Chlorine in PDB 7ora: Crystal Structure of the T478K Mutant Receptor Binding Domain of Sars- Cov-2 Spike Glycoprotein in Complex with Covox-45 and Covox-253 Fabs

The structure of Crystal Structure of the T478K Mutant Receptor Binding Domain of Sars- Cov-2 Spike Glycoprotein in Complex with Covox-45 and Covox-253 Fabs, PDB code: 7ora 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)	51.50 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.57, 182.385, 142.412, 90, 93.04, 90
R / Rfree (%)	20.4 / 24.5

The binding sites of Chlorine atom in the Crystal Structure of the T478K Mutant Receptor Binding Domain of Sars- Cov-2 Spike Glycoprotein in Complex with Covox-45 and Covox-253 Fabs (pdb code 7ora). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of the T478K Mutant Receptor Binding Domain of Sars- Cov-2 Spike Glycoprotein in Complex with Covox-45 and Covox-253 Fabs, PDB code: 7ora:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in the Crystal Structure of the T478K Mutant Receptor Binding Domain of Sars- Cov-2 Spike Glycoprotein in Complex with Covox-45 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 T478K Mutant Receptor Binding Domain of Sars- Cov-2 Spike Glycoprotein in Complex with Covox-45 and Covox-253 Fabs within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl301 b:62.1 occ:1.00 N A:ASN74 3.2 55.5 1.0 O A:ARG72 3.2 49.2 1.0 ND2 A:ASN74 3.7 52.4 1.0 CG A:ASN74 3.7 50.5 1.0 CA A:ASP73 3.8 52.8 1.0 CB A:ASN74 3.8 48.6 1.0 C A:ARG72 3.9 49.2 1.0 C A:ASP73 4.0 57.9 1.0 CG A:ARG72 4.0 46.0 1.0 CA A:ASN74 4.1 51.4 1.0 N A:ASP73 4.1 49.2 1.0 OD1 A:ASN74 4.3 45.0 1.0 O A:ASP54 4.6 45.5 1.0 CD A:ARG72 4.9 39.9 1.0 CB A:ARG72 5.0 44.0 1.0

Chlorine binding site 2 out of 6 in the Crystal Structure of the T478K Mutant Receptor Binding Domain of Sars- Cov-2 Spike Glycoprotein in Complex with Covox-45 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 T478K Mutant Receptor Binding Domain of Sars- Cov-2 Spike Glycoprotein in Complex with Covox-45 and Covox-253 Fabs within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl302 b:72.9 occ:1.00 O A:LYS58 3.6 37.2 1.0 N A:LYS58 3.6 41.1 1.0 CA A:ASN57 3.9 43.2 1.0 C A:ASN57 4.3 44.5 1.0 CB A:ASN57 4.3 45.7 1.0 OD1 A:ASN57 4.4 40.3 1.0 CG A:ASN57 4.4 44.6 1.0 O A:SER56 4.4 44.6 1.0 C A:LYS58 4.5 37.1 1.0 CZ A:TYR59 4.6 33.0 1.0 OH A:TYR59 4.6 45.0 1.0 CA A:LYS58 4.6 35.5 1.0 CE1 A:TYR59 4.7 36.6 1.0 ND2 A:ASN57 5.0 47.6 1.0

Chlorine binding site 3 out of 6 in the Crystal Structure of the T478K Mutant Receptor Binding Domain of Sars- Cov-2 Spike Glycoprotein in Complex with Covox-45 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 T478K Mutant Receptor Binding Domain of Sars- Cov-2 Spike Glycoprotein in Complex with Covox-45 and Covox-253 Fabs within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl301 b:61.2 occ:1.00 O B:HOH409 3.2 41.6 1.0 NE2 B:GLN37 3.4 48.3 1.0 OE1 B:GLN37 4.2 51.3 1.0 CD B:GLN37 4.2 46.6 1.0 CD2 B:LEU47 4.4 38.3 1.0 CD B:PRO59 4.5 47.1 1.0 CE2 B:PHE62 4.9 47.5 1.0

