Calcium in PDB 7wqv: Crystal Structure of A Neutralizing Monoclonal Antibody (AB08) in Complex with Sars-Cov-2 Receptor-Binding Domain (Rbd)

The structure of Crystal Structure of A Neutralizing Monoclonal Antibody (AB08) in Complex with Sars-Cov-2 Receptor-Binding Domain (Rbd), PDB code: 7wqv was solved by J.Zha, L.Meng, X.Zhang, D.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.93 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	92.643, 116.742, 180.72, 90, 90.31, 90
R / Rfree (%)	22 / 25.1

The structure of Crystal Structure of A Neutralizing Monoclonal Antibody (AB08) in Complex with Sars-Cov-2 Receptor-Binding Domain (Rbd) also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of A Neutralizing Monoclonal Antibody (AB08) in Complex with Sars-Cov-2 Receptor-Binding Domain (Rbd) (pdb code 7wqv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of A Neutralizing Monoclonal Antibody (AB08) in Complex with Sars-Cov-2 Receptor-Binding Domain (Rbd), PDB code: 7wqv:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of A Neutralizing Monoclonal Antibody (AB08) in Complex with Sars-Cov-2 Receptor-Binding Domain (Rbd)


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 A Neutralizing Monoclonal Antibody (AB08) in Complex with Sars-Cov-2 Receptor-Binding Domain (Rbd) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1202 b:49.5 occ:1.00 O B:HOH1306 2.4 57.6 1.0 OE1 B:GLU1085 2.4 52.7 1.0 OE2 B:GLU1085 2.5 49.2 1.0 O B:HOH1304 2.6 47.5 1.0 CD B:GLU1085 2.7 48.3 1.0 O B:VAL1110 3.7 40.1 1.0 CG B:GLU1085 4.2 50.9 1.0 C B:VAL1110 4.8 41.2 1.0 N B:VAL1110 4.8 45.7 1.0 CB B:GLU1085 5.0 42.6 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of A Neutralizing Monoclonal Antibody (AB08) in Complex with Sars-Cov-2 Receptor-Binding Domain (Rbd)


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 A Neutralizing Monoclonal Antibody (AB08) in Complex with Sars-Cov-2 Receptor-Binding Domain (Rbd) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1202 b:32.7 occ:1.00 OH D:TYR110 3.4 44.3 1.0 OH D:TYR1051 3.7 28.4 1.0 CZ D:TYR1051 3.8 33.7 1.0 CE1 D:TYR1051 4.1 44.6 1.0 CE2 D:TYR1051 4.3 34.3 1.0 CZ D:TYR110 4.5 41.1 1.0 CD1 D:TYR1051 4.8 36.9 1.0 CE2 D:TYR110 4.8 44.6 1.0 CD2 D:TYR1051 4.9 35.2 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of A Neutralizing Monoclonal Antibody (AB08) in Complex with Sars-Cov-2 Receptor-Binding Domain (Rbd)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of A Neutralizing Monoclonal Antibody (AB08) in Complex with Sars-Cov-2 Receptor-Binding Domain (Rbd) within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca1201 b:56.6 occ:1.00 O F:HOH1301 2.6 64.8 1.0 OE2 F:GLU1085 2.7 44.8 1.0 O F:HOH1302 2.9 59.5 1.0 CD F:GLU1085 3.5 50.7 1.0 OE1 F:GLU1085 3.7 50.4 1.0 O F:VAL1110 4.3 49.5 1.0 CG F:GLU1085 4.9 47.4 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of A Neutralizing Monoclonal Antibody (AB08) in Complex with Sars-Cov-2 Receptor-Binding Domain (Rbd)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of A Neutralizing Monoclonal Antibody (AB08) in Complex with Sars-Cov-2 Receptor-Binding Domain (Rbd) within 5.0Å range: probe atom residue distance (Å) B Occ L:Ca1201 b:43.4 occ:1.00 OE2 L:GLU1085 2.5 41.4 1.0 O L:HOH1303 2.5 53.5 1.0 O L:HOH1302 2.6 30.7 1.0 OE1 L:GLU1085 2.7 48.1 1.0 CD L:GLU1085 2.8 45.0 1.0 O L:VAL1110 3.5 45.9 1.0 CG L:GLU1085 4.2 47.0 1.0 CG2 L:THR1109 4.6 37.0 1.0 C L:VAL1110 4.6 45.2 1.0 N L:VAL1110 4.7 45.1 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of A Neutralizing Monoclonal Antibody (AB08) in Complex with Sars-Cov-2 Receptor-Binding Domain (Rbd)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of A Neutralizing Monoclonal Antibody (AB08) in Complex with Sars-Cov-2 Receptor-Binding Domain (Rbd) within 5.0Å range: probe atom residue distance (Å) B Occ N:Ca1201 b:43.8 occ:1.00 OE2 N:GLU1085 2.4 39.4 1.0 O N:HOH1304 2.4 63.4 1.0 OE1 N:GLU1085 2.5 51.0 1.0 O N:HOH1301 2.5 42.2 1.0 CD N:GLU1085 2.8 44.6 1.0 CG N:GLU1085 4.3 42.0 1.0 O N:VAL1110 4.4 42.2 1.0 CG2 N:THR1109 4.7 34.4 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of A Neutralizing Monoclonal Antibody (AB08) in Complex with Sars-Cov-2 Receptor-Binding Domain (Rbd)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of A Neutralizing Monoclonal Antibody (AB08) in Complex with Sars-Cov-2 Receptor-Binding Domain (Rbd) within 5.0Å range: probe atom residue distance (Å) B Occ P:Ca1202 b:45.5 occ:1.00 OE1 P:GLU1085 2.4 54.0 1.0 O P:HOH1302 2.4 46.2 1.0 O P:HOH1301 2.4 39.5 1.0 OE2 P:GLU1085 2.5 51.0 1.0 CD P:GLU1085 2.7 52.0 1.0 O P:VAL1110 3.7 46.7 1.0 CG P:GLU1085 4.2 51.4 1.0 N P:VAL1110 4.8 52.5 1.0 C P:VAL1110 4.8 43.9 1.0 CG2 P:THR1109 4.9 37.3 1.0 CB P:GLU1085 5.0 43.2 1.0

L.Meng, J.Zha, D.Li, X.Zhang. Crystal Structure of A Neutralizing Monoclonal Antibody (AB08) in Complex with Sars-Cov-2 Receptor-Binding Domain (Rbd) To Be Published.