Chlorine in PDB 7q0i: Crystal Structure of the N-Terminal Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-43

The structure of Crystal Structure of the N-Terminal Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-43, PDB code: 7q0i 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)	143.10 / 2.39
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	117.83, 66.964, 143.238, 90, 92.54, 90
R / Rfree (%)	20.2 / 24.2

The binding sites of Chlorine atom in the Crystal Structure of the N-Terminal Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-43 (pdb code 7q0i). 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 N-Terminal Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-43, PDB code: 7q0i:
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 N-Terminal Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-43


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 N-Terminal Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-43 within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl301 b:62.1 occ:1.00 N H:GLY108 3.4 45.3 1.0 N H:TYR109 3.7 43.3 1.0 CA H:GLY108 4.0 41.7 1.0 N H:TYR110 4.0 46.2 1.0 CD2 H:TYR111 4.0 58.9 1.0 N H:PHE107 4.0 47.5 1.0 C H:GLY108 4.3 42.5 1.0 O H:PHE105 4.3 72.1 1.0 CD2 H:TYR110 4.4 53.4 1.0 C H:PHE107 4.5 40.6 1.0 CE2 H:TYR111 4.5 59.5 1.0 CA H:PHE107 4.6 41.8 1.0 C H:CYS106 4.6 56.2 1.0 CB H:TYR110 4.7 59.9 1.0 CB H:PHE107 4.7 50.5 1.0 O H:TYR100 4.7 66.0 1.0 CA H:TYR109 4.7 45.9 1.0 N H:TYR111 4.7 57.6 1.0 CB H:SER102 4.7 87.3 1.0 CA H:CYS106 4.7 58.2 1.0 C H:PHE105 4.8 60.0 1.0 CA H:TYR110 4.8 48.3 1.0 CB H:TYR109 4.9 44.9 1.0 N H:SER102 4.9 72.0 1.0 C H:TYR109 4.9 48.7 1.0 CG H:TYR110 5.0 55.7 1.0

Chlorine binding site 2 out of 6 in the Crystal Structure of the N-Terminal Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-43


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 N-Terminal Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-43 within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl302 b:61.7 occ:1.00 O H:HOH417 3.2 47.3 1.0 O H:VAL134 3.5 45.5 1.0 N H:VAL134 3.7 42.2 1.0 C H:VAL134 4.3 42.4 1.0 CA H:VAL134 4.4 37.1 1.0 CA H:SER133 4.6 41.5 1.0 CB H:VAL134 4.6 36.5 1.0 C H:SER133 4.6 38.3 1.0 CG1 H:VAL220 4.7 38.9 1.0

Chlorine binding site 3 out of 6 in the Crystal Structure of the N-Terminal Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-43


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 N-Terminal Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-43 within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl303 b:83.9 occ:1.00 OH H:TYR189 3.1 56.0 1.0 N H:GLU161 3.2 42.3 1.0 CB H:PRO160 3.5 33.8 1.0 CB H:GLU161 3.5 33.8 1.0 CZ H:TYR189 3.7 41.4 1.0 CE1 H:TYR189 3.8 43.2 1.0 CA H:GLU161 3.9 31.4 1.0 CG H:GLU161 4.0 34.8 1.0 OG1 H:THR123 4.1 40.2 1.0 O H:GLU161 4.1 43.6 1.0 C H:PRO160 4.1 41.5 1.0 CA H:PRO160 4.1 36.8 1.0 C H:GLU161 4.5 41.0 1.0 CE2 H:TYR189 4.7 31.7 1.0 CG H:PRO160 4.7 32.4 1.0 CE1 H:PHE159 4.7 36.4 1.0 CG2 H:THR123 4.8 31.8 1.0 CD1 H:TYR189 4.9 33.0 1.0

Chlorine binding site 4 out of 6 in the Crystal Structure of the N-Terminal Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-43


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 N-Terminal Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-43 within 5.0Å range: probe atom residue distance (Å) B Occ L:Cl403 b:69.0 occ:1.00 O L:HOH527 2.8 42.7 1.0 N L:GLY40 3.0 57.5 1.0 CA L:GLY40 3.5 46.9 1.0 NE2 L:GLN37 3.9 44.2 1.0 N L:GLN41 4.0 72.3 1.0 O L:LYS38 4.1 60.5 1.0 C L:PRO39 4.1 54.0 1.0 C L:GLY40 4.2 59.0 1.0 O L:GLN41 4.3 51.1 1.0 CD L:GLN37 4.3 42.2 1.0 CA L:PRO39 4.3 53.2 1.0 CG L:GLN37 4.5 39.4 1.0 OE1 L:GLN37 4.9 46.3 1.0

