Sodium in PDB 6t99: Crystal Structrue of Rsl W31YW76Y Lectin Mutant in Complex with Alpha- Methylfucoside

The structure of Crystal Structrue of Rsl W31YW76Y Lectin Mutant in Complex with Alpha- Methylfucoside, PDB code: 6t99 was solved by J.Houser, S.Kozmon, M.Wimmerova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.72 / 2.70
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	36.602, 44.425, 116.574, 96.42, 98.70, 103.36
R / Rfree (%)	22 / 26.5

The binding sites of Sodium atom in the Crystal Structrue of Rsl W31YW76Y Lectin Mutant in Complex with Alpha- Methylfucoside (pdb code 6t99). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structrue of Rsl W31YW76Y Lectin Mutant in Complex with Alpha- Methylfucoside, PDB code: 6t99:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structrue of Rsl W31YW76Y Lectin Mutant in Complex with Alpha- Methylfucoside


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structrue of Rsl W31YW76Y Lectin Mutant in Complex with Alpha- Methylfucoside within 5.0Å range: probe atom residue distance (Å) B Occ E:Na103 b:43.5 occ:1.00 OG1 F:THR6 2.1 37.6 1.0 OG E:SER67 2.5 45.0 1.0 O E:TYR65 2.5 31.9 1.0 OD1 E:ASN48 2.7 33.3 1.0 CB F:THR6 3.3 38.1 1.0 CG2 F:THR6 3.4 38.8 1.0 C E:TYR65 3.5 33.4 1.0 CB E:SER67 3.5 44.4 1.0 O E:ASN48 3.6 33.3 1.0 CG E:ASN48 3.8 34.8 1.0 C E:ASN48 3.9 32.8 1.0 CA E:VAL49 4.0 31.6 1.0 N E:SER50 4.0 30.9 1.0 N E:SER67 4.0 44.1 1.0 N E:VAL49 4.0 32.3 1.0 C E:VAL49 4.1 29.9 1.0 OG E:SER50 4.1 32.2 1.0 N F:THR6 4.2 35.4 1.0 CB E:TYR65 4.2 29.2 1.0 CA F:THR6 4.3 35.9 1.0 N E:ALA66 4.3 38.1 1.0 C E:ALA66 4.3 43.5 1.0 CA E:SER67 4.4 44.1 1.0 CA E:TYR65 4.4 31.2 1.0 CB E:ASN48 4.4 34.6 1.0 CA E:ALA66 4.5 40.8 1.0 CG2 E:THR72 4.6 36.5 1.0 O E:VAL49 4.8 26.9 1.0 CB E:SER50 4.8 30.5 1.0 CA E:ASN48 4.8 33.5 1.0 ND2 E:ASN48 4.8 34.0 1.0 OG1 E:THR72 5.0 37.4 1.0 C F:THR6 5.0 35.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structrue of Rsl W31YW76Y Lectin Mutant in Complex with Alpha- Methylfucoside


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structrue of Rsl W31YW76Y Lectin Mutant in Complex with Alpha- Methylfucoside within 5.0Å range: probe atom residue distance (Å) B Occ H:Na103 b:44.0 occ:1.00 O G:SER53 2.7 29.6 1.0 O H:SER10 3.0 36.1 1.0 C H:SER10 3.4 35.5 1.0 CB H:SER10 3.5 34.8 1.0 CA H:SER10 3.8 34.9 1.0 C G:SER53 3.9 30.1 1.0 N H:SER10 4.0 32.8 1.0 N H:TRP11 4.1 37.7 1.0 OG H:SER10 4.1 37.7 1.0 OG1 G:THR52 4.1 35.8 1.0 CB G:TRP54 4.2 34.3 1.0 CA G:TRP54 4.4 33.1 1.0 CA H:TRP11 4.5 40.0 1.0 N G:TRP54 4.6 31.8 1.0 N G:SER53 4.7 30.3 1.0 CA G:SER53 4.9 29.9 1.0

J.Houser, S.Kozmon, D.Mishra, Z.Hammerova, M.Wimmerova, J.Koca. The Ch-Pi Interaction in Protein - Carbohydrate Binding: Bioinformatics and in Vitro Quantification. Chemistry 2020.
ISSN: ISSN 0947-6539
PubMed: 32208534
DOI: 10.1002/CHEM.202000593