Chlorine in PDB 8cwi: Fab Arm of Antibody 10G4 Bound to Cov-2 Receptor Binding Domain (Rbd)

The structure of Fab Arm of Antibody 10G4 Bound to Cov-2 Receptor Binding Domain (Rbd), PDB code: 8cwi was solved by D.B.Langley, D.Christ, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.56 / 1.87
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.691, 88.639, 81.398, 90, 95.03, 90
R / Rfree (%)	17 / 20.5

The structure of Fab Arm of Antibody 10G4 Bound to Cov-2 Receptor Binding Domain (Rbd) also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Chlorine atom in the Fab Arm of Antibody 10G4 Bound to Cov-2 Receptor Binding Domain (Rbd) (pdb code 8cwi). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Fab Arm of Antibody 10G4 Bound to Cov-2 Receptor Binding Domain (Rbd), PDB code: 8cwi:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Fab Arm of Antibody 10G4 Bound to Cov-2 Receptor Binding Domain (Rbd)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Fab Arm of Antibody 10G4 Bound to Cov-2 Receptor Binding Domain (Rbd) within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl301 b:27.7 occ:1.00 O H:HOH496 3.0 33.9 1.0 O H:HOH467 3.1 31.4 1.0 N L:PHE98 3.2 24.3 1.0 O L:HOH582 3.3 48.5 1.0 N H:TRP47 3.3 22.9 1.0 CA L:THR97 3.7 23.6 1.0 CA H:GLU46 3.8 24.8 1.0 CD2 L:PHE98 4.0 25.1 1.0 O L:HOH484 4.0 31.8 1.0 C L:THR97 4.0 24.3 1.0 C H:GLU46 4.0 22.8 1.0 CB L:PHE98 4.0 20.2 1.0 CA L:PHE98 4.2 21.8 1.0 CB H:TRP47 4.2 23.1 1.0 CB L:THR97 4.3 25.1 1.0 CA H:TRP47 4.3 23.0 1.0 O L:TYR96 4.3 23.6 1.0 CG2 L:THR97 4.3 28.7 1.0 O H:LEU45 4.4 24.2 1.0 O L:HOH579 4.4 44.6 1.0 O L:PHE98 4.4 27.9 1.0 CB H:GLU46 4.4 28.8 1.0 CG L:PHE98 4.5 21.8 1.0 O H:TRP47 4.5 27.5 1.0 CG H:GLU46 4.7 38.9 1.0 C L:PHE98 4.8 25.1 1.0 N L:THR97 4.8 23.3 1.0 N H:GLU46 4.8 26.2 1.0 O H:HOH524 4.9 41.7 1.0 MG L:MG301 4.9 41.7 1.0 C H:TRP47 4.9 23.3 1.0

Chlorine binding site 2 out of 3 in the Fab Arm of Antibody 10G4 Bound to Cov-2 Receptor Binding Domain (Rbd)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Fab Arm of Antibody 10G4 Bound to Cov-2 Receptor Binding Domain (Rbd) within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl302 b:41.5 occ:1.00 N H:GLY122 3.2 25.4 1.0 NZ H:LYS121 3.4 36.6 1.0 CD H:LYS121 3.8 35.5 1.0 CA H:LYS121 4.0 26.5 1.0 CE H:LYS121 4.0 38.3 1.0 CA H:GLY122 4.0 29.1 1.0 C H:LYS121 4.1 26.5 1.0 CB H:SER207 4.4 34.0 1.0 CG H:LYS121 4.6 28.4 1.0 O H:GLY122 4.7 25.5 1.0 CB H:LYS121 4.9 26.6 1.0 O H:THR120 4.9 27.0 1.0 C H:GLY122 4.9 28.5 1.0 N H:LYS121 5.0 25.8 1.0

Chlorine binding site 3 out of 3 in the Fab Arm of Antibody 10G4 Bound to Cov-2 Receptor Binding Domain (Rbd)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Fab Arm of Antibody 10G4 Bound to Cov-2 Receptor Binding Domain (Rbd) within 5.0Å range: probe atom residue distance (Å) B Occ L:Cl302 b:52.7 occ:1.00 O L:HOH558 3.0 52.4 1.0 NE L:ARG26 3.1 56.6 1.0 N L:GLN3 3.3 33.8 1.0 NE2 L:GLN27 3.3 54.8 1.0 CB L:ARG26 3.4 44.4 1.0 O L:ASN1 3.5 45.1 1.0 CG L:ARG26 3.6 47.9 1.0 CA L:ILE2 3.8 34.4 1.0 CG L:GLN27 3.9 47.4 1.0 NH1 L:ARG26 3.9 58.3 1.0 CD L:ARG26 4.0 53.0 1.0 CZ L:ARG26 4.0 58.0 1.0 CB L:GLN3 4.0 34.2 1.0 C L:ILE2 4.0 34.5 1.0 CD L:GLN27 4.1 54.5 1.0 CA L:GLN3 4.3 30.9 1.0 C L:ASN1 4.4 43.3 1.0 CA L:ARG26 4.5 40.6 1.0 N L:ILE2 4.6 35.6 1.0 C L:ARG26 4.6 42.9 1.0 N L:GLN27 4.6 37.6 1.0 CG2 L:ILE2 4.7 32.3 1.0 CB L:ILE2 4.7 32.9 1.0 O L:GLN3 5.0 32.2 1.0

D.B.Langley, D.Christ. Neutralization of Cov-2 Omicron Lineages By Affinity-Matured Class 5 Antibodies To Be Published.