Fluorine in PDB 5o7v: Crystal Structure of the 5F-Tryptophan Rsl Lectin in Complex with Lewis X Tetrasaccharide

The structure of Crystal Structure of the 5F-Tryptophan Rsl Lectin in Complex with Lewis X Tetrasaccharide, PDB code: 5o7v was solved by A.Varrot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.92 / 1.28
Space group	F 2 3
Cell size a, b, c (Å), α, β, γ (°)	129.883, 129.883, 129.883, 90.00, 90.00, 90.00
R / Rfree (%)	12.2 / 14.8

The structure of Crystal Structure of the 5F-Tryptophan Rsl Lectin in Complex with Lewis X Tetrasaccharide also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Sodium	(Na)	4 atoms

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>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of the 5F-Tryptophan Rsl Lectin in Complex with Lewis X Tetrasaccharide (pdb code 5o7v). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 14 binding sites of Fluorine where determined in the Crystal Structure of the 5F-Tryptophan Rsl Lectin in Complex with Lewis X Tetrasaccharide, PDB code: 5o7v:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 14 in the Crystal Structure of the 5F-Tryptophan Rsl Lectin in Complex with Lewis X Tetrasaccharide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the 5F-Tryptophan Rsl Lectin in Complex with Lewis X Tetrasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:F10 b:12.3 occ:1.00 F A:FTR10 0.0 12.3 1.0 CZ3 A:FTR10 1.3 10.3 1.0 CE3 A:FTR10 2.4 9.9 1.0 CH2 A:FTR10 2.4 9.8 1.0 CG A:ARG17 3.1 7.6 1.0 CG2 A:THR8 3.2 9.0 1.0 CD1 A:ILE61 3.5 10.1 1.0 CD2 A:FTR10 3.6 9.9 1.0 CZ2 A:FTR10 3.6 9.7 1.0 CB A:ARG17 3.8 7.4 1.0 CG1 A:ILE61 3.9 9.0 1.0 CE2 A:FTR10 4.1 10.0 1.0 N A:ARG17 4.3 6.9 1.0 OG A:SER52 4.4 10.0 1.0 CG1 A:ILE59 4.5 13.5 1.0 CD A:ARG17 4.5 8.2 1.0 CB A:THR8 4.5 7.9 1.0 CB A:SER52 4.5 9.2 1.0 O A:THR8 4.5 8.4 1.0 C A:THR8 4.6 7.3 1.0 CA A:ARG17 4.7 7.2 1.0 OG1 A:THR8 4.7 9.4 1.0 NE A:ARG17 4.7 8.5 1.0 CG2 A:ILE61 4.8 7.7 1.0 C A:ILE16 4.9 7.2 1.0 N A:SER9 4.9 7.2 1.0 CG A:FTR10 5.0 9.5 1.0 CB A:ILE61 5.0 8.2 1.0 CD1 A:ILE59 5.0 13.1 1.0

Fluorine binding site 2 out of 14 in the Crystal Structure of the 5F-Tryptophan Rsl Lectin in Complex with Lewis X Tetrasaccharide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the 5F-Tryptophan Rsl Lectin in Complex with Lewis X Tetrasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:F31 b:12.2 occ:1.00 F A:FTR31 0.0 12.2 1.0 CZ3 A:FTR31 1.3 10.9 1.0 CE3 A:FTR31 2.3 9.8 1.0 CH2 A:FTR31 2.4 10.7 1.0 CA A:GLY35 3.3 9.9 1.0 CD1 A:FTR36 3.4 9.1 1.0 CD2 A:FTR31 3.6 9.6 1.0 NE1 A:FTR36 3.6 8.3 1.0 CZ2 A:FTR31 3.6 11.2 1.0 N A:GLY35 3.7 10.2 1.0 C A:GLY35 3.8 8.9 1.0 N A:FTR36 3.9 8.6 1.0 CE2 A:FTR31 4.1 10.6 1.0 CG A:FTR36 4.4 8.8 1.0 O A:GLY35 4.5 9.9 1.0 CE2 A:FTR36 4.6 9.5 1.0 C A:LYS34 4.7 10.8 1.0 O A:HOH246 4.7 32.3 1.0 CG A:FTR31 5.0 9.8 1.0

