Calcium in PDB 7pi3: Pfcyrpa Bound to Fab Fragments From Monoclonal Antibodies Cy.003, Cy.004 and Cy.007

The structure of Pfcyrpa Bound to Fab Fragments From Monoclonal Antibodies Cy.003, Cy.004 and Cy.007, PDB code: 7pi3 was solved by R.J.Ragotte, M.K.Higgins, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.64 / 3.27
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	164.842, 164.842, 382.311, 90, 90, 90
R / Rfree (%)	28.5 / 29.8

The binding sites of Calcium atom in the Pfcyrpa Bound to Fab Fragments From Monoclonal Antibodies Cy.003, Cy.004 and Cy.007 (pdb code 7pi3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Pfcyrpa Bound to Fab Fragments From Monoclonal Antibodies Cy.003, Cy.004 and Cy.007, PDB code: 7pi3:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Pfcyrpa Bound to Fab Fragments From Monoclonal Antibodies Cy.003, Cy.004 and Cy.007


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Pfcyrpa Bound to Fab Fragments From Monoclonal Antibodies Cy.003, Cy.004 and Cy.007 within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca401 b:190.6 occ:0.00 OD1 F:ASP121 2.9 163.0 1.0 ND1 F:HIS124 3.0 148.8 1.0 NZ A:LYS128 3.0 140.2 1.0 CA F:GLY123 3.0 148.2 1.0 OD2 F:ASP127 3.1 151.1 1.0 N F:GLY123 3.2 149.4 1.0 CE1 F:HIS124 3.5 149.2 1.0 OD2 F:ASP120 3.6 162.6 1.0 N F:HIS124 3.6 145.4 1.0 C F:GLY123 3.6 146.7 1.0 OE2 A:GLU120 3.9 118.9 1.0 CG F:ASP120 3.9 161.2 1.0 CG F:ASP121 4.0 162.2 1.0 CA F:CA402 4.0 112.3 0.0 OD1 F:ASP120 4.1 161.6 1.0 CG F:ASP127 4.1 148.7 1.0 CG F:HIS124 4.2 147.0 1.0 OD2 F:ASP121 4.3 164.6 1.0 CE A:LYS128 4.4 139.5 1.0 C F:GLY122 4.5 150.8 1.0 OD1 F:ASP127 4.5 149.1 1.0 O F:GLY123 4.6 146.7 1.0 N F:GLY122 4.7 153.0 1.0 CB F:HIS124 4.7 145.3 1.0 CA F:HIS124 4.7 144.7 1.0 NE2 F:HIS124 4.8 148.7 1.0 CB F:ASP120 4.9 158.4 1.0 CD A:LYS128 5.0 138.8 1.0 N F:ASP121 5.0 155.5 1.0

Calcium binding site 2 out of 8 in the Pfcyrpa Bound to Fab Fragments From Monoclonal Antibodies Cy.003, Cy.004 and Cy.007


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Pfcyrpa Bound to Fab Fragments From Monoclonal Antibodies Cy.003, Cy.004 and Cy.007 within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca402 b:112.3 occ:0.00 OD2 F:ASP120 2.5 162.6 1.0 OD1 F:ASP127 2.7 149.1 1.0 OE2 F:GLU131 2.9 167.1 1.0 ND2 G:ASN48 3.1 155.8 1.0 CG F:ASP127 3.6 148.7 1.0 OE1 F:GLU131 3.6 166.6 1.0 CD F:GLU131 3.7 165.1 1.0 CG F:ASP120 3.7 161.2 1.0 OD2 F:ASP127 3.8 151.1 1.0 ND1 F:HIS124 3.9 148.8 1.0 OH G:TYR67 3.9 168.2 1.0 CA F:CA401 4.0 190.6 0.0 CE1 G:TYR67 4.1 165.8 1.0 CZ G:TYR67 4.2 166.8 1.0 CG G:ASN48 4.4 154.9 1.0 CG F:HIS124 4.4 147.0 1.0 OD1 F:ASP120 4.5 161.6 1.0 CB F:HIS124 4.5 145.3 1.0 CE1 F:HIS124 4.6 149.2 1.0 CB F:ASP120 4.7 158.4 1.0 CB F:ASP127 4.9 144.6 1.0

Calcium binding site 3 out of 8 in the Pfcyrpa Bound to Fab Fragments From Monoclonal Antibodies Cy.003, Cy.004 and Cy.007


