Chlorine in PDB 7q3r: Crystal Structure of Sars-Cov-2 Rbd in Complex with the Neutralizing Nanobodies Vhh-F04 and Vhh-G09

The structure of Crystal Structure of Sars-Cov-2 Rbd in Complex with the Neutralizing Nanobodies Vhh-F04 and Vhh-G09, PDB code: 7q3r 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)	45.91 / 1.92
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	180.578, 180.578, 48.025, 90, 90, 120
R / Rfree (%)	18.2 / 20.9

The binding sites of Chlorine atom in the Crystal Structure of Sars-Cov-2 Rbd in Complex with the Neutralizing Nanobodies Vhh-F04 and Vhh-G09 (pdb code 7q3r). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of Sars-Cov-2 Rbd in Complex with the Neutralizing Nanobodies Vhh-F04 and Vhh-G09, PDB code: 7q3r:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in the Crystal Structure of Sars-Cov-2 Rbd in Complex with the Neutralizing Nanobodies Vhh-F04 and Vhh-G09


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 Nanobodies Vhh-F04 and Vhh-G09 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl601 b:55.8 occ:1.00 N A:GLY504 3.0 41.5 1.0 CA A:GLY504 3.5 41.7 1.0 C A:GLY502 3.6 45.2 1.0 N A:VAL503 3.7 42.7 1.0 CA A:GLY502 3.8 40.4 1.0 CD2 A:TYR505 3.9 51.2 1.0 O A:HOH736 4.0 63.1 1.0 O A:GLY502 4.0 36.6 1.0 C A:VAL503 4.2 44.4 1.0 N A:TYR505 4.2 39.2 1.0 C A:GLY504 4.3 46.4 1.0 CE2 A:TYR505 4.3 56.1 1.0 O A:HOH837 4.4 58.7 1.0 O A:HOH848 4.5 55.7 1.0 CA A:VAL503 4.5 43.3 1.0 CG1 A:VAL503 4.7 50.5 1.0 N A:GLY502 4.8 37.0 1.0

Chlorine binding site 2 out of 5 in the Crystal Structure of Sars-Cov-2 Rbd in Complex with the Neutralizing Nanobodies Vhh-F04 and Vhh-G09


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 Nanobodies Vhh-F04 and Vhh-G09 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl602 b:56.9 occ:1.00 N A:SER383 3.3 46.0 1.0 CA A:VAL382 3.8 42.5 1.0 CG2 A:VAL382 3.9 51.2 1.0 CD1 A:LEU390 4.0 49.7 1.0 C A:VAL382 4.0 45.8 1.0 CD A:LYS386 4.1 69.1 1.0 CB A:SER383 4.1 53.2 1.0 OG A:SER383 4.1 58.0 1.0 CA A:SER383 4.2 44.4 1.0 NZ A:LYS386 4.3 85.0 1.0 CB A:LYS386 4.4 47.4 1.0 CB A:VAL382 4.4 45.6 1.0 CE A:LYS386 4.6 82.1 1.0 O A:SER383 4.6 51.4 1.0 O A:GLY381 4.7 48.0 1.0 CG A:LYS386 4.7 61.9 1.0 C A:SER383 4.9 47.8 1.0 N A:VAL382 4.9 42.0 1.0

Chlorine binding site 3 out of 5 in the Crystal Structure of Sars-Cov-2 Rbd in Complex with the Neutralizing Nanobodies Vhh-F04 and Vhh-G09


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 Nanobodies Vhh-F04 and Vhh-G09 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl603 b:68.8 occ:1.00 OG A:SER459 3.0 40.5 1.0 N A:SER459 3.7 35.2 1.0 NH1 A:ARG457 3.8 35.3 1.0 CB A:LYS458 3.8 40.5 1.0 O A:HOH783 3.8 41.4 1.0 CB A:SER459 3.9 39.7 1.0 CZ A:ARG457 3.9 40.9 1.0 NH2 A:ARG457 4.0 38.1 1.0 C A:LYS458 4.3 43.6 1.0 CA A:SER459 4.3 39.3 1.0 N A:LYS458 4.3 35.8 1.0 CA A:LYS458 4.4 40.4 1.0 CG A:ARG457 4.4 34.3 1.0 CE A:LYS458 4.4 56.2 1.0 O A:HOH735 4.5 63.9 1.0 NE A:ARG457 4.5 34.5 1.0 O A:SER459 4.6 39.0 1.0 CG A:LYS458 4.8 51.3 1.0 C A:SER459 4.8 40.3 1.0

Chlorine binding site 4 out of 5 in the Crystal Structure of Sars-Cov-2 Rbd in Complex with the Neutralizing Nanobodies Vhh-F04 and Vhh-G09


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Sars-Cov-2 Rbd in Complex with the Neutralizing Nanobodies Vhh-F04 and Vhh-G09 within 5.0Å range: probe atom residue distance (Å) B Occ F:Cl201 b:64.5 occ:1.00 N F:GLY66 3.0 55.9 1.0 O F:HOH304 3.2 54.5 1.0 O F:HOH318 3.2 59.8 1.0 O A:HOH838 3.4 56.8 1.0 CB F:TYR60 3.6 46.3 1.0 CA F:GLY66 3.7 58.3 1.0 N F:LYS65 3.8 58.4 1.0 CG F:TYR60 3.9 47.8 1.0 CD2 F:TYR60 3.9 49.5 1.0 CG1 F:VAL64 3.9 47.5 1.0 CB F:VAL64 3.9 49.9 1.0 C F:LYS65 4.0 59.6 1.0 CA F:LYS65 4.2 54.4 1.0 C F:VAL64 4.3 56.4 1.0 O F:HOH360 4.7 67.9 1.0 CA F:VAL64 4.7 53.7 1.0 CD1 F:TYR60 4.7 43.3 1.0 O F:HOH356 4.7 65.4 1.0 C F:GLY66 4.8 59.5 1.0 O F:ALA61 4.8 49.5 1.0 CE2 F:TYR60 4.8 47.1 1.0 O F:VAL64 5.0 55.7 1.0

Chlorine binding site 5 out of 5 in the Crystal Structure of Sars-Cov-2 Rbd in Complex with the Neutralizing Nanobodies Vhh-F04 and Vhh-G09


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Sars-Cov-2 Rbd in Complex with the Neutralizing Nanobodies Vhh-F04 and Vhh-G09 within 5.0Å range: probe atom residue distance (Å) B Occ F:Cl202 b:64.6 occ:1.00 N F:ASN74 3.1 47.6 1.0 O F:HOH350 3.2 54.6 1.0 CB F:ASN74 3.7 53.5 1.0 O F:ARG72 3.8 46.9 1.0 CG F:ASN74 3.8 58.1 1.0 CA F:ASP73 3.9 51.4 1.0 C F:ASP73 4.0 50.2 1.0 CA F:ASN74 4.0 49.7 1.0 ND2 F:ASN74 4.1 45.5 1.0 OD1 F:ASN74 4.2 48.6 1.0 C F:ARG72 4.3 53.8 1.0 N F:ASP73 4.4 51.9 1.0 CG F:ARG72 4.4 46.0 1.0 OD1 F:ASP73 4.8 57.3 1.0 O F:SER54 5.0 52.0 1.0 N F:ALA75 5.0 47.2 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.