chlorine binding site 8 out of 11 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Propargyl- Fucoside


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Photorhabdus Asymbiotica Lectin (Phl) in Complex with Propargyl- Fucoside within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl407 b:44.5 occ:1.00 N B:TRP163 3.0 21.4 1.0 O B:HOH713 3.1 39.9 1.0 CA B:PRO162 3.6 24.9 1.0 C B:PRO162 3.8 23.5 1.0 CB B:PRO162 3.8 24.9 1.0 CD1 B:TRP163 3.9 19.9 1.0 CB B:TRP163 3.9 20.4 1.0 CA B:TRP163 4.0 20.8 1.0 CG B:TRP163 4.3 19.6 1.0 CD2 B:LEU121 4.4 22.6 1.0 O B:HOH693 4.4 41.2 1.0 O B:TRP163 4.4 20.6 1.0 O B:HOH557 4.4 29.9 1.0 C B:TRP163 4.7 20.9 1.0 N B:PRO162 4.9 24.8 1.0 O B:HOH685 4.9 36.5 1.0 O B:PRO162 5.0 23.5 1.0

Chlorine binding site 9 out of 11 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Propargyl- Fucoside


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Photorhabdus Asymbiotica Lectin (Phl) in Complex with Propargyl- Fucoside within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl408 b:34.9 occ:1.00 N B:ASP364 3.2 26.2 1.0 NH1 B:ARG336 3.2 29.4 1.0 CA B:ILE363 3.6 28.5 1.0 CB B:ILE363 3.8 31.9 1.0 C B:ILE363 3.9 27.3 1.0 CB B:ASP364 4.0 28.8 1.0 CA B:ASP364 4.1 26.7 1.0 NH2 B:ARG336 4.2 28.0 1.0 CZ B:ARG336 4.2 27.1 1.0 O B:ASP364 4.4 27.3 1.0 CG2 B:ILE363 4.5 33.3 1.0 C B:ASP364 4.7 27.5 1.0 O B:LEU362 4.8 24.9 1.0 O B:HOH503 4.9 42.2 1.0 N B:ILE363 4.9 27.9 1.0 CG1 B:ILE363 5.0 34.0 1.0

Chlorine binding site 10 out of 11 in the Photorhabdus Asymbiotica Lectin (Phl) in Complex with Propargyl- Fucoside


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Photorhabdus Asymbiotica Lectin (Phl) in Complex with Propargyl- Fucoside within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl409 b:27.5 occ:1.00 OG1 B:THR178 3.1 25.2 1.0 N B:VAL227 3.2 23.1 1.0 O B:HOH706 3.3 27.0 1.0 O B:HOH642 3.4 42.2 1.0 O B:HOH580 3.6 40.3 1.0 CA B:VAL226 3.6 23.8 1.0 O B:HOH582 3.7 26.8 1.0 O B:VAL227 3.7 22.9 1.0 C B:VAL226 3.9 23.9 1.0 CG1 B:VAL226 3.9 24.4 1.0 CB B:THR178 4.1 24.7 1.0 O B:HOH716 4.1 39.9 1.0 NA B:NA402 4.2 28.9 1.0 CG1 B:VAL227 4.2 26.8 1.0 CB B:VAL226 4.3 25.4 1.0 CA B:VAL227 4.3 22.6 1.0 O B:PRO225 4.4 24.5 1.0 C B:VAL227 4.4 23.4 1.0 CG2 B:THR178 4.5 24.6 1.0 CG2 B:VAL226 4.6 26.6 1.0 O B:HOH709 4.7 36.9 1.0 N B:VAL226 4.8 22.9 1.0 CB B:VAL227 4.9 24.2 1.0 O B:HOH647 4.9 17.5 1.0 O B:HOH618 4.9 23.9 1.0

G.Jancarikova, M.Herczeg, E.Fujdiarova, J.Houser, K.E.Kover, A.Borbas, M.Wimmerova, M.Csavas. Synthesis of Alpha-L-Fucopyranoside-Presenting Glycoclusters and Investigation of Their Interaction with Photorhabdus Asymbiotica Lectin (Phl). Chemistry V. 24 4055 2018.
ISSN: ISSN 1521-3765
PubMed: 29341313
DOI: 10.1002/CHEM.201705853