Chlorine in PDB 7or9: Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and Covox-278 Fabs

The structure of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and Covox-278 Fabs, PDB code: 7or9 was solved by D.Zhou, J.Ren, D.I.Stuart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.23 / 2.34
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.73, 114.47, 177.93, 90, 90, 90
R / Rfree (%)	19.4 / 23

The binding sites of Chlorine atom in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and Covox-278 Fabs (pdb code 7or9). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and Covox-278 Fabs, PDB code: 7or9:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and Covox-278 Fabs


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 the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and Covox-278 Fabs within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl902 b:80.8 occ:1.00 N E:THR430 3.4 65.0 1.0 O E:THR430 3.7 66.4 1.0 CD1 E:PHE429 4.0 62.8 1.0 CA E:THR430 4.2 63.9 1.0 CB E:THR430 4.2 63.3 1.0 CA E:PHE429 4.2 61.4 1.0 C E:THR430 4.3 68.2 1.0 C E:PHE429 4.3 61.0 1.0 CE2 E:PHE464 4.5 49.6 1.0 CE1 E:PHE429 4.5 60.2 1.0 O E:ASP428 4.6 60.4 1.0 CB E:SER514 4.6 45.9 1.0 CZ E:PHE464 4.7 51.6 1.0 OG1 E:THR430 4.8 69.8 1.0 CG E:PHE429 4.8 60.7 1.0 CG E:PRO426 4.9 48.2 1.0 N E:PHE515 4.9 61.8 1.0 OG E:SER514 5.0 57.1 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and Covox-278 Fabs


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 the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and Covox-278 Fabs within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl903 b:67.1 occ:1.00 O E:HOH1019 3.0 47.6 1.0 N E:LYS417 3.3 43.2 1.0 NE2 E:GLN409 3.4 44.4 1.0 OH B:TYR92 3.7 59.4 1.0 O B:HOH413 3.7 59.4 1.0 CG E:LYS417 3.8 50.1 1.0 CB E:LYS417 3.8 40.9 1.0 CD E:LYS417 3.8 55.7 1.0 OH A:TYR52 4.0 52.2 1.0 CE E:LYS417 4.1 63.2 1.0 CA E:LYS417 4.2 41.1 1.0 CA E:GLY416 4.2 46.2 1.0 C E:GLY416 4.2 43.9 1.0 NZ E:LYS417 4.3 75.0 1.0 CD E:GLN409 4.4 50.5 1.0 OE1 E:GLN409 4.5 49.0 1.0 O E:HOH1016 4.7 44.1 1.0 CZ B:TYR92 4.7 55.8 1.0 CE1 B:TYR92 4.8 50.1 1.0 N E:ILE418 4.9 42.7 1.0 OE2 E:GLU406 5.0 55.4 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and Covox-278 Fabs


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 the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and Covox-278 Fabs within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl301 b:59.0 occ:1.00 OH A:TYR151 3.0 52.4 1.0 N A:VAL156 3.2 60.9 1.0 CA A:PRO155 3.5 49.0 1.0 CG A:GLU154 3.5 55.5 1.0 C A:PRO155 3.8 58.3 1.0 CB A:ALA174 3.8 57.4 1.0 CE2 A:TYR151 3.8 45.9 1.0 CZ A:TYR151 3.9 48.6 1.0 CB A:GLU154 4.0 54.8 1.0 CB A:PRO155 4.1 58.5 1.0 CD2 A:LEU184 4.1 47.3 1.0 CD A:GLU154 4.1 60.6 1.0 O A:VAL156 4.2 65.0 1.0 CA A:VAL156 4.2 51.4 1.0 CA A:GLU154 4.3 49.9 1.0 OE2 A:GLU154 4.3 67.8 1.0 CB A:VAL156 4.3 56.9 1.0 N A:PRO155 4.7 56.5 1.0 C A:VAL156 4.7 58.1 1.0 OE1 A:GLU154 4.9 75.4 1.0 O A:PRO155 4.9 64.0 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and Covox-278 Fabs


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 the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and Covox-278 Fabs within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl302 b:83.7 occ:1.00 NH1 B:ARG62 3.1 79.2 1.0 CG B:ARG62 3.8 72.2 1.0 N B:ARG62 3.8 82.2 1.0 CB B:PRO60 3.8 71.1 1.0 CB B:ARG62 3.9 78.7 1.0 CD B:ARG62 4.0 70.0 1.0 N B:ASP61 4.0 79.2 1.0 CZ B:ARG62 4.2 83.1 1.0 NH1 B:ARG78 4.3 100.9 1.0 OE2 B:GLU80 4.4 84.3 1.0 CA B:ARG62 4.5 72.6 1.0 NE B:ARG62 4.6 78.4 1.0 CA B:PRO60 4.6 71.3 1.0 C B:PRO60 4.6 72.9 1.0 C B:ASP61 4.7 81.0 1.0 CA B:ASP61 4.7 76.0 1.0 CB B:ASP61 4.7 80.5 1.0

C.Liu, H.M.Ginn, W.Dejnirattisai, P.Supasa, B.Wang, A.Tuekprakhon, R.Nutalai, D.Zhou, A.J.Mentzer, Y.Zhao, H.M.Duyvesteyn, C.Lopez-Camacho, J.Slon-Campos, T.S.Walter, D.Skelly, S.A.Johnson, T.G.Ritter, C.Mason, F.G.Naveca, V.Nascimento, F.Nascimento, P.C.Resende, A.Pauvolid-Correa, M.M.Siqueira, C.Dold, N.Temperton, T.Dong, A.J.Pollard, J.C.Knight, D.Crook, T.Lambe, E.Clutterbuck, S.Bibi, A.Flaxman, M.Bittaye, S.Belij-Rammerstorfer, S.C.Gilbert, T.Malik, M.W.Carroll, P.Klenerman, E.Barnes, S.J.Dunachie, V.Baillie, N.Serafin, Z.Ditse, N.G.Paterson, M.A.Williams, D.R.Hall, S.Madhi, M.C.Nunes, P.Goulder, E.E.Fry, J.Mongkolsapaya, J.Ren, D.I.Stuart, G.R.Screaton. Reduced Neutralization of Sars-Cov-2 B.1.617 By Vaccine and Convalescent Serum Cell 2021.
DOI: 10.1016/J.CELL.2021.06.020