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

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

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:

Chlorine

(Cl)

4 atoms

The binding sites of Iodine 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 Iodine atom.
In total 4 binding sites of Iodine 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 Iodine binding site number: 1; 2; 3; 4;

Iodine 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 Iodine with other atoms in the I 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 A:I304 b:197.7 occ:1.00 N A:GLY26 3.7 52.6 1.0 O E:HOH713 3.7 54.6 1.0 OG E:SER477 4.1 71.8 1.0 ND2 A:ASN76 4.4 47.1 1.0 CA A:SER25 4.4 52.9 1.0 CA A:GLY26 4.4 53.4 1.0 CB E:SER477 4.5 59.6 1.0 C A:SER25 4.6 54.4 1.0 N A:LEU27 4.6 54.5 1.0 O A:LEU27 4.8 51.3 1.0 C A:GLY26 4.9 56.4 1.0 CB A:SER25 5.0 57.3 1.0

Iodine 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 Iodine with other atoms in the I 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 A:I305 b:149.9 occ:1.00 ND1 A:HIS168 3.4 45.2 1.0 OD1 B:ASP167 3.7 69.9 1.0 CE1 A:HIS168 3.7 46.9 1.0 O A:VAL167 4.5 45.2 1.0 O B:GLU165 4.5 56.1 1.0 CB B:THR164 4.6 46.4 1.0 CG B:ASP167 4.7 63.7 1.0 CG A:HIS168 4.7 40.9 1.0 OG1 B:THR164 4.7 45.7 1.0 CA B:ASP167 4.8 52.5 1.0 CB B:ASP167 4.8 53.8 1.0 CG2 B:THR164 4.9 41.4 1.0

Iodine 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 Iodine with other atoms in the I 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:I306 b:150.2 occ:1.00 O B:HOH428 3.1 47.1 1.0 O A:PRO171 3.6 41.3 1.0 N A:SER183 3.7 43.7 1.0 CA A:LEU182 3.7 43.9 1.0 OG B:SER176 3.8 49.5 1.0 CB B:SER162 3.8 43.9 1.0 O A:SER181 3.8 49.1 1.0 C A:LEU182 4.1 43.5 1.0 OG A:SER183 4.1 44.3 1.0 CB A:PHE170 4.2 39.0 1.0 OG B:SER162 4.2 50.2 1.0 CG1 A:VAL173 4.4 47.8 1.0 CB A:LEU182 4.4 46.7 1.0 CB A:SER183 4.5 39.7 1.0 C A:SER181 4.6 43.5 1.0 N A:LEU182 4.6 39.1 1.0 C A:PRO171 4.6 43.5 1.0 CA A:SER183 4.7 43.0 1.0 N A:VAL173 4.7 47.2 1.0 CG2 A:VAL173 4.7 43.5 1.0 CA A:ALA172 4.8 47.7 1.0 O B:SER176 4.9 41.6 1.0

Iodine 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 Iodine with other atoms in the I 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:I304 b:179.8 occ:1.00 N B:GLY42 3.3 66.1 1.0 CA B:GLY42 4.1 65.5 1.0 CA B:HIS41 4.1 68.2 1.0 C B:HIS41 4.2 66.9 1.0 ND1 B:HIS41 4.3 74.8 1.0 O B:LYS40 4.3 63.7 1.0 NE2 B:GLN39 4.3 44.0 1.0 CD B:GLN39 4.4 49.5 1.0 N B:GLN43 4.6 67.9 1.0 OE1 A:GLN39 4.6 54.7 1.0 CE1 B:HIS41 4.7 74.5 1.0 CG B:HIS41 4.7 75.5 1.0 OE1 B:GLN39 4.7 51.7 1.0 O B:GLN43 4.8 52.7 1.0 C B:GLY42 4.8 66.2 1.0 O B:HOH401 4.8 48.1 1.0 CG B:GLN39 4.9 49.4 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