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Arsenic in PDB 7tp3: Crystal Structure of Sars-Cov-2 Receptor Binding Domain in Complex with Neutralizing Antibody K288.2

Protein crystallography data

The structure of Crystal Structure of Sars-Cov-2 Receptor Binding Domain in Complex with Neutralizing Antibody K288.2, PDB code: 7tp3 was solved by M.Yuan, X.Zhu, I.A.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.50 / 2.33
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 72.462, 88.553, 131.495, 90, 90, 90
R / Rfree (%) 18.5 / 23.1

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Crystal Structure of Sars-Cov-2 Receptor Binding Domain in Complex with Neutralizing Antibody K288.2 (pdb code 7tp3). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 3 binding sites of Arsenic where determined in the Crystal Structure of Sars-Cov-2 Receptor Binding Domain in Complex with Neutralizing Antibody K288.2, PDB code: 7tp3:
Jump to Arsenic binding site number: 1; 2; 3;

Arsenic binding site 1 out of 3 in 7tp3

Go back to Arsenic Binding Sites List in 7tp3
Arsenic binding site 1 out of 3 in the Crystal Structure of Sars-Cov-2 Receptor Binding Domain in Complex with Neutralizing Antibody K288.2


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Crystal Structure of Sars-Cov-2 Receptor Binding Domain in Complex with Neutralizing Antibody K288.2 within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:As601

b:207.4
occ:1.00
AS Z:CAC601 0.0 207.4 1.0
O2 Z:CAC601 1.7 130.8 1.0
O1 Z:CAC601 1.7 72.6 1.0
C2 Z:CAC601 2.0 116.8 1.0
C1 Z:CAC601 2.0 105.8 1.0
ND2 Z:ASN354 4.1 75.8 1.0

Arsenic binding site 2 out of 3 in 7tp3

Go back to Arsenic Binding Sites List in 7tp3
Arsenic binding site 2 out of 3 in the Crystal Structure of Sars-Cov-2 Receptor Binding Domain in Complex with Neutralizing Antibody K288.2


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Crystal Structure of Sars-Cov-2 Receptor Binding Domain in Complex with Neutralizing Antibody K288.2 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:As301

b:191.5
occ:1.00
AS L:CAC301 0.0 191.5 1.0
O1 L:CAC301 1.7 92.8 1.0
O2 L:CAC301 1.7 118.5 1.0
C1 L:CAC301 2.0 104.0 1.0
C2 L:CAC301 2.0 97.2 1.0
O L:ASP9 4.0 48.8 1.0
O L:GLY101 4.3 45.5 1.0
C L:GLY101 4.7 54.6 1.0
CB L:ASP9 4.8 59.7 1.0
O L:GLY100 4.8 47.2 1.0
C L:ASP9 4.8 50.9 1.0
N L:LYS103 4.9 47.5 1.0
CB L:LYS103 5.0 39.7 1.0
CA L:ASP9 5.0 49.9 1.0

Arsenic binding site 3 out of 3 in 7tp3

Go back to Arsenic Binding Sites List in 7tp3
Arsenic binding site 3 out of 3 in the Crystal Structure of Sars-Cov-2 Receptor Binding Domain in Complex with Neutralizing Antibody K288.2


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 3 of Crystal Structure of Sars-Cov-2 Receptor Binding Domain in Complex with Neutralizing Antibody K288.2 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:As302

b:211.2
occ:1.00
AS L:CAC302 0.0 211.2 1.0
O1 L:CAC302 1.7 130.9 1.0
O2 L:CAC302 1.7 170.1 1.0
C1 L:CAC302 2.0 114.7 1.0
C2 L:CAC302 2.0 106.0 1.0
OD2 L:ASP81 4.4 92.1 1.0
CD L:PRO59 4.4 74.4 1.0
CG L:PRO59 4.6 79.3 1.0
SD L:MET58 4.8 111.0 1.0
CD L:ARG45 5.0 83.8 1.0

Reference:

W.T.He, M.Yuan, S.Callaghan, R.Musharrafieh, G.Song, M.Silva, N.Beutler, W.H.Lee, P.Yong, J.L.Torres, M.Melo, P.Zhou, F.Zhao, X.Zhu, L.Peng, D.Huang, F.Anzanello, J.Ricketts, M.Parren, E.Garcia, M.Ferguson, W.Rinaldi, S.A.Rawlings, D.Nemazee, D.M.Smith, B.Briney, Y.Safonova, T.F.Rogers, J.M.Dan, Z.Zhang, D.Weiskopf, A.Sette, S.Crotty, D.J.Irvine, A.B.Ward, I.A.Wilson, D.R.Burton, R.Andrabi. Broadly Neutralizing Antibodies to Sars-Related Viruses Can Be Readily Induced in Rhesus Macaques. Sci Transl Med V. 14 L9605 2022.
ISSN: ESSN 1946-6242
PubMed: 35947674
DOI: 10.1126/SCITRANSLMED.ABL9605
Page generated: Mon Jul 7 01:03:45 2025

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