Chlorine binding site 4 out of 6 in the Crystal Structure of the T478K Mutant Receptor Binding Domain of Sars- Cov-2 Spike Glycoprotein in Complex with Covox-45 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 T478K Mutant Receptor Binding Domain of Sars- Cov-2 Spike Glycoprotein in Complex with Covox-45 and Covox-253 Fabs within 5.0Å range: probe atom residue distance (Å) B Occ F:Cl402 b:41.2 occ:1.00 N F:TRP47 3.2 41.8 1.0 NH1 F:ARG44 3.3 47.7 1.0 N G:PHE99 3.3 34.7 1.0 CA G:THR98 3.8 38.8 1.0 CA F:GLU46 3.8 35.1 1.0 CB F:TRP47 3.8 31.1 1.0 CD1 G:PHE99 3.9 35.1 1.0 C F:GLU46 4.0 35.0 1.0 O F:LEU45 4.0 50.1 1.0 C G:THR98 4.0 37.6 1.0 CB G:PHE99 4.0 35.0 1.0 NH2 F:ARG44 4.0 61.3 1.0 CA F:TRP47 4.1 37.6 1.0 CZ F:ARG44 4.1 53.5 1.0 CA G:PHE99 4.2 36.7 1.0 CB G:THR98 4.3 33.0 1.0 CG F:GLU46 4.4 54.3 1.0 CG2 G:THR98 4.5 37.7 1.0 CG G:PHE99 4.5 37.3 1.0 O G:TYR97 4.5 41.9 1.0 O G:PHE99 4.6 43.5 1.0 CB F:GLU46 4.6 40.7 1.0 O F:TRP47 4.7 43.8 1.0 N F:GLU46 4.7 43.5 1.0 C F:LEU45 4.8 43.4 1.0 C G:PHE99 4.8 46.1 1.0 O G:HOH314 4.9 26.0 1.0 N G:THR98 4.9 34.9 1.0 C F:TRP47 4.9 37.2 1.0 CE1 G:PHE99 5.0 34.1 1.0

Chlorine binding site 5 out of 6 in the Crystal Structure of the T478K Mutant Receptor Binding Domain of Sars- Cov-2 Spike Glycoprotein in Complex with Covox-45 and Covox-253 Fabs


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 the T478K Mutant Receptor Binding Domain of Sars- Cov-2 Spike Glycoprotein in Complex with Covox-45 and Covox-253 Fabs within 5.0Å range: probe atom residue distance (Å) B Occ F:Cl403 b:68.9 occ:1.00 ND1 F:HIS174 2.8 56.3 1.0 CE1 F:HIS174 3.4 54.8 1.0 O F:VAL173 3.6 53.2 1.0 OD1 G:ASP168 3.9 69.0 1.0 CG F:HIS174 3.9 51.7 1.0 CA F:HIS174 4.2 38.4 1.0 CB F:HIS174 4.4 46.2 1.0 NE2 F:HIS174 4.6 56.9 1.0 C F:VAL173 4.6 48.1 1.0 CB G:THR165 4.7 42.9 1.0 CG2 G:THR165 4.7 46.8 1.0 OG1 G:THR165 4.9 45.2 1.0 N F:HIS174 4.9 42.5 1.0 CD2 F:HIS174 4.9 43.5 1.0 CG G:ASP168 5.0 61.5 1.0

Chlorine binding site 6 out of 6 in the Crystal Structure of the T478K Mutant Receptor Binding Domain of Sars- Cov-2 Spike Glycoprotein in Complex with Covox-45 and Covox-253 Fabs


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of the T478K Mutant Receptor Binding Domain of Sars- Cov-2 Spike Glycoprotein in Complex with Covox-45 and Covox-253 Fabs within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl301 b:41.5 occ:1.00 O H:HOH415 3.0 27.6 1.0 N L:PHE99 3.3 27.8 1.0 N H:TRP47 3.4 33.9 1.0 NH1 H:ARG44 3.5 41.5 1.0 CA L:THR98 3.6 35.5 1.0 CB H:TRP47 3.9 31.2 1.0 C L:THR98 3.9 27.4 1.0 CB L:THR98 4.0 35.9 1.0 NH2 H:ARG44 4.1 56.6 1.0 CG2 L:THR98 4.1 36.2 1.0 CA H:GLU46 4.1 30.3 1.0 CD1 L:PHE99 4.2 26.6 1.0 CB L:PHE99 4.2 31.2 1.0 CA H:TRP47 4.2 34.4 1.0 CA L:PHE99 4.3 27.6 1.0 C H:GLU46 4.3 33.0 1.0 CZ H:ARG44 4.3 54.1 1.0 O H:LEU45 4.4 34.2 1.0 O L:PHE99 4.5 40.8 1.0 O L:TYR97 4.5 43.8 1.0 CG H:GLU46 4.7 41.3 1.0 O H:TRP47 4.7 35.5 1.0 N L:THR98 4.7 33.0 1.0 CG L:PHE99 4.7 29.2 1.0 C L:PHE99 4.8 32.6 1.0 CB H:GLU46 4.9 32.4 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