Chlorine in PDB 7orb: Crystal Structure of the L452R Mutant Receptor Binding Domain of Sars- Cov-2 Spike Glycoprotein in Complex with Covox-75 and Covox-253 Fabs

The structure of Crystal Structure of the L452R Mutant Receptor Binding Domain of Sars- Cov-2 Spike Glycoprotein in Complex with Covox-75 and Covox-253 Fabs, PDB code: 7orb 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)	73.67 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	93.239, 149.425, 115.04, 90, 92.03, 90
R / Rfree (%)	21.3 / 25.1

The binding sites of Chlorine atom in the Crystal Structure of the L452R Mutant Receptor Binding Domain of Sars- Cov-2 Spike Glycoprotein in Complex with Covox-75 and Covox-253 Fabs (pdb code 7orb). 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 L452R Mutant Receptor Binding Domain of Sars- Cov-2 Spike Glycoprotein in Complex with Covox-75 and Covox-253 Fabs, PDB code: 7orb:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of the L452R Mutant Receptor Binding Domain of Sars- Cov-2 Spike Glycoprotein in Complex with Covox-75 and Covox-253 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 L452R Mutant Receptor Binding Domain of Sars- Cov-2 Spike Glycoprotein in Complex with Covox-75 and Covox-253 Fabs within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl504 b:54.9 occ:1.00 NH1 H:ARG44 3.2 59.0 1.0 N H:TRP47 3.3 55.2 1.0 N L:PHE99 3.4 45.2 1.0 NH2 H:ARG44 3.7 53.4 1.0 CB H:TRP47 3.8 48.9 1.0 CA L:THR98 3.9 41.6 1.0 CZ H:ARG44 3.9 66.1 1.0 OE1 H:GLU46 4.0 86.0 1.0 O H:LEU45 4.1 47.5 1.0 CA H:GLU46 4.1 51.9 1.0 CA H:TRP47 4.1 49.0 1.0 CD2 L:PHE99 4.2 44.0 1.0 C H:GLU46 4.2 59.8 1.0 C L:THR98 4.2 48.0 1.0 CB L:PHE99 4.2 42.5 1.0 CA L:PHE99 4.3 43.7 1.0 CB L:THR98 4.3 38.7 1.0 CD H:GLU46 4.4 89.9 1.0 CG2 L:THR98 4.5 40.0 1.0 O H:TRP47 4.5 51.5 1.0 O L:PHE99 4.5 40.0 1.0 OE2 H:GLU46 4.7 92.3 1.0 CG L:PHE99 4.7 48.0 1.0 O L:TYR97 4.7 70.0 1.0 C H:TRP47 4.8 45.7 1.0 C H:LEU45 4.9 49.2 1.0 C L:PHE99 4.9 40.8 1.0 N H:GLU46 4.9 52.9 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of the L452R Mutant Receptor Binding Domain of Sars- Cov-2 Spike Glycoprotein in Complex with Covox-75 and Covox-253 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 L452R Mutant Receptor Binding Domain of Sars- Cov-2 Spike Glycoprotein in Complex with Covox-75 and Covox-253 Fabs within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl502 b:51.5 occ:1.00 O C:HOH601 3.0 43.8 1.0 N C:TRP47 3.1 55.1 1.0 NH1 C:ARG44 3.3 58.3 1.0 N D:PHE99 3.3 49.0 1.0 CB C:TRP47 3.8 42.9 1.0 CA C:GLU46 3.8 48.6 1.0 CA D:THR98 3.8 48.1 1.0 NH2 C:ARG44 3.8 66.8 1.0 C C:GLU46 3.9 56.6 1.0 O C:LEU45 4.0 48.4 1.0 CD1 D:PHE99 4.0 48.3 1.0 CA C:TRP47 4.0 41.9 1.0 CZ C:ARG44 4.0 68.1 1.0 C D:THR98 4.1 47.7 1.0 CB D:PHE99 4.1 39.2 1.0 CA D:PHE99 4.2 45.1 1.0 CB D:THR98 4.3 37.0 1.0 CG2 D:THR98 4.4 38.5 1.0 O C:TRP47 4.5 47.6 1.0 O D:PHE99 4.5 43.8 1.0 CG D:PHE99 4.5 44.3 1.0 CB C:GLU46 4.7 62.2 1.0 N C:GLU46 4.7 51.2 1.0 O D:TYR97 4.7 66.2 1.0 C C:LEU45 4.8 49.6 1.0 C C:TRP47 4.8 42.7 1.0 O D:HOH1312 4.8 37.0 1.0 C D:PHE99 4.8 47.5 1.0 N D:THR98 4.9 45.1 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of the L452R Mutant Receptor Binding Domain of Sars- Cov-2 Spike Glycoprotein in Complex with Covox-75 and Covox-253 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 L452R Mutant Receptor Binding Domain of Sars- Cov-2 Spike Glycoprotein in Complex with Covox-75 and Covox-253 Fabs within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl407 b:72.7 occ:1.00 O F:HOH437 2.5 52.8 1.0 ND1 E:HIS178 3.0 60.9 1.0 CE1 E:HIS178 3.4 56.3 1.0 OD1 F:ASP167 4.0 63.8 1.0 CB F:THR164 4.2 46.4 1.0 CG E:HIS178 4.3 54.9 1.0 CG2 F:THR164 4.3 62.4 1.0 O E:VAL177 4.5 50.7 1.0 OG1 F:THR164 4.5 51.0 1.0 NE2 E:HIS178 4.7 54.7 1.0 CA E:HIS178 4.8 44.9 1.0 O F:GLU165 4.8 59.8 1.0 CB E:HIS178 4.9 50.9 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of the L452R Mutant Receptor Binding Domain of Sars- Cov-2 Spike Glycoprotein in Complex with Covox-75 and Covox-253 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 L452R Mutant Receptor Binding Domain of Sars- Cov-2 Spike Glycoprotein in Complex with Covox-75 and Covox-253 Fabs within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl408 b:76.3 occ:1.00 N E:VAL166 3.4 46.0 1.0 O E:HOH514 3.5 49.2 1.0 CA E:THR165 3.8 54.1 1.0 O E:HOH556 3.9 57.0 1.0 O E:VAL166 3.9 34.3 1.0 O E:VAL164 4.0 46.2 1.0 O E:HOH501 4.1 54.9 1.0 C E:THR165 4.1 49.9 1.0 CG2 E:THR179 4.4 54.0 1.0 O6 E:BTB404 4.4 70.2 1.0 CA E:VAL166 4.4 39.0 1.0 CB E:THR165 4.5 48.3 1.0 C E:VAL166 4.6 41.9 1.0 O E:HOH531 4.6 43.9 1.0 CB E:VAL166 4.6 38.6 1.0 C7 E:BTB404 4.7 66.2 1.0 N E:BTB404 4.8 82.8 1.0 N E:THR165 4.8 50.9 1.0 C E:VAL164 4.8 49.5 1.0 CB E:THR179 4.9 42.0 1.0 C6 E:BTB404 5.0 77.7 1.0 CG2 E:VAL166 5.0 38.1 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