Chlorine in PDB 7nx6: Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and EY6A Fabs

The structure of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and EY6A Fabs, PDB code: 7nx6 was solved by D.Zhou, J.Ren, D.Stuart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	105.85 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.391, 120.146, 211.706, 90, 90, 90
R / Rfree (%)	20.7 / 24.8

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 EY6A Fabs (pdb code 7nx6). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 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 EY6A Fabs, PDB code: 7nx6:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and EY6A 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 EY6A Fabs within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl301 b:63.6 occ:1.00 O H:GLY100 2.9 69.0 1.0 O H:HOH420 3.0 48.5 1.0 OH H:TYR32 3.3 51.5 1.0 O H:HOH419 3.4 50.7 1.0 NZ H:LYS98 3.6 47.8 1.0 C H:GLY100 3.9 66.3 1.0 CZ H:TYR32 4.1 45.9 1.0 CE1 H:TYR32 4.1 51.1 1.0 CE H:LYS102 4.2 58.0 1.0 CA H:GLY100 4.3 56.5 1.0 CE H:LYS98 4.5 38.5 1.0 OD2 H:ASP109 4.5 49.5 1.0 CG H:LYS102 4.6 60.2 1.0 O H:HOH406 4.9 47.6 1.0

Chlorine binding site 2 out of 7 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and EY6A 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 EY6A Fabs within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl302 b:56.0 occ:1.00 OG H:SER30 2.8 62.3 1.0 N H:SER30 3.5 43.9 1.0 N H:PHE29 3.7 46.3 1.0 CB H:SER30 3.7 40.5 1.0 CG2 H:THR28 3.8 47.5 1.0 C H:THR28 4.1 43.7 1.0 CA H:THR28 4.1 50.5 1.0 CA H:SER30 4.2 53.5 1.0 C H:PHE29 4.5 45.3 1.0 CA H:PHE29 4.5 42.0 1.0 CB H:THR28 4.6 54.0 1.0 OD1 H:ASN77 4.7 64.9 1.0 O H:THR28 4.8 50.8 1.0 CB H:PHE29 4.8 41.5 1.0 C H:SER30 5.0 52.0 1.0

Chlorine binding site 3 out of 7 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and EY6A 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 EY6A Fabs within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl707 b:78.2 occ:1.00 OG1 E:THR500 3.0 75.8 1.0 CB E:GLN498 3.3 54.1 1.0 CD E:PRO499 3.3 60.0 1.0 N E:THR500 3.6 61.7 1.0 N E:PRO499 3.7 60.7 1.0 C E:GLN498 3.9 55.8 1.0 CG E:PRO499 3.9 57.1 1.0 CB E:THR500 4.0 62.1 1.0 CA E:GLN498 4.0 47.0 1.0 CG2 E:THR500 4.2 65.9 1.0 O E:VAL445 4.2 71.7 1.0 CG E:GLN498 4.2 71.9 1.0 CA E:THR500 4.3 56.8 1.0 CD E:GLN498 4.5 88.5 1.0 C E:PRO499 4.5 61.2 1.0 O E:GLN498 4.5 61.2 1.0 CA E:PRO499 4.6 62.2 1.0 NE2 E:GLN498 4.9 79.2 1.0 CB E:PRO499 4.9 57.8 1.0 OE1 E:GLN498 4.9 71.3 1.0 C E:THR500 4.9 63.1 1.0 C E:VAL445 5.0 65.8 1.0

Chlorine binding site 4 out of 7 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and EY6A 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 EY6A Fabs within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl708 b:57.5 occ:1.00 O E:HOH801 3.1 29.3 1.0 NZ E:LYS417 3.3 47.0 1.0 NH2 E:ARG403 3.3 39.0 1.0 O E:HOH832 3.5 46.7 1.0 CE1 B:TYR92 3.6 39.6 1.0 CD1 B:TYR92 3.8 43.4 1.0 CE E:LYS417 3.9 36.2 1.0 OH E:TYR453 3.9 46.5 1.0 O2 E:SO4706 3.9 58.7 1.0 CB A:SER101 4.1 44.5 1.0 CD E:LYS417 4.1 35.8 1.0 O B:HOH409 4.2 46.0 1.0 CZ E:ARG403 4.4 37.1 1.0 CE2 B:TYR33 4.4 46.0 1.0 OE2 E:GLU406 4.5 39.5 1.0 CZ B:TYR92 4.5 48.0 1.0 OG A:SER101 4.5 47.3 1.0 CZ E:TYR453 4.6 40.8 1.0 NE E:ARG403 4.8 37.4 1.0 CG B:TYR92 4.8 41.3 1.0 CE2 E:TYR453 4.8 31.2 1.0 OH B:TYR33 4.8 55.2 1.0 CD A:PRO102 4.9 45.4 1.0