Chlorine binding site 5 out of 6 in the Crystal Structure of the N-Terminal Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-43


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 N-Terminal Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-43 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl302 b:68.4 occ:1.00 N A:TYR109 3.3 40.8 1.0 N A:TYR110 3.4 56.2 1.0 N A:GLY108 3.5 42.2 1.0 CD2 A:TYR110 3.7 55.2 1.0 CA A:GLY108 4.0 40.3 1.0 C A:GLY108 4.1 45.5 1.0 CB A:TYR110 4.1 52.1 1.0 CA A:TYR109 4.2 45.4 1.0 N A:PHE107 4.3 44.7 1.0 CA A:TYR110 4.3 52.4 1.0 C A:TYR109 4.3 55.7 1.0 CB A:TYR109 4.3 45.0 1.0 N A:TYR111 4.4 55.3 1.0 CD2 A:TYR111 4.4 60.2 1.0 CG A:TYR110 4.4 52.6 1.0 C A:PHE107 4.5 41.0 1.0 O A:PHE105 4.7 61.1 1.0 CB A:PHE107 4.7 36.2 1.0 CE2 A:TYR110 4.7 51.8 1.0 CA A:PHE107 4.7 35.3 1.0 CD2 A:TYR109 4.8 40.5 1.0 C A:TYR110 4.8 54.1 1.0 CB A:SER102 4.9 113.8 1.0 O A:TYR100 4.9 64.2 1.0

Chlorine binding site 6 out of 6 in the Crystal Structure of the N-Terminal Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-43


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 N-Terminal Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-43 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl303 b:90.7 occ:1.00 N A:TRP47 3.0 40.1 1.0 N B:PHE99 3.3 48.4 1.0 O B:TYR97 3.6 44.4 1.0 CA A:GLU46 3.7 41.2 1.0 CB A:TRP47 3.7 44.4 1.0 CD2 B:PHE99 3.7 36.6 1.0 C A:GLU46 3.8 45.8 1.0 CB B:PHE99 3.9 40.8 1.0 CA A:TRP47 3.9 38.9 1.0 CA B:VAL98 3.9 40.0 1.0 O A:LEU45 4.0 52.9 1.0 C B:VAL98 4.1 42.8 1.0 CA B:PHE99 4.2 45.3 1.0 CG B:PHE99 4.3 38.8 1.0 C B:TYR97 4.5 40.9 1.0 O B:PHE99 4.5 46.0 1.0 N A:GLU46 4.6 43.6 1.0 CG A:GLU46 4.6 50.5 1.0 CB A:GLU46 4.6 47.6 1.0 O A:TRP47 4.6 42.6 1.0 C A:LEU45 4.7 53.0 1.0 N B:VAL98 4.7 35.3 1.0 CE2 B:PHE99 4.8 39.4 1.0 C A:TRP47 4.8 41.1 1.0 C B:PHE99 4.9 53.2 1.0 CG1 B:VAL98 5.0 36.0 1.0 CB B:VAL98 5.0 35.6 1.0

C.Liu, D.Zhou, R.Nutalai, H.M.Duyvesteyn, A.Tuekprakhon, H.M.Ginn, W.Dejnirattisai, P.Supasa, A.J.Mentzer, B.Wang, J.B.Case, Y.Zhao, D.T.Skelly, R.E.Chen, S.A.Johnson, T.G.Ritter, C.Mason, T.Malik, N.Temperton, N.G.Paterson, M.A.Williams, D.R.Hall, D.K.Clare, A.Howe, P.J.Goulder, E.E.Fry, M.S.Diamond, J.Mongkolsapaya, J.Ren, D.I.Stuart, G.R.Screaton. The Antibody Response to Sars-Cov-2 Beta Underscores the Antigenic Distance to Other Variants Cell Host Microbe 2021.
ISSN: ESSN 1934-6069
DOI: 10.1016/J.CHOM.2021.11.013