Calcium in PDB 7l2c: Crystallographic Structure of Neutralizing Antibody 2-51 in Complex with Sars-Cov-2 Spike N-Terminal Domain (Ntd)

The structure of Crystallographic Structure of Neutralizing Antibody 2-51 in Complex with Sars-Cov-2 Spike N-Terminal Domain (Ntd), PDB code: 7l2c was solved by G.Cerutti, E.R.Reddem, L.Shapiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	88.03 / 3.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	66.791, 115.785, 137.606, 90, 99.97, 90
R / Rfree (%)	21.6 / 27.2

The structure of Crystallographic Structure of Neutralizing Antibody 2-51 in Complex with Sars-Cov-2 Spike N-Terminal Domain (Ntd) also contains other interesting chemical elements:

Arsenic

(As)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 39;

Binding sites:

The binding sites of Calcium atom in the Crystallographic Structure of Neutralizing Antibody 2-51 in Complex with Sars-Cov-2 Spike N-Terminal Domain (Ntd) (pdb code 7l2c). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 39 binding sites of Calcium where determined in the Crystallographic Structure of Neutralizing Antibody 2-51 in Complex with Sars-Cov-2 Spike N-Terminal Domain (Ntd), PDB code: 7l2c:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 39 in the Crystallographic Structure of Neutralizing Antibody 2-51 in Complex with Sars-Cov-2 Spike N-Terminal Domain (Ntd)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystallographic Structure of Neutralizing Antibody 2-51 in Complex with Sars-Cov-2 Spike N-Terminal Domain (Ntd) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca408 b:61.8 occ:1.00 CE1 A:TYR200 3.4 66.8 1.0 O A:ASP198 3.8 52.0 1.0 CD1 A:TYR200 3.9 64.9 1.0 O A:GLY199 4.2 68.6 1.0 CZ A:TYR200 4.5 65.3 1.0 CG1 B:VAL227 4.6 58.9 1.0 C A:GLY199 4.6 67.2 1.0 OH B:TYR170 4.7 56.7 1.0 CA A:GLY199 4.7 72.3 1.0 OH A:TYR200 4.7 64.3 1.0 CB A:PRO230 4.8 52.9 1.0 C A:ASP198 5.0 64.2 1.0 CA A:GLY232 5.0 62.7 1.0

Calcium binding site 2 out of 39 in the Crystallographic Structure of Neutralizing Antibody 2-51 in Complex with Sars-Cov-2 Spike N-Terminal Domain (Ntd)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystallographic Structure of Neutralizing Antibody 2-51 in Complex with Sars-Cov-2 Spike N-Terminal Domain (Ntd) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca409 b:60.4 occ:1.00 O A:ILE231 3.3 60.4 1.0 O B:VAL171 3.4 51.5 1.0 OG1 A:THR167 3.9 56.2 1.0 CB A:THR167 3.9 57.8 1.0 CE1 B:TYR170 4.0 55.4 1.0 CB B:SER172 4.0 61.2 1.0 OG B:SER172 4.2 74.8 1.0 C A:ILE231 4.3 56.7 1.0 C B:VAL171 4.5 53.1 1.0 OH B:TYR170 4.5 56.7 1.0 CZ B:TYR170 4.5 53.0 1.0 CA B:SER172 4.5 61.3 1.0 CG2 A:THR167 4.6 58.7 1.0 O A:PRO230 4.7 54.9 1.0 CD1 B:TYR170 4.7 55.4 1.0 O A:THR167 4.8 54.3 1.0 N B:SER172 5.0 56.5 1.0 CA A:ILE231 5.0 54.5 1.0

Calcium binding site 3 out of 39 in the Crystallographic Structure of Neutralizing Antibody 2-51 in Complex with Sars-Cov-2 Spike N-Terminal Domain (Ntd)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystallographic Structure of Neutralizing Antibody 2-51 in Complex with Sars-Cov-2 Spike N-Terminal Domain (Ntd) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca410 b:66.7 occ:1.00 CG1 A:VAL227 4.3 57.0 1.0 OH A:TYR170 4.5 74.7 1.0 CE1 B:TYR200 4.5 81.4 1.0 O A:LEU226 4.6 68.8 1.0 O B:ASP198 4.7 76.1 1.0 O B:GLY199 4.9 67.0 1.0

Calcium binding site 4 out of 39 in the Crystallographic Structure of Neutralizing Antibody 2-51 in Complex with Sars-Cov-2 Spike N-Terminal Domain (Ntd)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystallographic Structure of Neutralizing Antibody 2-51 in Complex with Sars-Cov-2 Spike N-Terminal Domain (Ntd) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca411 b:74.9 occ:1.00 O7 A:NAG401 3.5 120.6 1.0 C7 A:NAG401 4.6 130.2 1.0 O A:CYS15 4.7 75.6 1.0

Calcium binding site 5 out of 39 in the Crystallographic Structure of Neutralizing Antibody 2-51 in Complex with Sars-Cov-2 Spike N-Terminal Domain (Ntd)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystallographic Structure of Neutralizing Antibody 2-51 in Complex with Sars-Cov-2 Spike N-Terminal Domain (Ntd) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca412 b:95.4 occ:1.00 OH A:TYR28 3.6 108.4 1.0 CZ A:TYR28 3.8 97.6 1.0 O6 A:NAG402 4.0 100.6 1.0 CE2 A:TYR28 4.2 97.0 1.0 O5 A:NAG402 4.4 107.6 1.0 CE1 A:TYR28 4.4 92.4 1.0 ND2 A:ASN61 4.6 102.2 1.0

