Chlorine in PDB 7q3q: Crystal Structure of Sars-Cov-2 Rbd in Complex with the Neutralizing Nanobody Vhh-12

The structure of Crystal Structure of Sars-Cov-2 Rbd in Complex with the Neutralizing Nanobody Vhh-12, PDB code: 7q3q was solved by I.Fernandez, R.Pederzoli, F.A.Rey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.41 / 2.30
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	62.451, 62.451, 218.525, 90, 90, 90
R / Rfree (%)	18.5 / 22

The binding sites of Chlorine atom in the Crystal Structure of Sars-Cov-2 Rbd in Complex with the Neutralizing Nanobody Vhh-12 (pdb code 7q3q). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Sars-Cov-2 Rbd in Complex with the Neutralizing Nanobody Vhh-12, PDB code: 7q3q:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of Sars-Cov-2 Rbd in Complex with the Neutralizing Nanobody Vhh-12


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Sars-Cov-2 Rbd in Complex with the Neutralizing Nanobody Vhh-12 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl201 b:48.0 occ:1.00 O B:HOH303 3.4 41.1 1.0 N B:LYS56 3.4 47.5 1.0 CB B:ARG54 3.5 44.2 1.0 N B:PHE57 3.5 41.4 1.0 CD2 B:PHE57 3.6 42.4 1.0 NH1 B:ARG54 3.6 38.3 1.0 CD B:ARG54 3.7 38.9 1.0 CB B:LYS56 3.8 45.1 1.0 CD1 B:ILE106 3.8 31.8 1.0 OG1 B:THR35 3.8 46.7 1.0 N B:TRP55 3.9 43.5 1.0 CG B:ARG54 3.9 38.4 1.0 CD1 B:TRP55 4.0 46.6 1.0 CA B:LYS56 4.0 44.9 1.0 NE1 B:TRP55 4.1 41.0 1.0 C B:LYS56 4.2 45.2 1.0 CB B:PHE57 4.3 40.0 1.0 CA B:ARG54 4.3 43.4 1.0 CG B:PHE57 4.4 42.1 1.0 CA B:PHE57 4.5 45.0 1.0 CG B:TRP55 4.5 44.7 1.0 CE2 B:PHE57 4.5 42.4 1.0 C B:TRP55 4.5 40.1 1.0 C B:ARG54 4.5 41.9 1.0 CZ B:ARG54 4.6 44.4 1.0 NE B:ARG54 4.6 44.8 1.0 CE2 B:TRP55 4.6 37.5 1.0 CA B:TRP55 4.7 41.9 1.0 CG2 B:ILE106 4.7 36.9 1.0 CD2 B:TRP55 4.8 46.9 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of Sars-Cov-2 Rbd in Complex with the Neutralizing Nanobody Vhh-12


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Sars-Cov-2 Rbd in Complex with the Neutralizing Nanobody Vhh-12 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl202 b:61.4 occ:1.00 O B:HOH315 3.0 48.3 1.0 N B:GLY122 3.0 50.2 1.0 N B:CYS98 3.2 46.0 1.0 CA B:GLY120 3.4 47.9 1.0 C B:GLY120 3.4 57.0 1.0 N B:GLN121 3.4 52.7 1.0 CA B:GLY122 3.6 47.4 1.0 CA B:TYR97 3.7 45.3 1.0 O B:TYR96 3.9 45.5 1.0 CB B:CYS98 3.9 50.5 1.0 C B:TYR97 3.9 47.9 1.0 CB B:ALA8 4.0 52.8 1.0 C B:GLN121 4.0 61.0 1.0 O B:GLY120 4.1 48.8 1.0 CA B:CYS98 4.1 39.9 1.0 N B:GLY120 4.2 53.0 1.0 C B:GLY122 4.3 51.5 1.0 CA B:GLN121 4.3 60.1 1.0 O B:CYS98 4.3 49.9 1.0 CB B:TYR97 4.6 46.9 1.0 N B:TYR97 4.7 47.9 1.0 C B:TYR96 4.7 48.1 1.0 C B:CYS98 4.7 48.3 1.0 N B:THR123 4.7 51.9 1.0 CD2 B:TYR97 4.8 52.5 1.0 O B:GLY122 4.8 61.2 1.0 OG1 B:THR123 4.9 51.6 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of Sars-Cov-2 Rbd in Complex with the Neutralizing Nanobody Vhh-12


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Sars-Cov-2 Rbd in Complex with the Neutralizing Nanobody Vhh-12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl604 b:76.0 occ:1.00 N A:GLY496 3.2 51.2 1.0 O A:HOH715 3.3 51.6 1.0 CA A:GLY496 3.9 47.9 1.0 O A:GLY496 4.0 49.1 1.0 C A:TYR495 4.2 47.5 1.0 CA A:TYR495 4.2 43.0 1.0 C A:GLY496 4.3 51.8 1.0 CD1 A:TYR495 4.4 48.2 1.0 CB A:TYR495 4.8 40.3 1.0 CD A:ARG403 4.8 49.3 1.0 CD2 A:TYR505 4.9 70.9 1.0

I.Fernandez, F.A.Rey. Nanobodies Against Sars-Cov-2 Neutralize Variants of Concern and Explore Conformational Differences on the Spike Protein To Be Published.