Chlorine 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:

Sodium

(Na)

3 atoms

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

Chlorine binding site 1 out of 2 in the Wbbb D232C Kdo Adduct


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Wbbb D232C Kdo Adduct within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl503 b:52.5 occ:1.00 HH11 A:ARG168 2.7 48.4 1.0 HD1 A:TYR377 2.9 39.8 1.0 HD3 A:ARG168 3.0 39.5 1.0 HB3 A:ARG168 3.1 37.0 1.0 HG2 A:ARG168 3.2 43.3 1.0 O A:HOH655 3.5 34.3 1.0 NH1 A:ARG168 3.6 40.3 1.0 HA A:TYR377 3.7 47.0 1.0 HE1 A:PHE376 3.7 54.1 1.0 CG A:ARG168 3.7 36.1 1.0 CD1 A:TYR377 3.8 33.1 1.0 CD A:ARG168 3.8 32.9 1.0 CB A:ARG168 3.9 30.8 1.0 HE1 A:TYR377 3.9 43.4 1.0 HH12 A:ARG168 4.0 48.4 1.0 O A:HOH739 4.2 37.8 1.0 HD1 A:PHE376 4.2 45.2 1.0 CE1 A:TYR377 4.3 36.1 1.0 HA A:ARG168 4.3 41.6 1.0 CE1 A:PHE376 4.4 45.1 1.0 HD2 A:ARG168 4.5 39.5 1.0 CZ A:ARG168 4.5 42.7 1.0 NE A:ARG168 4.5 33.8 1.0 HB2 A:ARG168 4.6 37.0 1.0 CA A:TYR377 4.6 39.1 1.0 HG3 A:ARG168 4.6 43.3 1.0 CD1 A:PHE376 4.7 37.7 1.0 CA A:ARG168 4.7 34.7 1.0 CG A:TYR377 4.9 35.9 1.0 H A:ASN169 4.9 31.3 1.0 HB3 A:TYR377 5.0 42.9 1.0 O A:TYR377 5.0 42.0 1.0

Chlorine binding site 2 out of 2 in the Wbbb D232C Kdo Adduct


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Wbbb D232C Kdo Adduct within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl503 b:58.9 occ:1.00 HB3 B:ARG168 3.0 43.2 1.0 HH11 B:ARG168 3.0 51.0 1.0 HD3 B:ARG168 3.2 48.1 1.0 O B:HOH653 3.3 40.6 1.0 HD1 B:TYR377 3.4 45.2 1.0 HG2 B:ARG168 3.5 52.1 1.0 HE1 B:PHE376 3.5 60.2 1.0 CB B:ARG168 3.8 36.0 1.0 NH1 B:ARG168 3.8 42.5 1.0 CG B:ARG168 3.9 43.4 1.0 CD B:ARG168 4.0 40.1 1.0 HE1 B:TYR377 4.1 48.9 1.0 HA B:ARG168 4.1 50.0 1.0 CD1 B:TYR377 4.2 37.7 1.0 HA B:TYR377 4.2 58.1 1.0 HH12 B:ARG168 4.2 51.0 1.0 CE1 B:PHE376 4.4 50.2 1.0 H B:ASN169 4.5 42.1 1.0 CA B:ARG168 4.5 41.7 1.0 HB2 B:ARG168 4.5 43.2 1.0 CE1 B:TYR377 4.5 40.7 1.0 HD1 B:PHE376 4.5 57.0 1.0 HD2 B:ARG168 4.6 48.1 1.0 CZ B:ARG168 4.8 45.6 1.0 NE B:ARG168 4.8 41.5 1.0 HG3 B:ARG168 4.9 52.1 1.0 OE2 B:GLU210 4.9 58.2 1.0 CD1 B:PHE376 4.9 47.5 1.0 O B:HOH722 5.0 41.2 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