Calcium in PDB 7tow: Antibody DH1058 Fab Fragment Bound to Sars-Cov-2 Fusion Peptide

The structure of Antibody DH1058 Fab Fragment Bound to Sars-Cov-2 Fusion Peptide, PDB code: 7tow was solved by S.Gobeil, P.Acharya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.21 / 2.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.916, 76.788, 119.786, 90, 100.85, 90
R / Rfree (%)	16.7 / 23.4

The binding sites of Calcium atom in the Antibody DH1058 Fab Fragment Bound to Sars-Cov-2 Fusion Peptide (pdb code 7tow). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Antibody DH1058 Fab Fragment Bound to Sars-Cov-2 Fusion Peptide, PDB code: 7tow:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Antibody DH1058 Fab Fragment Bound to Sars-Cov-2 Fusion Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Antibody DH1058 Fab Fragment Bound to Sars-Cov-2 Fusion Peptide within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca301 b:29.8 occ:1.00 O E:HOH903 3.0 22.5 1.0 OG H:SER52 3.1 17.9 1.0 N H:GLU54 3.2 14.7 1.0 N H:ARG56 3.3 17.2 1.0 CB H:ARG56 3.3 19.3 1.0 CB H:GLU54 3.3 20.3 1.0 CA H:GLU54 3.4 16.4 1.0 C H:GLU54 3.5 21.6 1.0 CE1 H:TYR53 3.5 24.9 1.0 CD1 H:TYR53 3.6 19.9 1.0 N H:GLY55 3.7 14.6 1.0 CA H:ARG56 3.8 15.5 1.0 CB H:SER52 3.9 14.8 1.0 CG H:ARG56 4.0 23.5 1.0 O H:GLU54 4.0 19.7 1.0 CD H:ARG56 4.3 31.8 1.0 N H:ASN57 4.3 17.2 1.0 C H:GLY55 4.3 19.1 1.0 OE1 E:GLU819 4.4 19.7 1.0 C H:SER52 4.4 12.3 1.0 CZ H:TYR53 4.5 23.5 1.0 C H:TYR53 4.5 14.6 1.0 N H:TYR53 4.5 14.5 1.0 C H:ARG56 4.6 18.8 1.0 CA H:GLY55 4.6 11.8 1.0 O H:HOH534 4.6 27.0 1.0 CG H:GLU54 4.6 27.4 1.0 O H:SER52 4.6 14.1 1.0 NE H:ARG56 4.7 44.3 1.0 CG H:TYR53 4.7 21.7 1.0 CA H:SER52 4.8 16.6 1.0 OE1 H:GLU54 4.9 44.8 1.0 CA H:TYR53 5.0 16.0 1.0 OH H:TYR53 5.0 26.5 1.0

Calcium binding site 2 out of 3 in the Antibody DH1058 Fab Fragment Bound to Sars-Cov-2 Fusion Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Antibody DH1058 Fab Fragment Bound to Sars-Cov-2 Fusion Peptide within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca302 b:21.3 occ:1.00 O H:HOH499 3.1 16.9 1.0 N H:TRP47 3.2 12.2 1.0 O H:HOH515 3.3 27.4 1.0 N L:PHE99 3.4 12.8 1.0 CA H:GLU46 3.6 15.5 1.0 CA L:THR98 3.7 12.5 1.0 CD2 L:PHE99 3.9 12.9 1.0 C H:GLU46 3.9 14.2 1.0 O H:LEU45 4.0 17.6 1.0 C L:THR98 4.0 17.3 1.0 CB L:PHE99 4.0 16.7 1.0 CG H:GLU46 4.1 14.4 1.0 CB H:TRP47 4.1 15.8 1.0 O L:ILE97 4.2 16.5 1.0 CA H:TRP47 4.2 18.0 1.0 CA L:PHE99 4.3 15.1 1.0 CB H:GLU46 4.3 16.7 1.0 CB L:THR98 4.4 13.8 1.0 CG L:PHE99 4.4 17.0 1.0 N H:GLU46 4.6 15.4 1.0 O H:HOH468 4.6 24.0 1.0 CG2 L:THR98 4.7 16.5 1.0 O H:TRP47 4.7 15.1 1.0 O L:PHE99 4.7 15.0 1.0 C H:LEU45 4.7 17.6 1.0 O L:HOH401 4.7 22.0 1.0 N L:THR98 4.8 14.6 1.0 CE2 L:PHE99 4.9 17.8 1.0 C L:ILE97 4.9 14.5 1.0 C H:TRP47 5.0 13.5 1.0 C L:PHE99 5.0 20.3 1.0

Calcium binding site 3 out of 3 in the Antibody DH1058 Fab Fragment Bound to Sars-Cov-2 Fusion Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Antibody DH1058 Fab Fragment Bound to Sars-Cov-2 Fusion Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:21.4 occ:1.00 O A:HOH431 3.2 19.2 1.0 O A:HOH517 3.2 27.2 1.0 N B:PHE99 3.2 15.2 1.0 N A:TRP47 3.3 15.7 1.0 CA B:THR98 3.6 13.1 1.0 CA A:GLU46 3.8 14.2 1.0 CD2 B:PHE99 3.9 13.8 1.0 C B:THR98 3.9 15.9 1.0 CB A:TRP47 4.0 16.7 1.0 CB B:PHE99 4.1 10.4 1.0 C A:GLU46 4.1 15.2 1.0 O B:ILE97 4.1 16.2 1.0 CB B:THR98 4.2 14.4 1.0 O A:LEU45 4.2 17.1 1.0 CA B:PHE99 4.2 15.4 1.0 CA A:TRP47 4.2 17.1 1.0 CG B:PHE99 4.4 13.4 1.0 CG2 B:THR98 4.5 17.3 1.0 O B:HOH402 4.5 19.3 1.0 O B:PHE99 4.6 11.3 1.0 CG A:GLU46 4.6 12.7 1.0 CB A:GLU46 4.6 15.2 1.0 N B:THR98 4.6 16.5 1.0 O A:HOH460 4.7 26.1 1.0 O A:TRP47 4.8 15.4 1.0 N A:GLU46 4.8 14.1 1.0 C B:ILE97 4.8 14.2 1.0 C A:LEU45 4.9 15.7 1.0 C B:PHE99 4.9 15.8 1.0 CE2 B:PHE99 4.9 11.1 1.0

S.M.Gobeil, R.Henderson, V.Stalls, K.Janowska, X.Huang, A.May, M.Speakman, E.Beaudoin, K.Manne, D.Li, R.Parks, M.Barr, M.Deyton, M.Martin, K.Mansouri, R.J.Edwards, G.D.Sempowski, K.O.Saunders, K.Wiehe, W.Williams, B.Korber, B.F.Haynes, P.Acharya. Structural Diversity of the Sars-Cov-2 Omicron Spike. Biorxiv 2022.
PubMed: 35118469
DOI: 10.1101/2022.01.25.477784