Sodium 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:

Fluorine	(F)	14 atoms
Chlorine	(Cl)	1 atom

The binding sites of Sodium 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 Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of the 5F-Tryptophan Rsl Lectin in Complex with Lewis X Tetrasaccharide, PDB code: 5o7v:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 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 Sodium with other atoms in the Na 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:Na103 b:11.9 occ:1.00 O A:HOH203 2.3 16.4 0.5 O A:HOH231 2.3 23.6 0.5 O A:HOH231 2.3 16.9 0.5 O A:HOH281 2.4 11.3 1.0 O A:HOH211 2.4 11.1 1.0 O A:HOH203 2.4 18.4 0.5 O A:HOH240 2.4 16.6 1.0 O A:HOH280 2.5 20.7 1.0 O A:HOH235 4.1 27.8 1.0 OXT A:ASN90 4.3 16.1 1.0 O A:ASN90 4.4 13.3 1.0 OG1 A:THR87 4.5 12.2 1.0 O A:ALA85 4.6 11.8 1.0 C A:ASN90 4.8 12.4 1.0

Sodium binding site 2 out of 4 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 Sodium with other atoms in the Na 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:Na104 b:12.5 occ:1.00 O A:HOH250 2.3 12.6 1.0 O A:VAL50 2.3 7.6 1.0 O A:HOH230 2.5 13.1 1.0 O A:HOH270 2.8 16.6 1.0 C A:VAL50 3.5 6.2 1.0 O A:HOH267 3.9 13.7 1.0 CB A:THR51 4.2 7.3 1.0 O A:HOH232 4.2 12.3 1.0 CA A:THR51 4.3 6.7 1.0 N A:THR51 4.3 6.4 1.0 OG1 A:THR51 4.5 8.2 1.0 N A:VAL50 4.5 6.3 1.0 CA A:VAL50 4.6 6.5 1.0 CG1 A:VAL50 4.9 7.5 1.0

Sodium binding site 3 out of 4 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 Sodium with other atoms in the Na 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:Na111 b:20.9 occ:1.00 O B:ASN79 2.2 25.8 1.0 O A:ASN79 2.3 17.9 1.0 O B:HOH251 2.5 24.2 1.0 O A:HOH241 2.6 27.2 1.0 O B:HOH248 2.7 15.9 1.0 C B:ASN79 3.4 26.4 1.0 C A:ASN79 3.4 17.8 1.0 CA A:ASN79 4.0 17.4 1.0 ND2 A:ASN79 4.1 18.2 1.0 CA B:GLY80 4.1 15.1 1.0 N B:GLY80 4.2 16.6 1.0 CH2 A:FTR76 4.2 15.6 1.0 OD1 B:ASN79 4.3 25.3 0.7 ND2 B:ASN79 4.3 20.7 0.7 CG B:ASN79 4.3 25.1 0.7 CA B:ASN79 4.4 28.4 1.0 F B:FTR76 4.5 18.8 1.0 CG A:ASN79 4.5 17.7 1.0 CH2 B:FTR76 4.6 13.4 1.0 N A:GLY80 4.6 16.1 1.0 F A:FTR76 4.8 20.7 1.0 O A:GLY78 4.8 23.2 1.0 C3 B:GAL104 4.9 20.9 0.8 CZ3 A:FTR76 4.9 17.1 1.0 CZ3 B:FTR76 4.9 14.8 1.0 CB A:ASN79 4.9 17.4 1.0 O3 B:GAL104 4.9 23.7 0.8 CA A:GLY80 4.9 17.8 1.0 O A:HOH238 5.0 38.3 1.0 CZ2 A:FTR76 5.0 15.5 1.0 OD1 A:ASN79 5.0 19.4 1.0

Sodium binding site 4 out of 4 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 Sodium with other atoms in the Na 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 B:Na101 b:11.4 occ:1.00 O B:VAL50 2.3 7.9 1.0 O B:HOH269 2.3 13.2 1.0 O B:HOH229 2.5 12.9 1.0 C B:VAL50 3.5 6.4 1.0 O B:HOH258 3.9 8.0 0.3 CB B:THR51 4.2 7.8 1.0 O B:HOH223 4.2 14.8 1.0 CA B:THR51 4.2 7.1 1.0 N B:THR51 4.3 6.8 1.0 OG1 B:THR51 4.5 8.6 1.0 N B:VAL50 4.5 7.0 1.0 CA B:VAL50 4.6 7.2 1.0 CG1 B:VAL50 4.8 8.3 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