Sodium in PDB 8cse: Wbbb in Complex with Alpha-Rha-(1-3)-Beta-Glcnac Acceptor

The structure of Wbbb in Complex with Alpha-Rha-(1-3)-Beta-Glcnac Acceptor, PDB code: 8cse 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)	37.76 / 2.30
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	92.38, 158.02, 117.58, 90, 90, 90
R / Rfree (%)	16.7 / 22.5

The binding sites of Sodium atom in the Wbbb in Complex with Alpha-Rha-(1-3)-Beta-Glcnac Acceptor (pdb code 8cse). 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 in Complex with Alpha-Rha-(1-3)-Beta-Glcnac Acceptor, PDB code: 8cse:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Wbbb in Complex with Alpha-Rha-(1-3)-Beta-Glcnac Acceptor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Wbbb in Complex with Alpha-Rha-(1-3)-Beta-Glcnac Acceptor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:51.0 occ:1.00 O A:LEU209 2.3 39.4 1.0 O A:ASN206 2.8 40.2 1.0 O A:TYR207 2.9 34.0 1.0 C A:LEU209 3.5 40.3 1.0 C A:TYR207 3.5 36.5 1.0 C A:ASN206 3.9 39.7 1.0 N A:LEU209 4.0 36.5 1.0 CA A:TYR207 4.0 37.0 1.0 CA A:LEU209 4.2 41.2 1.0 OE1 A:GLU403 4.2 62.3 1.0 C A:PHE208 4.3 37.2 1.0 N A:PHE208 4.4 35.3 1.0 NH2 A:ARG168 4.4 42.8 1.0 OE1 A:GLU210 4.5 54.0 1.0 ND2 A:ASN206 4.5 46.5 1.0 CB A:LEU209 4.5 39.9 1.0 N A:TYR207 4.5 36.6 1.0 N A:GLU210 4.6 41.0 1.0 CA A:PHE208 4.7 38.5 1.0 O A:PHE208 4.7 37.5 1.0 CA A:GLU210 4.8 43.4 1.0 CG A:ASN206 4.9 47.9 1.0 NE A:ARG168 5.0 39.2 1.0

Sodium binding site 2 out of 4 in the Wbbb in Complex with Alpha-Rha-(1-3)-Beta-Glcnac Acceptor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Wbbb in Complex with Alpha-Rha-(1-3)-Beta-Glcnac Acceptor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:44.3 occ:1.00 OG1 A:THR333 2.7 45.8 1.0 O A:LEU327 2.8 48.8 1.0 O A:ILE324 2.8 37.5 1.0 O A:ASN325 3.2 38.4 1.0 CG2 A:THR333 3.5 40.1 1.0 C A:ASN325 3.5 39.5 1.0 CA A:ASN325 3.7 39.4 1.0 CB A:THR333 3.7 43.0 1.0 C A:LEU327 3.7 48.8 1.0 C A:ILE324 3.9 37.9 1.0 N A:LEU327 3.9 43.8 1.0 CA A:LEU327 4.1 43.4 1.0 CB A:LEU327 4.1 44.8 1.0 N A:ASN325 4.2 37.4 1.0 N A:GLU326 4.3 37.2 1.0 OD1 A:ASN325 4.6 40.6 1.0 CA A:THR333 4.6 42.5 1.0 C A:GLU326 4.6 43.7 1.0 N A:ALA328 4.8 51.0 1.0 O A:GLY329 4.9 50.2 1.0 CA A:GLU326 5.0 39.8 1.0

Sodium binding site 3 out of 4 in the Wbbb in Complex with Alpha-Rha-(1-3)-Beta-Glcnac Acceptor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Wbbb in Complex with Alpha-Rha-(1-3)-Beta-Glcnac Acceptor within 5.0Å range: probe atom residue distance (Å) B Occ B:Na502 b:55.9 occ:1.00 O B:ASN206 2.3 43.2 1.0 O B:LEU209 2.4 46.4 1.0 O B:HOH732 2.7 55.2 1.0 O B:HOH723 2.7 49.4 1.0 C B:LEU209 3.5 47.5 1.0 C B:ASN206 3.6 46.0 1.0 OE2 B:GLU403 3.9 85.9 1.0 O B:TYR207 4.0 44.2 1.0 O B:HOH739 4.1 44.2 1.0 N B:LEU209 4.1 42.2 1.0 CA B:LEU209 4.2 46.0 1.0 CB B:LEU209 4.2 42.9 1.0 C B:TYR207 4.3 47.5 1.0 CA B:ASN206 4.4 46.7 1.0 CA B:TYR207 4.4 45.7 1.0 N B:TYR207 4.5 48.4 1.0 N B:GLU210 4.5 45.8 1.0 OE1 B:GLU403 4.6 75.4 1.0 CD B:GLU403 4.7 81.8 1.0 CA B:GLU210 4.7 50.5 1.0 CB B:ASN206 4.8 48.9 1.0 C B:PHE208 4.8 42.4 1.0 OD1 B:ASN206 4.9 56.9 1.0 N B:PHE208 5.0 43.8 1.0 C B:GLU210 5.0 46.7 1.0

Sodium binding site 4 out of 4 in the Wbbb in Complex with Alpha-Rha-(1-3)-Beta-Glcnac Acceptor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Wbbb in Complex with Alpha-Rha-(1-3)-Beta-Glcnac Acceptor within 5.0Å range: probe atom residue distance (Å) B Occ B:Na503 b:53.2 occ:1.00 O B:LEU327 2.2 42.8 1.0 O B:HOH651 2.5 49.4 1.0 O B:HOH676 2.7 41.8 1.0 O B:ASN325 2.7 37.5 1.0 C B:LEU327 3.4 43.5 1.0 C B:ASN325 3.6 37.4 1.0 N B:LEU327 4.0 41.5 1.0 O B:HOH733 4.0 50.0 1.0 CA B:ASN325 4.2 36.0 1.0 C B:GLU326 4.3 40.5 1.0 CA B:LEU327 4.3 41.8 1.0 N B:ALA328 4.4 40.8 1.0 N B:GLU326 4.5 36.3 1.0 CA B:ALA328 4.5 44.6 1.0 O B:ILE324 4.5 36.6 1.0 O B:HOH626 4.6 38.4 1.0 CA B:GLU326 4.6 38.9 1.0 O B:ALA328 4.7 51.5 1.0 OD1 B:ASN325 4.7 38.3 1.0 C B:ALA328 4.8 48.6 1.0 OG1 B:THR333 4.8 42.3 1.0 CG B:ASN325 4.8 40.7 1.0 O B:GLU326 4.9 44.7 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