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

Protein crystallography data

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

Chlorine Binding Sites:

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 7q0i

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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 7q0i

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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 7q0i

Go back to Chlorine Binding Sites List in 7q0i
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 7q0i

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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 7q0i

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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 7q0i

Go back to Chlorine Binding Sites List in 7q0i
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

Reference:

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
Page generated: Fri Dec 24 05:46:48 2021

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