Fluorine binding site 3 out of 14 in the Crystal Structure of the 5F-Tryptophan Rsl Lectin in Complex with Lewis X Tetrasaccharide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of the 5F-Tryptophan Rsl Lectin in Complex with Lewis X Tetrasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:F36 b:9.4 occ:1.00 F A:FTR36 0.0 9.4 1.0 CZ3 A:FTR36 1.4 8.7 1.0 CH2 A:FTR36 2.3 8.1 1.0 CE3 A:FTR36 2.4 8.3 1.0 O A:ARG29 3.0 8.3 1.0 C A:ARG29 3.3 7.9 1.0 N A:CYS30 3.4 8.3 1.0 CA A:CYS30 3.5 8.1 1.0 CG2 A:VAL18 3.6 8.3 1.0 O A:ILE16 3.6 7.7 1.0 C A:CYS30 3.6 8.5 1.0 CD2 A:FTR36 3.6 9.0 1.0 CZ2 A:FTR36 3.6 8.5 1.0 N A:FTR31 3.7 8.1 1.0 N A:VAL18 3.8 6.8 1.0 C A:ILE16 4.0 7.2 1.0 CG2 A:ILE16 4.1 7.2 1.0 CB A:ARG29 4.1 8.3 1.0 CB A:VAL18 4.1 8.0 1.0 CE2 A:FTR36 4.1 9.5 1.0 CA A:ARG17 4.1 7.2 1.0 C A:ARG17 4.2 6.9 1.0 CA A:ARG29 4.3 7.9 1.0 O A:CYS30 4.3 9.3 1.0 CB A:ILE16 4.3 7.5 1.0 CB A:FTR31 4.3 9.4 1.0 N A:ARG17 4.3 6.9 1.0 CA A:VAL18 4.5 6.8 1.0 CA A:FTR31 4.6 8.2 1.0 CA A:ILE16 4.8 7.0 1.0 CG A:FTR36 5.0 8.8 1.0

Fluorine binding site 4 out of 14 in the Crystal Structure of the 5F-Tryptophan Rsl Lectin in Complex with Lewis X Tetrasaccharide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of the 5F-Tryptophan Rsl Lectin in Complex with Lewis X Tetrasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:F53 b:12.2 occ:1.00 F A:FTR53 0.0 12.2 1.0 CZ3 A:FTR53 1.4 10.7 1.0 CE3 A:FTR53 2.3 10.6 1.0 CH2 A:FTR53 2.4 11.3 1.0 CG A:ARG62 3.1 8.2 1.0 CG2 A:THR51 3.4 8.1 1.0 CD2 A:FTR53 3.6 10.4 1.0 CZ2 A:FTR53 3.6 11.4 1.0 CB A:ARG62 3.7 7.7 1.0 O A:THR51 4.1 8.0 1.0 CE2 A:FTR53 4.1 11.5 1.0 N A:ARG62 4.3 7.2 1.0 C A:THR51 4.3 7.1 1.0 CD A:ARG62 4.4 8.8 1.0 N A:SER52 4.5 7.4 1.0 CA A:SER52 4.5 8.1 1.0 CB A:THR51 4.6 7.3 1.0 CA A:ARG62 4.6 7.6 1.0 NE A:ARG62 4.7 9.3 1.0 O A:HIS60 4.8 11.3 1.0 C A:ILE61 4.8 7.6 1.0 C A:SER52 4.9 8.7 1.0 OG1 A:THR51 4.9 8.2 1.0 CG A:FTR53 4.9 11.2 1.0 CZ A:ARG62 5.0 8.9 1.0

