Nickel in PDB 9atm: Sars-Cov-2 Eg.5 Rbd Bound to the Vir-7229 and the S2H97 Fab Fragments

The structure of Sars-Cov-2 Eg.5 Rbd Bound to the Vir-7229 and the S2H97 Fab Fragments, PDB code: 9atm was solved by T.Rietz, Y.J.Park, J.Errico, N.Czudnochowski, J.C.Nix, D.Corti, G.Snell, A.D.Marco, D.Pinto, E.Cameroni, Seattle Structural Genomics Center Forinfectious Disease (Ssgcid), D.Veesler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.78 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.728, 149.698, 167.078, 90, 90, 90
R / Rfree (%)	19.4 / 22.7

The structure of Sars-Cov-2 Eg.5 Rbd Bound to the Vir-7229 and the S2H97 Fab Fragments also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Nickel atom in the Sars-Cov-2 Eg.5 Rbd Bound to the Vir-7229 and the S2H97 Fab Fragments (pdb code 9atm). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Sars-Cov-2 Eg.5 Rbd Bound to the Vir-7229 and the S2H97 Fab Fragments, PDB code: 9atm:

Nickel binding site 1 out of 1 in the Sars-Cov-2 Eg.5 Rbd Bound to the Vir-7229 and the S2H97 Fab Fragments


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Sars-Cov-2 Eg.5 Rbd Bound to the Vir-7229 and the S2H97 Fab Fragments within 5.0Å range: probe atom residue distance (Å) B Occ L:Ni301 b:99.2 occ:1.00 O H:HOH451 3.0 67.7 1.0 OD2 L:ASP142 3.4 65.8 1.0 OD1 L:ASP142 3.6 64.6 1.0 CG L:ASP142 3.9 60.3 1.0 OG1 H:THR193 4.2 69.0 1.0 O H:GLY172 4.5 65.4 1.0 OE1 L:GLN171 4.7 70.5 1.0 CA H:GLY172 4.8 68.9 1.0 NE2 L:GLN171 4.8 69.0 1.0 OG L:SER141 4.9 62.1 1.0 C H:GLY172 4.9 66.4 1.0 CD L:GLN171 5.0 64.1 1.0

L.E.Rosen, M.A.Tortorici, A.De Marco, D.Pinto, W.B.Foreman, A.L.Taylor, Y.J.Park, D.Bohan, T.Rietz, J.M.Errico, K.Hauser, H.V.Dang, J.W.Chartron, M.Giurdanella, G.Cusumano, C.Saliba, F.Zatta, K.R.Sprouse, A.Addetia, S.K.Zepeda, J.Brown, J.Lee, E.Dellota Jr., A.Rajesh, J.Noack, Q.Tao, Y.Dacosta, B.Tsu, R.Acosta, S.Subramanian, G.D.De Melo, L.Kergoat, I.Zhang, Z.Liu, B.Guarino, M.A.Schmid, G.Schnell, J.L.Miller, F.A.Lempp, N.Czudnochowski, E.Cameroni, S.P.J.Whelan, H.Bourhy, L.A.Purcell, F.Benigni, J.Di Iulio, M.S.Pizzuto, A.Lanzavecchia, A.Telenti, G.Snell, D.Corti, D.Veesler, T.N.Starr. A Potent Pan-Sarbecovirus Neutralizing Antibody Resilient to Epitope Diversification. Cell 2024.
ISSN: ISSN 1097-4172
PubMed: 39383863
DOI: 10.1016/J.CELL.2024.09.026