Calcium in PDB 6a4k: Human Antibody 32D6 Fab in Complex with H1N1 Influenza A Virus HA1

The structure of Human Antibody 32D6 Fab in Complex with H1N1 Influenza A Virus HA1, PDB code: 6a4k was solved by C.C.Lee, T.P.Ko, L.L.Lin, A.H.J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.15
Space group	P 31 1 2
Cell size a, b, c (Å), α, β, γ (°)	181.743, 181.743, 248.091, 90.00, 90.00, 120.00
R / Rfree (%)	17.5 / 23.3

The binding sites of Calcium atom in the Human Antibody 32D6 Fab in Complex with H1N1 Influenza A Virus HA1 (pdb code 6a4k). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Human Antibody 32D6 Fab in Complex with H1N1 Influenza A Virus HA1, PDB code: 6a4k:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Human Antibody 32D6 Fab in Complex with H1N1 Influenza A Virus HA1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Antibody 32D6 Fab in Complex with H1N1 Influenza A Virus HA1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:69.5 occ:1.00 OG1 A:THR249 3.4 54.0 1.0 O A:TRP248 3.5 48.4 1.0 O A:HOH612 3.6 43.9 1.0 OD2 A:ASP114 3.9 56.0 1.0 CB A:THR249 4.4 52.5 1.0 CA A:THR249 4.4 51.5 1.0 CD2 A:TYR223 4.5 62.4 1.0 C A:TRP248 4.6 46.9 1.0 CE2 A:TYR223 4.6 64.1 1.0 CZ3 A:TRP248 4.7 46.6 1.0 CH2 A:TRP248 4.7 45.3 1.0 OE2 A:GLU117 4.8 60.7 1.0 CE3 A:TRP248 4.8 47.2 1.0 CG A:ASP114 4.9 51.6 1.0 OE1 A:GLU117 4.9 69.8 1.0 CZ2 A:TRP248 4.9 43.1 1.0 CD2 A:TRP248 5.0 45.2 1.0

Calcium binding site 2 out of 5 in the Human Antibody 32D6 Fab in Complex with H1N1 Influenza A Virus HA1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Antibody 32D6 Fab in Complex with H1N1 Influenza A Virus HA1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:72.8 occ:1.00 O B:HOH604 2.9 43.9 1.0 O B:TRP248 3.6 63.0 1.0 OD2 B:ASP114 3.8 57.4 1.0 OG1 B:THR249 4.0 67.9 1.0 OE2 B:GLU117 4.2 73.3 1.0 CD1 B:TYR223 4.3 73.5 1.0 CE1 B:TYR223 4.3 74.9 1.0 CA B:THR249 4.5 64.7 1.0 CB B:THR249 4.5 63.6 1.0 OE1 B:GLU117 4.6 87.4 1.0 C B:TRP248 4.7 59.3 1.0 CD B:GLU117 4.8 76.6 1.0 CG B:ASP114 4.8 57.6 1.0 CZ3 B:TRP248 4.8 57.6 1.0 CE3 B:TRP248 4.9 57.9 1.0 CH2 B:TRP248 5.0 57.6 1.0

Calcium binding site 3 out of 5 in the Human Antibody 32D6 Fab in Complex with H1N1 Influenza A Virus HA1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human Antibody 32D6 Fab in Complex with H1N1 Influenza A Virus HA1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca502 b:71.7 occ:1.00 O C:HOH609 3.1 64.7 1.0 OD2 C:ASP114 3.4 57.8 1.0 O C:TRP248 3.6 51.4 1.0 OG1 C:THR249 3.7 52.3 1.0 OE2 C:GLU117 4.3 58.3 1.0 CD1 C:TYR223 4.3 65.6 1.0 CE1 C:TYR223 4.3 67.0 1.0 CZ3 C:TRP248 4.5 56.2 1.0 CG C:ASP114 4.6 53.8 1.0 CA C:THR249 4.6 49.6 1.0 CB C:THR249 4.6 49.0 1.0 CE3 C:TRP248 4.7 55.9 1.0 CH2 C:TRP248 4.7 57.5 1.0 C C:TRP248 4.7 49.6 1.0 OE1 C:GLU117 4.9 59.7 1.0 CD C:GLU117 4.9 55.6 1.0 CD2 C:TRP248 5.0 58.4 1.0 CZ2 C:TRP248 5.0 56.2 1.0

Calcium binding site 4 out of 5 in the Human Antibody 32D6 Fab in Complex with H1N1 Influenza A Virus HA1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Human Antibody 32D6 Fab in Complex with H1N1 Influenza A Virus HA1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca502 b:71.5 occ:1.00 O D:HOH612 3.4 47.7 1.0 O D:TRP248 3.7 55.0 1.0 OG1 D:THR249 3.9 54.9 1.0 OD1 D:ASP114 4.0 70.3 1.0 OE2 D:GLU117 4.0 62.4 1.0 CE2 D:TYR223 4.3 66.2 1.0 CD2 D:TYR223 4.3 66.0 1.0 CA D:THR249 4.5 53.4 1.0 OE1 D:GLU117 4.5 71.0 1.0 CB D:THR249 4.5 52.6 1.0 CD D:GLU117 4.5 62.8 1.0 CZ3 D:TRP248 4.7 61.9 1.0 C D:TRP248 4.8 54.1 1.0 CH2 D:TRP248 4.8 61.5 1.0 CE3 D:TRP248 4.9 63.7 1.0

Calcium binding site 5 out of 5 in the Human Antibody 32D6 Fab in Complex with H1N1 Influenza A Virus HA1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Human Antibody 32D6 Fab in Complex with H1N1 Influenza A Virus HA1 within 5.0Å range: probe atom residue distance (Å) B Occ O:Ca301 b:0.5 occ:0.50 O O:HOH419 4.7 67.7 0.5 O O:ARG59 4.9 44.8 1.0

C.C.Lee, C.Y.Yang, L.L.Lin, T.P.Ko, A.H.Chang, S.S.Chang, A.H.Wang. An Effective Neutralizing Antibody Against Influenza Virus H1N1 From Human B Cells. Sci Rep V. 9 4546 2019.
ISSN: ESSN 2045-2322
PubMed: 30872685
DOI: 10.1038/S41598-019-40937-4