Fluorine binding site 5 out of 14 in the Crystal Structure of the 5F-Tryptophan Rsl Lectin in Complex with Lewis X Tetrasaccharide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of the 5F-Tryptophan Rsl Lectin in Complex with Lewis X Tetrasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:F74 b:19.9 occ:1.00 F A:FTR74 0.0 19.9 1.0 CZ3 A:FTR74 1.3 15.4 1.0 CH2 A:FTR74 2.3 15.8 1.0 CE3 A:FTR74 2.3 12.9 1.0 CG2 B:THR82 3.2 15.3 1.0 O A:FTR81 3.5 15.3 1.0 CD2 A:FTR74 3.6 11.3 1.0 CZ2 A:FTR74 3.6 14.3 1.0 N A:LYS83 3.6 13.4 1.0 O B:HOH226 3.7 31.1 1.0 CG A:LYS83 3.8 21.9 1.0 C A:THR82 3.9 14.0 1.0 O B:HOH261 3.9 36.1 1.0 O A:HOH251 4.0 14.0 1.0 OE2 A:GLU43 4.0 23.0 1.0 CA A:THR82 4.0 16.2 1.0 C A:FTR81 4.0 13.5 1.0 O B:HOH207 4.1 39.8 1.0 CE2 A:FTR74 4.1 11.9 1.0 N A:THR82 4.1 15.2 1.0 CA A:LYS83 4.4 13.6 1.0 CD A:GLU43 4.4 18.7 1.0 CB B:THR82 4.6 14.0 1.0 CB A:LYS83 4.6 16.6 1.0 O A:THR82 4.7 16.0 1.0 OG1 B:THR82 4.8 18.2 1.0 CB A:FTR81 4.9 11.3 1.0 OE1 A:GLU43 4.9 19.5 1.0 CG A:FTR74 4.9 10.0 1.0 CE A:LYS83 5.0 26.0 0.4 CD A:LYS83 5.0 24.4 1.0

Fluorine binding site 6 out of 14 in the Crystal Structure of the 5F-Tryptophan Rsl Lectin in Complex with Lewis X Tetrasaccharide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of the 5F-Tryptophan Rsl Lectin in Complex with Lewis X Tetrasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:F76 b:20.7 occ:1.00 F A:FTR76 0.0 20.7 1.0 CZ3 A:FTR76 1.4 17.1 1.0 CE3 A:FTR76 2.3 13.4 1.0 CH2 A:FTR76 2.4 15.6 1.0 ND2 B:ASN79 2.7 20.7 0.7 CA A:GLY80 3.3 17.8 1.0 CD1 A:FTR81 3.3 11.1 1.0 NE1 A:FTR81 3.5 10.0 1.0 CD2 A:FTR76 3.6 13.1 1.0 CZ2 A:FTR76 3.7 15.5 1.0 O A:ASN79 3.8 17.9 1.0 C A:GLY80 3.8 15.1 1.0 N A:GLY80 3.8 16.1 1.0 CG B:ASN79 3.9 25.1 0.7 N A:FTR81 4.0 13.9 1.0 C3 A:FUC105 4.0 11.5 1.0 C A:ASN79 4.1 17.8 1.0 O3 A:FUC105 4.1 11.6 1.0 O A:HOH263 4.1 15.8 0.7 CE2 A:FTR76 4.2 12.7 1.0 CG A:FTR81 4.2 10.7 1.0 O B:HOH251 4.3 24.2 1.0 OD1 B:ASN79 4.4 25.3 0.7 CB A:ALA40 4.4 14.4 1.0 CE2 A:FTR81 4.4 10.3 1.0 O A:GLY80 4.5 16.1 1.0 C4 A:FUC105 4.6 10.8 1.0 O B:HOH204 4.6 29.7 1.0 NA A:NA111 4.8 20.9 1.0 CD2 A:FTR81 4.8 9.6 1.0 CG A:FTR76 4.9 11.2 1.0

