Calcium in PDB 7deo: Crystal Structure of Sars-Cov-2 Rbd in Complex with A Neutralizing Antibody Scfv

The structure of Crystal Structure of Sars-Cov-2 Rbd in Complex with A Neutralizing Antibody Scfv, PDB code: 7deo was solved by D.Fu, G.Zhang, X.Li, Z.Rao, Y.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.49 / 2.50
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	156.08, 160.609, 42.239, 90, 90, 90
R / Rfree (%)	18.7 / 23.2

The binding sites of Calcium atom in the Crystal Structure of Sars-Cov-2 Rbd in Complex with A Neutralizing Antibody Scfv (pdb code 7deo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Sars-Cov-2 Rbd in Complex with A Neutralizing Antibody Scfv, PDB code: 7deo:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Sars-Cov-2 Rbd in Complex with A Neutralizing Antibody Scfv


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Sars-Cov-2 Rbd in Complex with A Neutralizing Antibody Scfv within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:20.5 occ:1.00 O A:ARG104 2.2 16.0 1.0 O A:PRO100 2.3 17.6 1.0 O A:HOH686 2.3 22.9 1.0 OD1 A:ASP99 2.4 20.6 1.0 O A:GLY102 2.4 16.1 1.0 O A:HOH690 2.5 16.0 1.0 C A:ARG104 3.4 16.8 1.0 C A:GLY102 3.5 17.9 1.0 C A:PRO100 3.5 18.2 1.0 CG A:ASP99 3.5 21.4 1.0 N A:GLY102 3.8 21.1 1.0 O A:HOH691 3.9 28.7 1.0 O A:HOH642 3.9 20.7 1.0 C A:PRO101 4.0 23.4 1.0 N A:PRO100 4.1 19.2 1.0 OD2 A:ASP99 4.1 19.4 1.0 N A:ARG104 4.2 19.2 1.0 CA A:GLY102 4.2 17.0 1.0 CA A:ARG104 4.3 17.8 1.0 C A:LEU103 4.3 20.2 1.0 O A:PRO101 4.4 20.2 1.0 C A:ASP99 4.4 22.3 1.0 CA A:PRO100 4.4 20.7 1.0 N A:PHE105 4.4 19.4 1.0 N A:PRO101 4.5 19.4 1.0 CD A:PRO100 4.5 20.2 1.0 CA A:PRO101 4.5 21.7 1.0 N A:LEU103 4.5 17.1 1.0 O A:LEU103 4.5 22.6 1.0 CA A:PHE105 4.5 21.5 1.0 CG A:PRO100 4.6 22.5 1.0 CB A:ASP99 4.7 17.9 1.0 O A:ASP99 4.7 19.6 1.0 N A:ARG106 4.8 23.9 1.0 CA A:LEU103 4.8 19.9 1.0 C A:PHE105 4.8 24.2 1.0 CA A:ASP99 4.9 17.5 1.0 CB A:PRO100 5.0 19.6 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Sars-Cov-2 Rbd in Complex with A Neutralizing Antibody Scfv


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Sars-Cov-2 Rbd in Complex with A Neutralizing Antibody Scfv within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca501 b:27.1 occ:1.00 O C:ARG104 2.3 23.6 1.0 O C:PRO100 2.3 18.6 1.0 O C:GLY102 2.3 24.6 1.0 O C:HOH666 2.3 24.1 1.0 OD1 C:ASP99 2.5 28.0 1.0 O C:HOH660 3.0 30.3 1.0 C C:GLY102 3.4 23.3 1.0 C C:ARG104 3.5 26.3 1.0 C C:PRO100 3.5 23.8 1.0 CG C:ASP99 3.6 29.6 1.0 N C:GLY102 3.7 28.0 1.0 O D:HOH1128 3.8 23.7 1.0 C C:PRO101 3.9 27.0 1.0 N C:PRO100 4.0 25.5 1.0 N C:ARG104 4.1 27.1 1.0 CA C:GLY102 4.1 23.7 1.0 C C:LEU103 4.2 25.6 1.0 OD2 C:ASP99 4.2 31.5 1.0 C C:ASP99 4.2 23.3 1.0 CA C:ARG104 4.3 25.6 1.0 O C:PRO101 4.3 21.3 1.0 CA C:PRO100 4.4 25.9 1.0 O C:LEU103 4.4 29.4 1.0 N C:PRO101 4.4 24.8 1.0 N C:LEU103 4.4 22.3 1.0 CA C:PRO101 4.5 23.3 1.0 O D:HOH1170 4.5 38.0 1.0 N C:PHE105 4.5 25.3 1.0 O C:ASP99 4.5 20.6 1.0 CA C:PHE105 4.6 29.8 1.0 CD C:PRO100 4.6 28.2 1.0 CB C:ASP99 4.7 23.0 1.0 CA C:LEU103 4.8 26.5 1.0 CG C:PRO100 4.9 25.9 1.0 CA C:ASP99 4.9 24.2 1.0 N C:ARG106 4.9 25.0 1.0

D.Fu, G.Zhang, X.Li, Z.Rao, Y.Guo. Crystal Structure of Sars-Cov-2 Rbd in Complex with A Neutralizing Antibody Scfv To Be Published.