Chlorine binding site 5 out of 7 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and EY6A 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 Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and EY6A Fabs within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl301 b:51.1 occ:1.00 N A:VAL156 3.3 47.4 1.0 OH A:TYR151 3.3 42.9 1.0 CA A:PRO155 3.4 43.3 1.0 CG A:GLU154 3.6 46.1 1.0 CB A:ALA174 3.7 46.9 1.0 C A:PRO155 3.8 47.8 1.0 CB A:GLU154 3.8 45.8 1.0 CE2 A:TYR151 3.9 47.5 1.0 CB A:PRO155 4.0 48.5 1.0 CD2 A:LEU184 4.0 47.5 1.0 CD A:GLU154 4.0 54.8 1.0 CZ A:TYR151 4.1 43.8 1.0 CA A:GLU154 4.2 40.0 1.0 OE2 A:GLU154 4.2 66.5 1.0 O A:VAL156 4.2 50.8 1.0 CG2 A:VAL156 4.4 40.1 1.0 CA A:VAL156 4.4 51.8 1.0 N A:PRO155 4.6 42.2 1.0 OE1 A:GLU154 4.7 72.6 1.0 CB A:VAL156 4.8 47.3 1.0 C A:VAL156 4.8 51.0 1.0 CG1 A:VAL156 4.9 48.2 1.0 N A:ALA174 4.9 49.1 1.0 CA A:ALA174 4.9 42.1 1.0 C A:GLU154 4.9 42.6 1.0 O A:PRO155 5.0 53.0 1.0

Chlorine binding site 6 out of 7 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and EY6A 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 Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and EY6A Fabs within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl302 b:77.5 occ:1.00 N A:ALA87 2.8 56.6 1.0 CA A:GLY86 3.5 44.9 1.0 CB A:ALA87 3.5 45.6 1.0 C A:GLY86 3.6 50.5 1.0 CA A:ALA87 3.7 51.1 1.0 CB A:PRO14 4.7 52.5 1.0 O A:GLY86 4.7 53.9 1.0 N A:GLY86 4.9 48.3 1.0 C A:ALA87 5.0 48.5 1.0

Chlorine binding site 7 out of 7 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and EY6A Fabs


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-222 and EY6A Fabs within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl308 b:83.6 occ:1.00 O E:HOH844 2.8 60.8 1.0 OG B:SER32 3.4 54.5 1.0 N B:SER32 3.4 42.5 1.0 N B:SER31 3.4 51.2 1.0 CB B:PRO30 3.6 46.8 1.0 O E:HOH848 3.8 61.1 1.0 CB B:SER32 3.8 50.8 1.0 O E:HOH865 3.9 49.3 1.0 OE1 E:GLN498 3.9 71.3 1.0 C B:PRO30 4.0 53.0 1.0 CA B:PRO30 4.1 52.2 1.0 CA B:SER31 4.2 47.7 1.0 O E:GLY496 4.2 54.4 1.0 CA B:SER32 4.2 42.7 1.0 C B:SER31 4.2 43.2 1.0 CB B:SER31 4.3 45.4 1.0 CD E:GLN498 4.4 88.5 1.0 OH E:TYR449 4.4 71.8 1.0 O B:HOH457 4.7 56.4 1.0 O E:TYR495 4.8 56.4 1.0 NE2 E:GLN498 4.8 79.2 1.0 CA E:GLY496 4.9 58.7 1.0 CG B:PRO30 5.0 52.5 1.0 O B:PRO30 5.0 52.2 1.0 C E:GLY496 5.0 53.2 1.0

W.Dejnirattisai, D.Zhou, P.Supasa, C.Liu, A.J.Mentzer, H.M.Ginn, Y.Zhao, H.M.Duyvesteyn, A.Tuekprakhon, R.Nutalai, B.Wang, G.C.Paesen, C.Lopez-Camacho, J.Slon-Campos, T.S.Walter, D.Skelly, F.G.Naveca, V.Nascimento, F.Nascimento, P.C.Resende, A.Pauvolid-Correa, M.M.Siqueira, C.Dold, R.Levin, T.Dong, A.J.Pollard, J.C.Knight, D.Crook, T.Lambe, E.Clutterbuck, S.Bibi, A.Flaxman, M.Bittaye, S.Belij-Rammerstorfer, S.Gilbert, M.W.Carroll, P.Klenerman, E.Barnes, S.J.Dunachie, N.G.Paterson, M.A.Williams, D.R.Hall, R.J.Hulswit, T.A.Bowden, E.E.Fry, J.Mongkolsapaya, J.Ren, D.I.Stuart, G.R.Screaton. Antibody Evasion By the P.1 Strain of Sars-Cov-2 Cell(Cambridge,Mass.) 2021.
ISSN: ISSN 0092-8674
DOI: 10.1016/J.CELL.2021.03.055