Fluorine binding site 7 out of 14 in the Crystal Structure of the 5F-Tryptophan Rsl Lectin in Complex with Lewis X Tetrasaccharide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of the 5F-Tryptophan Rsl Lectin in Complex with Lewis X Tetrasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:F81 b:11.4 occ:1.00 F A:FTR81 0.0 11.4 1.0 CZ3 A:FTR81 1.4 9.9 1.0 CE3 A:FTR81 2.4 9.9 1.0 CH2 A:FTR81 2.4 10.0 1.0 O A:FTR74 3.0 9.2 1.0 O A:ILE61 3.4 8.5 1.0 C A:FTR74 3.4 9.4 1.0 CG2 A:VAL63 3.4 9.1 1.0 N A:FTR76 3.5 9.9 1.0 CD2 A:FTR81 3.6 9.6 1.0 N A:VAL63 3.6 7.3 1.0 CZ2 A:FTR81 3.6 9.7 1.0 N A:CYS75 3.6 9.9 1.0 C A:CYS75 3.7 10.2 1.0 CA A:CYS75 3.7 9.4 1.0 C A:ILE61 3.8 7.6 1.0 CB A:VAL63 3.9 8.6 1.0 CB A:FTR74 4.0 9.2 1.0 CG2 A:ILE61 4.1 7.7 1.0 CE2 A:FTR81 4.1 10.3 1.0 CB A:ILE61 4.1 8.2 1.0 CA A:ARG62 4.1 7.6 1.0 CB A:FTR76 4.1 10.8 1.0 C A:ARG62 4.2 7.2 1.0 N A:ARG62 4.2 7.2 1.0 CA A:FTR74 4.3 8.5 1.0 CA A:VAL63 4.4 7.6 1.0 CA A:FTR76 4.4 10.4 1.0 O A:CYS75 4.5 12.1 1.0 CA A:ILE61 4.6 8.0 1.0 CD1 A:PHE41 4.9 14.0 1.0 CE1 A:PHE41 4.9 14.0 1.0 CG A:FTR81 4.9 10.7 1.0

Fluorine binding site 8 out of 14 in the Crystal Structure of the 5F-Tryptophan Rsl Lectin in Complex with Lewis X Tetrasaccharide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of the 5F-Tryptophan Rsl Lectin in Complex with Lewis X Tetrasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ B:F10 b:12.4 occ:1.00 F B:FTR10 0.0 12.4 1.0 CZ3 B:FTR10 1.3 10.8 1.0 CH2 B:FTR10 2.3 10.4 1.0 CE3 B:FTR10 2.4 10.6 1.0 CG B:ARG17 3.2 8.1 1.0 CG2 B:THR8 3.3 9.2 1.0 CD1 B:ILE61 3.6 10.2 1.0 CZ2 B:FTR10 3.6 10.4 1.0 CD2 B:FTR10 3.6 10.2 1.0 CB B:ARG17 3.8 7.9 1.0 CG1 B:ILE61 3.9 9.6 1.0 CE2 B:FTR10 4.1 10.8 1.0 N B:ARG17 4.3 7.1 1.0 OG B:SER52 4.4 10.1 1.0 CG1 B:ILE59 4.4 14.1 1.0 CB B:SER52 4.5 9.4 1.0 CD B:ARG17 4.5 8.4 1.0 CB B:THR8 4.5 8.4 1.0 O B:THR8 4.6 8.1 1.0 C B:THR8 4.7 7.1 1.0 CA B:ARG17 4.7 7.3 1.0 OG1 B:THR8 4.7 9.4 1.0 CG2 B:ILE61 4.7 8.4 1.0 NE B:ARG17 4.8 9.1 1.0 N B:SER9 4.9 7.1 1.0 C B:ILE16 4.9 7.2 1.0 CG B:FTR10 4.9 10.3 1.0 CB B:ILE61 4.9 8.4 1.0 CD1 B:ILE59 5.0 13.8 1.0

