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Chlorine in PDB 7ps1: Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-27 Fab

Protein crystallography data

The structure of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-27 Fab, PDB code: 7ps1 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) 56.62 / 2.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 193.396, 85.745, 57.447, 90, 99.73, 90
R / Rfree (%) 18.4 / 21.5

Other elements in 7ps1:

The structure of Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-27 Fab also contains other interesting chemical elements:

Iodine (I) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-27 Fab (pdb code 7ps1). 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 Receptor Binding Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-27 Fab, PDB code: 7ps1:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 7ps1

Go back to Chlorine Binding Sites List in 7ps1
Chlorine binding site 1 out of 4 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-27 Fab


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 Beta Variant Spike Glycoprotein in Complex with Beta-27 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl604

b:84.1
occ:1.00
N E:THR430 3.7 68.3 1.0
O E:THR430 3.9 75.1 1.0
CD1 E:PHE429 4.3 60.3 1.0
CB E:THR430 4.4 71.7 1.0
CA E:THR430 4.4 70.0 1.0
CA E:PHE429 4.4 66.5 1.0
O E:PHE515 4.5 99.5 1.0
CE2 E:PHE464 4.5 47.5 1.0
O E:ASP428 4.6 74.9 1.0
C E:THR430 4.6 71.9 1.0
C E:PHE429 4.6 68.5 1.0
CG E:PRO426 4.7 59.2 1.0
CZ E:PHE464 4.8 46.9 1.0
CE1 E:PHE429 4.8 58.5 1.0
OG1 E:THR430 4.9 79.4 1.0
CB E:SER514 4.9 54.1 1.0

Chlorine binding site 2 out of 4 in 7ps1

Go back to Chlorine Binding Sites List in 7ps1
Chlorine binding site 2 out of 4 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-27 Fab


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 Beta Variant Spike Glycoprotein in Complex with Beta-27 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl605

b:76.6
occ:1.00
NZ E:LYS484 3.6 60.8 1.0
CD1 E:PHE490 3.7 50.6 1.0
CG E:PHE490 3.8 50.1 1.0
CE1 E:PHE490 4.1 44.4 1.0
CE E:LYS484 4.1 60.1 1.0
CB E:PHE490 4.2 43.8 1.0
CD2 E:PHE490 4.2 46.0 1.0
CD E:LYS484 4.3 56.5 1.0
CZ E:PHE490 4.5 45.2 1.0
CE2 E:PHE490 4.6 46.5 1.0

Chlorine binding site 3 out of 4 in 7ps1

Go back to Chlorine Binding Sites List in 7ps1
Chlorine binding site 3 out of 4 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-27 Fab


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 Beta Variant Spike Glycoprotein in Complex with Beta-27 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl303

b:80.9
occ:1.00
N A:VAL125 3.3 49.1 1.0
CA A:SER124 3.8 44.7 1.0
O A:VAL125 3.9 47.7 1.0
C A:SER124 4.0 50.0 1.0
OE2 B:GLU123 4.1 90.5 1.0
CA A:VAL125 4.2 47.2 1.0
CB A:VAL125 4.4 48.2 1.0
CB A:SER124 4.4 47.1 1.0
C A:VAL125 4.4 48.9 1.0
CG1 A:VAL211 4.4 50.8 1.0
O A:PRO123 4.5 46.2 1.0
CG2 A:VAL125 4.8 44.3 1.0
CG2 A:VAL211 4.8 55.8 1.0
OG A:SER124 5.0 54.9 1.0
N A:SER124 5.0 46.3 1.0

Chlorine binding site 4 out of 4 in 7ps1

Go back to Chlorine Binding Sites List in 7ps1
Chlorine binding site 4 out of 4 in the Crystal Structure of the Receptor Binding Domain of Sars-Cov-2 Beta Variant Spike Glycoprotein in Complex with Beta-27 Fab


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 Beta Variant Spike Glycoprotein in Complex with Beta-27 Fab within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl303

b:79.3
occ:1.00
N B:GLY212 3.0 70.0 1.0
O B:ASN210 3.7 60.9 1.0
CA B:GLY212 3.8 70.7 1.0
N B:GLU213 3.9 80.0 1.0
C B:ARG211 3.9 67.8 1.0
CA B:ARG211 3.9 54.6 1.0
CD2 B:PHE209 4.2 48.1 1.0
CE2 B:PHE209 4.3 44.5 1.0
OH B:TYR186 4.3 54.2 1.0
C B:GLY212 4.3 78.8 1.0
CB B:PRO119 4.4 45.5 1.0
C B:ASN210 4.6 60.2 1.0
N B:ARG211 4.7 53.1 1.0
CG B:PRO119 4.8 47.1 1.0
C B:GLU213 4.9 94.9 1.0
CA B:GLU213 5.0 84.7 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: Sun Jul 13 05:52:41 2025

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