Calcium binding site 6 out of 39 in the Crystallographic Structure of Neutralizing Antibody 2-51 in Complex with Sars-Cov-2 Spike N-Terminal Domain (Ntd)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystallographic Structure of Neutralizing Antibody 2-51 in Complex with Sars-Cov-2 Spike N-Terminal Domain (Ntd) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca413 b:80.4 occ:1.00 OE2 A:GLU156 3.2 79.0 1.0 O5 A:NAG407 3.7 82.0 1.0 ND2 A:ASN122 4.1 75.4 1.0 C1 A:NAG407 4.1 86.7 1.0 C2 A:NAG407 4.1 96.7 1.0 CD A:GLU156 4.4 68.7 1.0 O6 A:NAG407 4.4 77.1 1.0 O A:GLU154 4.6 80.0 1.0 OE1 A:GLU154 4.6 79.8 1.0 C5 A:NAG407 4.6 78.4 1.0 C8 A:NAG407 4.8 78.8 1.0 C4 A:NAG407 4.8 86.2 1.0 C6 A:NAG407 4.8 81.2 1.0 N2 A:NAG407 5.0 86.0 1.0

Calcium binding site 7 out of 39 in the Crystallographic Structure of Neutralizing Antibody 2-51 in Complex with Sars-Cov-2 Spike N-Terminal Domain (Ntd)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystallographic Structure of Neutralizing Antibody 2-51 in Complex with Sars-Cov-2 Spike N-Terminal Domain (Ntd) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca407 b:92.0 occ:1.00 O7 B:NAG402 2.5 86.3 1.0 OE2 B:GLU132 2.7 83.7 1.0 C7 B:NAG402 3.5 88.2 1.0 OE1 B:GLU132 3.5 75.2 1.0 CD B:GLU132 3.5 81.1 1.0 C2 B:NAG402 3.7 93.6 1.0 N2 B:NAG402 4.0 93.2 1.0 ND2 B:ASN165 4.4 86.6 1.0 C1 B:NAG402 4.4 88.1 1.0 C8 B:NAG402 4.6 70.3 1.0 O5 B:NAG402 4.7 84.1 1.0 C3 B:NAG402 4.8 97.0 1.0 O3 B:NAG402 4.8 104.4 1.0 CG B:GLU132 5.0 78.3 1.0

Calcium binding site 8 out of 39 in the Crystallographic Structure of Neutralizing Antibody 2-51 in Complex with Sars-Cov-2 Spike N-Terminal Domain (Ntd)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystallographic Structure of Neutralizing Antibody 2-51 in Complex with Sars-Cov-2 Spike N-Terminal Domain (Ntd) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca408 b:71.8 occ:1.00 O B:ASN137 2.7 83.0 1.0 OD1 B:ASN137 3.1 90.1 1.0 O B:HOH508 3.5 36.3 1.0 OD1 B:ASP138 3.9 79.1 1.0 C B:ASN137 3.9 81.1 1.0 CG2 B:VAL83 4.2 60.5 1.0 CG B:ASN137 4.3 84.9 1.0 CA B:ASN137 4.6 76.0 1.0 NE2 B:GLN239 4.7 75.9 1.0 N B:ASP138 4.9 80.8 1.0 OE1 B:GLN239 4.9 58.7 1.0 CB B:ASN137 5.0 78.2 1.0

Calcium binding site 9 out of 39 in the Crystallographic Structure of Neutralizing Antibody 2-51 in Complex with Sars-Cov-2 Spike N-Terminal Domain (Ntd)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystallographic Structure of Neutralizing Antibody 2-51 in Complex with Sars-Cov-2 Spike N-Terminal Domain (Ntd) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca409 b:88.1 occ:1.00 OE1 B:GLU169 3.3 89.0 1.0 OE2 A:GLU169 3.8 83.9 1.0 CD B:GLU169 4.3 83.2 1.0 CD A:GLU169 4.4 80.8 1.0 OE2 B:GLU169 4.8 83.3 1.0 OE1 A:GLU169 4.8 78.8 1.0

Calcium binding site 10 out of 39 in the Crystallographic Structure of Neutralizing Antibody 2-51 in Complex with Sars-Cov-2 Spike N-Terminal Domain (Ntd)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystallographic Structure of Neutralizing Antibody 2-51 in Complex with Sars-Cov-2 Spike N-Terminal Domain (Ntd) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca410 b:73.0 occ:1.00 OE1 B:GLU156 2.5 85.4 1.0 ND2 B:ASN122 3.5 78.5 1.0 CD B:GLU156 3.6 90.4 1.0 O5 E:NAG1 3.6 66.6 1.0 C1 E:NAG1 3.8 82.5 1.0 CG B:GLU156 4.2 88.0 1.0 OE1 B:GLU154 4.3 85.2 1.0 CG B:ASN122 4.3 73.7 1.0 O6 E:NAG1 4.4 81.5 1.0 C2 E:NAG1 4.6 82.6 1.0 CG1 B:VAL120 4.6 66.2 1.0 OE2 B:GLU156 4.6 89.4 1.0 CB B:ASN122 4.8 67.6 1.0 CG2 B:VAL127 4.8 54.2 1.0 C5 E:NAG1 5.0 70.9 1.0

G.Cerutti, Y.Guo, T.Zhou, J.Gorman, M.Lee, M.Rapp, E.R.Reddem, J.Yu, F.Bahna, J.Bimela, Y.Huang, P.S.Katsamba, L.Liu, M.S.Nair, R.Rawi, A.S.Olia, P.Wang, G.Chuang, D.D.Ho, Z.Sheng, P.D.Kwong, L.Shapiro. Potent Sars-Cov-2 Neutralizing Antibodies Directed Against Spike N-Terminal Domain Target A Single Supersite Biorxiv 2021.
DOI: 10.1101/2021.01.10.426120