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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

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:

Chlorine (Cl) 4 atoms

Iodine Binding Sites:

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 7ps1

Go back to Iodine Binding Sites List in 7ps1
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 7ps1

Go back to Iodine Binding Sites List in 7ps1
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 7ps1

Go back to Iodine Binding Sites List in 7ps1
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 7ps1

Go back to Iodine Binding Sites List in 7ps1
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

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: Mon Aug 12 01:56:17 2024

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