Sodium in PDB 8csc: Wbbb D232N-Kdo Adduct

The structure of Wbbb D232N-Kdo Adduct, PDB code: 8csc 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)	39.96 / 1.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	92.6, 158.22, 117.57, 90, 90, 90
R / Rfree (%)	18.7 / 21.9

The structure of Wbbb D232N-Kdo Adduct also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Wbbb D232N-Kdo Adduct (pdb code 8csc). 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 D232N-Kdo Adduct, PDB code: 8csc:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Wbbb D232N-Kdo Adduct


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Wbbb D232N-Kdo Adduct within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:35.1 occ:1.00 OD1 A:ASN179 3.1 38.0 1.0 N A:SER320 3.2 29.3 1.0 OG A:SER320 3.3 30.1 1.0 O A:HOH652 3.4 32.4 1.0 OH A:TYR172 3.4 31.1 1.0 CB A:CYS319 3.6 31.4 1.0 CA A:ASN179 3.6 29.8 1.0 CB A:SER320 3.8 29.1 1.0 CA A:CYS319 3.8 29.5 1.0 CZ A:TYR172 4.0 29.9 1.0 C A:CYS319 4.0 29.2 1.0 CG A:ASN179 4.0 37.2 1.0 CA A:SER320 4.1 32.9 1.0 O A:ASN179 4.1 31.5 1.0 O A:HOH649 4.1 33.2 1.0 CB A:ASN179 4.2 33.1 1.0 O A:HOH729 4.4 28.3 1.0 CE2 A:TYR172 4.4 27.6 1.0 C A:ASN179 4.4 34.3 1.0 ND2 A:ASN234 4.4 34.5 0.5 N A:ASN179 4.5 28.7 1.0 CE1 A:TYR172 4.7 26.7 1.0 CD2 A:TYR321 4.9 27.8 1.0

Sodium binding site 2 out of 4 in the Wbbb D232N-Kdo Adduct


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Wbbb D232N-Kdo Adduct within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:44.1 occ:1.00 O A:HOH761 2.3 52.4 1.0 O A:LEU209 2.4 37.0 1.0 O A:HOH753 2.5 43.0 1.0 O A:ASN206 2.6 36.6 1.0 O A:TYR207 3.0 36.4 1.0 C A:TYR207 3.4 35.3 1.0 C A:LEU209 3.6 36.3 1.0 C A:ASN206 3.7 36.2 1.0 CA A:TYR207 3.9 34.6 1.0 N A:LEU209 4.0 36.5 1.0 CA A:LEU209 4.2 35.1 1.0 N A:PHE208 4.2 32.1 1.0 N A:TYR207 4.3 34.5 1.0 C A:PHE208 4.3 34.4 1.0 OE2 A:GLU403 4.4 85.2 1.0 NH2 A:ARG168 4.4 46.4 1.0 CB A:LEU209 4.6 35.9 1.0 OD1 A:ASN206 4.6 44.8 1.0 N A:GLU210 4.6 37.1 1.0 CG A:GLU403 4.6 61.0 1.0 O A:HOH760 4.7 52.3 1.0 CA A:PHE208 4.7 33.7 1.0 CG A:ASN206 4.8 44.2 1.0 NE A:ARG168 4.8 40.5 1.0 O A:PHE208 4.9 35.9 1.0 CA A:GLU210 4.9 37.8 1.0 ND2 A:ASN206 5.0 41.5 1.0 CD A:GLU403 5.0 71.4 1.0 CA A:ASN206 5.0 33.7 1.0 OE1 A:GLU210 5.0 51.0 1.0

Sodium binding site 3 out of 4 in the Wbbb D232N-Kdo Adduct


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Wbbb D232N-Kdo Adduct within 5.0Å range: probe atom residue distance (Å) B Occ B:Na503 b:69.9 occ:1.00 O B:LEU327 2.4 44.9 1.0 O B:HOH663 2.7 37.2 1.0 O B:ASN325 2.8 32.4 1.0 C B:LEU327 3.6 38.5 1.0 O B:HOH764 3.7 53.6 1.0 C B:ASN325 3.8 38.2 1.0 O B:HOH714 3.8 41.2 1.0 O B:HOH652 4.1 37.1 1.0 N B:LEU327 4.3 37.6 1.0 CA B:ASN325 4.4 31.9 1.0 N B:ALA328 4.5 37.0 1.0 OD1 B:ASN325 4.5 38.3 1.0 CA B:ALA328 4.5 42.5 1.0 CA B:LEU327 4.5 35.2 1.0 O B:ILE324 4.6 34.2 1.0 C B:GLU326 4.6 40.0 1.0 N B:GLU326 4.7 33.4 1.0 OG1 B:THR333 4.7 40.7 1.0 C B:ALA328 4.7 46.2 1.0 O B:ALA328 4.8 49.9 1.0 CG B:ASN325 4.9 35.5 1.0 CA B:GLU326 4.9 38.2 1.0 O B:HOH760 4.9 48.5 1.0

Sodium binding site 4 out of 4 in the Wbbb D232N-Kdo Adduct


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Wbbb D232N-Kdo Adduct within 5.0Å range: probe atom residue distance (Å) B Occ B:Na504 b:52.4 occ:1.00 O B:HOH691 2.3 51.0 1.0 O B:LEU209 2.4 43.2 1.0 O B:HOH747 2.4 44.1 1.0 O B:ASN206 2.4 43.0 1.0 O B:HOH777 2.7 46.9 1.0 C B:LEU209 3.4 44.0 1.0 C B:ASN206 3.6 43.1 1.0 O B:HOH791 3.8 40.8 1.0 CB B:LEU209 4.0 40.2 1.0 CA B:LEU209 4.1 43.8 1.0 N B:LEU209 4.2 40.6 1.0 O B:TYR207 4.3 39.4 1.0 CA B:ASN206 4.3 41.9 1.0 N B:GLU210 4.4 45.9 1.0 C B:TYR207 4.5 44.8 1.0 N B:TYR207 4.6 43.0 1.0 OD1 B:ASN206 4.6 70.0 1.0 CA B:TYR207 4.7 42.5 1.0 CA B:GLU210 4.7 47.1 1.0 CB B:ASN206 4.7 46.5 1.0 O B:VAL211 4.7 45.8 1.0 C B:GLU210 4.8 43.6 1.0 C B:PHE208 4.9 38.6 1.0 N B:VAL211 5.0 42.6 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