Sodium in PDB 8csd: Wbbb D232C Kdo Adduct

The structure of Wbbb D232C Kdo Adduct, PDB code: 8csd 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)	47.49 / 1.95
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	93.01, 156.73, 118.02, 90, 90, 90
R / Rfree (%)	16.2 / 19.9

The structure of Wbbb D232C Kdo Adduct also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

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

Sodium binding site 1 out of 3 in the Wbbb D232C 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 D232C Kdo Adduct within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:42.8 occ:1.00 O A:HOH751 2.2 49.2 1.0 O A:HOH674 2.2 54.1 1.0 O A:LEU209 2.3 33.1 1.0 O A:ASN206 2.5 32.5 1.0 OE1 A:GLU403 3.0 59.5 1.0 O A:TYR207 3.1 29.2 1.0 C A:LEU209 3.5 33.6 1.0 HA A:TYR207 3.5 37.1 1.0 C A:TYR207 3.5 37.6 1.0 C A:ASN206 3.7 35.2 1.0 HB3 A:LEU209 3.9 47.6 1.0 CA A:TYR207 4.0 30.9 1.0 H A:LEU209 4.0 37.7 1.0 N A:LEU209 4.0 31.4 1.0 CD A:GLU403 4.0 70.2 1.0 HH21 A:ARG168 4.0 47.8 1.0 HA A:GLU210 4.1 41.6 1.0 CA A:LEU209 4.2 32.6 1.0 N A:TYR207 4.3 31.4 1.0 N A:PHE208 4.3 29.1 1.0 C A:PHE208 4.4 28.0 1.0 HE A:ARG168 4.4 40.5 1.0 OE2 A:GLU403 4.5 76.8 1.0 OE2 A:GLU210 4.5 48.9 1.0 N A:GLU210 4.5 30.2 1.0 CB A:LEU209 4.6 39.7 1.0 OD1 A:ASN206 4.6 54.3 1.0 NH2 A:ARG168 4.7 39.8 1.0 O A:HOH647 4.7 44.4 1.0 HA A:ASN206 4.8 36.7 1.0 CA A:PHE208 4.8 29.1 1.0 CA A:GLU210 4.8 34.7 1.0 HA A:PHE208 4.8 35.0 1.0 CA A:ASN206 4.9 30.6 1.0 H A:PHE208 4.9 34.9 1.0 O A:PHE208 4.9 29.0 1.0

Sodium binding site 2 out of 3 in the Wbbb D232C 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 D232C Kdo Adduct within 5.0Å range: probe atom residue distance (Å) B Occ B:Na504 b:37.0 occ:1.00 O B:LEU209 2.2 34.4 1.0 O B:ASN206 2.3 41.9 1.0 O B:HOH710 2.3 45.5 1.0 O B:HOH759 2.4 36.4 1.0 O B:HOH705 2.4 33.8 1.0 C B:LEU209 3.4 33.5 1.0 C B:ASN206 3.5 40.8 1.0 HB2 B:LEU209 3.6 42.7 1.0 O B:HOH764 3.7 34.7 1.0 HA B:GLU210 4.0 46.1 1.0 H B:LEU209 4.0 38.4 1.0 HA B:TYR207 4.1 42.5 1.0 HA B:ASN206 4.1 41.9 1.0 CA B:LEU209 4.1 38.4 1.0 N B:LEU209 4.1 32.0 1.0 CB B:LEU209 4.2 35.6 1.0 HB3 B:LEU209 4.2 42.7 1.0 O B:TYR207 4.2 35.0 1.0 HB3 B:ASN206 4.2 45.7 1.0 C B:TYR207 4.3 35.5 1.0 CA B:ASN206 4.3 34.9 1.0 N B:GLU210 4.4 33.7 1.0 OE2 B:GLU403 4.4 88.0 1.0 N B:TYR207 4.5 38.4 1.0 CA B:TYR207 4.5 35.4 1.0 CA B:GLU210 4.6 38.5 1.0 OD1 B:ASN206 4.6 58.9 1.0 OE1 B:GLU403 4.7 80.0 1.0 O B:VAL211 4.7 36.5 1.0 CB B:ASN206 4.8 38.1 1.0 C B:PHE208 4.8 34.1 1.0 C B:GLU210 4.8 37.9 1.0 H B:VAL211 4.9 42.1 1.0 N B:PHE208 4.9 33.3 1.0 N B:VAL211 4.9 35.1 1.0 CD B:GLU403 5.0 81.8 1.0

Sodium binding site 3 out of 3 in the Wbbb D232C 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 D232C Kdo Adduct within 5.0Å range: probe atom residue distance (Å) B Occ B:Na505 b:50.8 occ:1.00 O B:LEU327 2.3 36.5 1.0 O B:HOH693 2.4 32.5 1.0 O B:ASN325 2.6 32.0 1.0 C B:LEU327 3.5 37.3 1.0 C B:ASN325 3.6 34.1 1.0 HA B:ASN325 3.6 38.7 1.0 O B:HOH754 3.7 51.5 1.0 HA B:ALA328 3.8 48.3 1.0 O B:HOH618 4.1 41.4 1.0 CA B:ASN325 4.1 32.2 1.0 N B:LEU327 4.2 33.9 1.0 HG1 B:THR333 4.2 39.1 1.0 H B:LEU327 4.2 40.7 1.0 O B:ILE324 4.4 29.8 1.0 OD1 B:ASN325 4.4 32.7 1.0 C B:GLU326 4.4 32.3 1.0 CA B:LEU327 4.4 31.1 1.0 N B:ALA328 4.5 30.4 1.0 CA B:ALA328 4.5 40.3 1.0 N B:GLU326 4.5 28.3 1.0 HB2 B:LEU327 4.5 40.5 1.0 HA B:GLU326 4.6 35.5 1.0 OG1 B:THR333 4.7 32.6 1.0 CG B:ASN325 4.8 32.4 1.0 CA B:GLU326 4.8 29.6 1.0 O B:ALA328 4.8 38.4 1.0 C B:ALA328 4.8 39.4 1.0 O B:GLU326 4.9 34.5 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