Fluorine binding site 9 out of 14 in the Crystal Structure of the 5F-Tryptophan Rsl Lectin in Complex with Lewis X Tetrasaccharide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of the 5F-Tryptophan Rsl Lectin in Complex with Lewis X Tetrasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ B:F31 b:12.6 occ:1.00 F B:FTR31 0.0 12.6 1.0 CZ3 B:FTR31 1.3 10.5 1.0 CH2 B:FTR31 2.3 11.0 1.0 CE3 B:FTR31 2.3 10.3 1.0 CA B:GLY35 3.3 10.1 1.0 CD1 B:FTR36 3.4 9.3 1.0 CD2 B:FTR31 3.6 9.7 1.0 CZ2 B:FTR31 3.6 10.8 1.0 NE1 B:FTR36 3.6 8.8 1.0 N B:GLY35 3.7 10.6 1.0 C B:GLY35 3.8 9.1 1.0 N B:FTR36 3.9 8.8 1.0 CE2 B:FTR31 4.1 10.2 1.0 CG B:FTR36 4.3 8.6 1.0 O B:GLY35 4.5 10.5 1.0 CE2 B:FTR36 4.6 8.9 1.0 O B:HOH241 4.7 33.6 1.0 C B:LYS34 4.8 11.0 1.0 CG B:FTR31 5.0 9.6 1.0 CA B:FTR36 5.0 8.8 1.0

Fluorine binding site 10 out of 14 in the Crystal Structure of the 5F-Tryptophan Rsl Lectin in Complex with Lewis X Tetrasaccharide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of the 5F-Tryptophan Rsl Lectin in Complex with Lewis X Tetrasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ B:F36 b:9.6 occ:1.00 F B:FTR36 0.0 9.6 1.0 CZ3 B:FTR36 1.4 8.5 1.0 CH2 B:FTR36 2.3 8.0 1.0 CE3 B:FTR36 2.4 8.7 1.0 O B:ARG29 3.0 8.7 1.0 C B:ARG29 3.3 8.2 1.0 N B:CYS30 3.4 8.4 1.0 CA B:CYS30 3.5 8.2 1.0 CG2 B:VAL18 3.6 8.8 1.0 O B:ILE16 3.6 7.9 1.0 C B:CYS30 3.6 8.6 1.0 CD2 B:FTR36 3.6 8.7 1.0 CZ2 B:FTR36 3.6 8.2 1.0 N B:FTR31 3.6 8.1 1.0 N B:VAL18 3.8 7.1 1.0 C B:ILE16 4.0 7.2 1.0 CB B:ARG29 4.1 9.0 1.0 CG2 B:ILE16 4.1 7.9 1.0 CB B:VAL18 4.1 8.4 1.0 CE2 B:FTR36 4.1 8.9 1.0 CA B:ARG17 4.2 7.3 1.0 CA B:ARG29 4.2 8.2 1.0 O B:CYS30 4.3 9.7 1.0 C B:ARG17 4.3 6.9 1.0 CB B:ILE16 4.3 7.5 1.0 CB B:FTR31 4.3 8.9 1.0 N B:ARG17 4.4 7.1 1.0 CA B:VAL18 4.6 7.5 1.0 CA B:FTR31 4.6 8.5 1.0 CA B:ILE16 4.8 7.2 1.0 CG B:FTR36 5.0 8.6 1.0

F.Tobola, M.Lelimousin, A.Varrot, E.Gillon, B.Darnhofer, O.Blixt, R.Birner-Gruenberger, A.Imberty, B.Wiltschi. Effect of Noncanonical Amino Acids on Protein-Carbohydrate Interactions: Structure, Dynamics, and Carbohydrate Affinity of A Lectin Engineered with Fluorinated Tryptophan Analogs. Acs Chem. Biol. V. 13 2211 2018.
ISSN: ESSN 1554-8937
PubMed: 29812892
DOI: 10.1021/ACSCHEMBIO.8B00377