Sodium in PDB 7qny: The Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-58 and Covox-158 Fabs

The structure of The Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-58 and Covox-158 Fabs, PDB code: 7qny 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)	69.37 / 2.84
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	72.762, 72.762, 416.202, 90, 90, 120
R / Rfree (%)	22.6 / 27.8

The binding sites of Sodium atom in the The Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-58 and Covox-158 Fabs (pdb code 7qny). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the The Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-58 and Covox-158 Fabs, PDB code: 7qny:

Sodium binding site 1 out of 1 in the The Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-58 and Covox-158 Fabs


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Receptor Binding Domain of Sars-Cov-2 Spike Glycoprotein in Complex with Covox-58 and Covox-158 Fabs within 5.0Å range: probe atom residue distance (Å) B Occ H:Na301 b:78.5 occ:1.00 OG H:SER101 2.5 112.8 1.0 CB H:SER101 3.4 105.8 1.0 O H:LEU99 3.4 96.8 1.0 N H:SER101 3.9 97.1 1.0 OD1 H:ASP103 3.9 95.2 1.0 OD2 H:ASP103 4.1 120.0 1.0 OE1 L:GLN49 4.2 198.2 1.0 CA H:SER101 4.3 111.8 1.0 CB H:LEU99 4.3 88.4 1.0 C H:LEU99 4.3 94.3 1.0 CG H:ASP103 4.5 107.3 1.0 CD2 E:LEU455 4.8 104.2 1.0 CD L:GLN49 4.9 205.9 1.0 C H:GLY100 5.0 96.0 1.0 CA H:LEU99 5.0 85.5 1.0

W.Dejnirattisai, J.Huo, D.Zhou, J.Zahradnik, P.Supasa, C.Liu, H.M.E.Duyvesteyn, H.M.Ginn, A.J.Mentzer, A.Tuekprakhon, R.Nutalai, B.Wang, A.Dijokaite, S.Khan, O.Avinoam, M.Bahar, D.Skelly, S.Adele, S.A.Johnson, A.Amini, T.G.Ritter, C.Mason, C.Dold, D.Pan, S.Assadi, A.Bellass, N.Omo-Dare, D.Koeckerling, A.Flaxman, D.Jenkin, P.K.Aley, M.Voysey, S.A.Costa Clemens, F.G.Naveca, V.Nascimento, F.Nascimento, C.Fernandes Da Costa, P.C.Resende, A.Pauvolid-Correa, M.M.Siqueira, V.Baillie, N.Serafin, G.Kwatra, K.Da Silva, S.A.Madhi, M.C.Nunes, T.Malik, P.J.M.Openshaw, J.K.Baillie, M.G.Semple, A.R.Townsend, K.A.Huang, T.K.Tan, M.W.Carroll, P.Klenerman, E.Barnes, S.J.Dunachie, B.Constantinides, H.Webster, D.Crook, A.J.Pollard, T.Lambe, N.G.Paterson, M.A.Williams, D.R.Hall, E.E.Fry, J.Mongkolsapaya, J.Ren, G.Schreiber, D.I.Stuart, G.R.Screaton. Sars-Cov-2 Omicron-B.1.1.529 Leads to Widespread Escape From Neutralizing Antibody Responses. Cell V. 185 467 2022.
ISSN: ISSN 1097-4172
PubMed: 35081335
DOI: 10.1016/J.CELL.2021.12.046