Sodium in PDB 8csf: Wbbb D232C-Kdo Adduct + Alpha-Rha(1,3)Glcnac Ternary Complex

The structure of Wbbb D232C-Kdo Adduct + Alpha-Rha(1,3)Glcnac Ternary Complex, PDB code: 8csf was solved by T.J.B.Forrester, M.S.Kimber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.78 / 2.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	92.5, 158.07, 116.68, 90, 90, 90
R / Rfree (%)	17.2 / 22.1

The binding sites of Sodium atom in the Wbbb D232C-Kdo Adduct + Alpha-Rha(1,3)Glcnac Ternary Complex (pdb code 8csf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Wbbb D232C-Kdo Adduct + Alpha-Rha(1,3)Glcnac Ternary Complex, PDB code: 8csf:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Wbbb D232C-Kdo Adduct + Alpha-Rha(1,3)Glcnac Ternary Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Wbbb D232C-Kdo Adduct + Alpha-Rha(1,3)Glcnac Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:67.5 occ:1.00 O A:HOH648 2.4 42.8 1.0 O A:LEU327 2.7 53.9 1.0 O A:ASN325 3.0 47.3 1.0 O A:HOH644 3.4 52.2 1.0 C A:LEU327 3.9 48.8 1.0 C A:ASN325 4.0 45.1 1.0 OD1 A:ASN325 4.4 48.9 1.0 CA A:ASN325 4.4 45.3 1.0 N A:LEU327 4.7 47.1 1.0 OG1 A:THR333 4.7 47.4 1.0 CA A:ALA328 4.7 50.0 1.0 O A:ALA328 4.7 64.9 1.0 O A:ILE324 4.8 38.1 1.0 N A:ALA328 4.8 47.8 1.0 CG A:ASN325 4.8 48.6 1.0 C A:ALA328 4.8 55.4 1.0 CA A:LEU327 4.9 46.8 1.0

Sodium binding site 2 out of 4 in the Wbbb D232C-Kdo Adduct + Alpha-Rha(1,3)Glcnac Ternary Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Wbbb D232C-Kdo Adduct + Alpha-Rha(1,3)Glcnac Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:51.2 occ:1.00 O A:LEU209 2.2 44.5 1.0 O A:HOH678 2.3 52.6 1.0 O A:ASN206 2.4 50.0 1.0 O A:HOH669 2.5 49.5 1.0 C A:LEU209 3.3 50.4 1.0 C A:ASN206 3.6 44.3 1.0 O A:HOH709 3.7 50.7 1.0 OE1 A:GLU403 4.0 89.2 1.0 CA A:LEU209 4.1 41.5 1.0 N A:LEU209 4.1 45.2 1.0 CB A:LEU209 4.1 38.5 1.0 O A:TYR207 4.2 41.9 1.0 C A:TYR207 4.3 47.9 1.0 N A:GLU210 4.4 50.8 1.0 CA A:ASN206 4.5 48.8 1.0 CA A:GLU210 4.5 49.4 1.0 N A:TYR207 4.6 51.2 1.0 CA A:TYR207 4.6 49.2 1.0 O A:VAL211 4.7 49.3 1.0 C A:GLU210 4.7 44.6 1.0 OD1 A:ASN206 4.8 65.0 1.0 C A:PHE208 4.8 45.5 1.0 N A:PHE208 4.8 45.9 1.0 CB A:ASN206 4.9 54.7 1.0 CD A:GLU403 5.0 89.1 1.0

Sodium binding site 3 out of 4 in the Wbbb D232C-Kdo Adduct + Alpha-Rha(1,3)Glcnac Ternary Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Wbbb D232C-Kdo Adduct + Alpha-Rha(1,3)Glcnac Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na502 b:39.7 occ:1.00 OG1 B:THR149 2.6 38.7 1.0 NE2 B:HIS118 2.8 48.0 1.0 ND1 B:HIS145 2.8 48.0 1.0 CE1 B:HIS145 3.1 47.2 1.0 CB B:THR149 3.5 44.9 1.0 O B:HIS145 3.5 36.1 1.0 CE1 B:HIS118 3.6 43.8 1.0 CA B:VAL146 3.7 35.9 1.0 CD2 B:HIS118 3.8 44.9 1.0 C B:HIS145 3.8 36.7 1.0 CB A:ALA186 3.9 45.2 1.0 N B:VAL146 3.9 36.2 1.0 CG B:HIS145 4.0 47.5 1.0 CG2 B:THR149 4.1 35.9 1.0 NE2 B:HIS145 4.3 43.8 1.0 CG2 B:VAL146 4.4 37.2 1.0 CB A:GLU183 4.4 35.3 1.0 C B:VAL146 4.6 38.2 1.0 O B:VAL146 4.7 39.8 1.0 CB B:VAL146 4.7 36.8 1.0 CB B:HIS145 4.8 39.1 1.0 CA B:THR149 4.8 40.3 1.0 CD2 B:HIS145 4.8 46.6 1.0 ND1 B:HIS118 4.8 46.9 1.0 OE1 B:GLU114 4.8 47.9 1.0 N B:THR149 4.9 38.6 1.0 CA B:HIS145 4.9 39.3 1.0 CG B:HIS118 4.9 49.0 1.0 CA A:GLU183 5.0 34.4 1.0

Sodium binding site 4 out of 4 in the Wbbb D232C-Kdo Adduct + Alpha-Rha(1,3)Glcnac Ternary Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Wbbb D232C-Kdo Adduct + Alpha-Rha(1,3)Glcnac Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na503 b:51.2 occ:1.00 O B:HOH726 1.8 51.3 1.0 O B:LEU327 2.6 52.0 1.0 OG1 B:THR333 2.7 46.3 1.0 O B:ILE324 3.1 41.1 1.0 O B:HOH734 3.2 60.6 1.0 O B:ASN325 3.5 50.0 1.0 C B:LEU327 3.6 53.4 1.0 CG2 B:THR333 3.6 37.5 1.0 CB B:THR333 3.7 44.9 1.0 C B:ASN325 3.8 45.4 1.0 N B:LEU327 4.0 51.5 1.0 CA B:ASN325 4.0 41.4 1.0 CA B:LEU327 4.1 50.4 1.0 CB B:LEU327 4.2 44.5 1.0 C B:ILE324 4.2 40.9 1.0 N B:ASN325 4.6 38.1 1.0 N B:ALA328 4.7 55.7 1.0 N B:GLU326 4.7 44.9 1.0 C B:GLU326 4.7 47.5 1.0 CA B:THR333 4.7 44.3 1.0 OD1 B:ASN325 4.7 47.0 1.0 O B:GLY329 4.8 57.7 1.0

T.J.B.Forrester, O.G.Ovchinnikova, Z.Li, E.N.Kitova, J.T.Nothof, A.Koizumi, J.S.Klassen, T.L.Lowary, C.Whitfield, M.S.Kimber. The Retaining Beta-Kdo Glycosyltransferase Wbbb Uses A Double-Displacement Mechanism with An Intermediate Adduct Rearrangement Step. Nat Commun V. 13 6277 2022.
ISSN: ESSN 2041-1723
PubMed: 36271007
DOI: 10.1038/S41467-022-33988-1