Chlorine in PDB 5dqd: Structure of S55-5 Fab in Complex with Lipid A Carbohydrate Backbone

The structure of Structure of S55-5 Fab in Complex with Lipid A Carbohydrate Backbone, PDB code: 5dqd was solved by O.Haji-Ghassemi, S.V.Evans, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.09 / 1.94
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.385, 64.793, 129.771, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 22.2

The binding sites of Chlorine atom in the Structure of S55-5 Fab in Complex with Lipid A Carbohydrate Backbone (pdb code 5dqd). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Structure of S55-5 Fab in Complex with Lipid A Carbohydrate Backbone, PDB code: 5dqd:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Structure of S55-5 Fab in Complex with Lipid A Carbohydrate Backbone


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of S55-5 Fab in Complex with Lipid A Carbohydrate Backbone within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl301 b:12.4 occ:1.00 O H:HOH468 3.0 20.9 1.0 O H:HOH434 3.1 29.1 1.0 N L:PHE98 3.2 8.8 1.0 N H:TRP47 3.3 10.9 1.0 CA L:THR97 3.6 10.2 1.0 CA H:GLU46 3.7 11.3 1.0 CD1 L:PHE98 3.8 11.6 1.0 C L:THR97 3.9 12.8 1.0 C H:GLU46 4.0 13.3 1.0 CB L:PHE98 4.1 10.1 1.0 O L:ARG96 4.1 11.9 1.0 O H:LEU45 4.1 15.4 1.0 CB L:THR97 4.2 14.0 1.0 CB H:TRP47 4.2 10.1 1.0 CA L:PHE98 4.2 11.0 1.0 CG H:GLU46 4.2 21.7 1.0 O L:HOH353 4.3 19.1 1.0 CA H:TRP47 4.4 13.8 1.0 CG2 L:THR97 4.4 14.7 1.0 CG L:PHE98 4.5 8.9 1.0 CB H:GLU46 4.5 15.6 1.0 O L:PHE98 4.6 8.3 1.0 O H:TRP47 4.7 11.8 1.0 N H:GLU46 4.7 14.0 1.0 N L:THR97 4.7 10.2 1.0 O H:HOH436 4.8 28.5 1.0 C H:LEU45 4.8 13.6 1.0 C L:ARG96 4.9 14.6 1.0 CE1 L:PHE98 4.9 11.3 1.0 C L:PHE98 4.9 12.6 1.0

Chlorine binding site 2 out of 2 in the Structure of S55-5 Fab in Complex with Lipid A Carbohydrate Backbone


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of S55-5 Fab in Complex with Lipid A Carbohydrate Backbone within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl302 b:15.2 occ:1.00 NE H:ARG100 3.7 14.2 1.0 CZ H:ARG100 3.7 12.8 1.0 CD H:ARG100 3.7 12.3 1.0 NH1 H:ARG100 3.8 10.6 1.0 NH2 H:ARG100 4.3 10.3 1.0 O H:HOH454 4.6 18.7 1.0 CG H:ARG100 4.6 18.3 1.0

O.Haji-Ghassemi, S.Muller-Loennies, T.Rodriguez, L.Brade, P.Kosma, H.Brade, S.V.Evans. Lipid A-Antibody Structures Reveal A Widely-Utilized Pocket Specific For Negatively Charged Groups Derived From Unrelated V-Genes J.Biol.Chem. 2015.
ISSN: ESSN 1083-351X