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Pfcyrpa Bound to Fab Fragments From Monoclonal Antibodies Cy.003, Cy.004 and Cy.007 within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca401 b:185.3 occ:0.00 OD1 M:ASP121 2.3 150.4 1.0 OE2 H:GLU120 2.4 164.4 1.0 OD2 M:ASP121 2.7 151.1 1.0 CG M:ASP121 2.8 149.6 1.0 CE H:LYS128 2.9 179.5 1.0 CD H:GLU120 3.4 162.8 1.0 CA M:GLY123 3.6 141.0 1.0 NZ H:LYS128 3.7 181.8 1.0 CD H:LYS128 3.8 176.2 1.0 N M:GLY123 3.8 141.1 1.0 OE1 H:GLU120 4.0 163.9 1.0 CB M:ASP121 4.3 145.2 1.0 CE1 M:HIS124 4.3 143.2 1.0 ND1 M:HIS124 4.4 142.5 1.0 CG H:GLU120 4.5 157.1 1.0 CB H:GLU120 4.6 152.1 1.0 OD1 M:ASP120 4.6 150.3 1.0 C M:GLY123 4.6 140.5 1.0 OD2 M:ASP127 4.9 142.5 1.0 N M:ASP121 4.9 143.1 1.0 CG M:ASP120 4.9 149.3 1.0 OD2 M:ASP120 4.9 150.7 1.0

Calcium binding site 4 out of 8 in the Pfcyrpa Bound to Fab Fragments From Monoclonal Antibodies Cy.003, Cy.004 and Cy.007


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Pfcyrpa Bound to Fab Fragments From Monoclonal Antibodies Cy.003, Cy.004 and Cy.007 within 5.0Å range: probe atom residue distance (Å) B Occ M:Ca401 b:136.4 occ:0.00 OD1 M:ASP127 2.2 140.5 1.0 OE2 M:GLU131 2.6 159.4 1.0 OD2 M:ASP120 2.6 150.7 1.0 CG M:ASP127 3.1 140.1 1.0 ND2 N:ASN48 3.1 155.7 1.0 OD2 M:ASP127 3.4 142.5 1.0 CD M:GLU131 3.5 156.3 1.0 ND1 M:HIS124 3.6 142.5 1.0 OE1 M:GLU131 3.7 157.5 1.0 CG M:ASP120 3.9 149.3 1.0 CB M:HIS124 3.9 139.0 1.0 CG M:HIS124 4.0 140.9 1.0 CB M:ASP127 4.4 135.7 1.0 CG N:ASN48 4.4 154.8 1.0 OG M:SER126 4.4 138.1 1.0 CE1 M:HIS124 4.5 143.2 1.0 CB M:ASP120 4.6 145.0 1.0 CA M:ASP127 4.7 134.3 1.0 N M:ASP127 4.7 134.3 1.0 CE1 N:TYR67 4.7 168.9 1.0 N M:HIS124 4.7 139.3 1.0 OD1 M:ASP120 4.8 150.3 1.0 OH N:TYR67 4.8 170.9 1.0 CA M:HIS124 4.9 138.6 1.0 CZ N:TYR67 4.9 169.7 1.0 CG M:GLU131 4.9 148.2 1.0 CD2 M:HIS124 5.0 142.3 1.0

Calcium binding site 5 out of 8 in the Pfcyrpa Bound to Fab Fragments From Monoclonal Antibodies Cy.003, Cy.004 and Cy.007


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Pfcyrpa Bound to Fab Fragments From Monoclonal Antibodies Cy.003, Cy.004 and Cy.007 within 5.0Å range: probe atom residue distance (Å) B Occ T:Ca401 b:233.5 occ:0.00 OD1 T:ASP121 2.1 186.2 1.0 NZ O:LYS128 2.5 193.9 1.0 CG T:ASP121 3.0 185.6 1.0 OD1 T:ASP120 3.1 185.9 1.0 CE O:LYS128 3.3 191.9 1.0 OD2 T:ASP121 3.4 187.9 1.0 CG T:ASP120 3.5 184.9 1.0 OD2 T:ASP120 3.6 186.3 1.0 OD2 T:ASP127 3.8 179.3 1.0 N T:GLY123 3.9 176.2 1.0 CA T:GLY123 4.1 176.0 1.0 N T:ASP121 4.1 179.1 1.0 CD O:LYS128 4.3 188.8 1.0 OE2 O:GLU120 4.3 177.8 1.0 CB T:ASP121 4.3 181.0 1.0 ND1 T:HIS124 4.3 181.1 1.0 CB T:ASP120 4.5 181.1 1.0 CE1 T:HIS124 4.6 181.7 1.0 CA T:ASP121 4.7 179.1 1.0 N T:GLY122 4.7 177.8 1.0 CG T:ASP127 4.9 176.9 1.0 C T:GLY123 5.0 175.6 1.0

Calcium binding site 6 out of 8 in the Pfcyrpa Bound to Fab Fragments From Monoclonal Antibodies Cy.003, Cy.004 and Cy.007


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Pfcyrpa Bound to Fab Fragments From Monoclonal Antibodies Cy.003, Cy.004 and Cy.007 within 5.0Å range: probe atom residue distance (Å) B Occ T:Ca402 b:235.5 occ:0.00 OD2 T:ASP120 2.5 186.3 1.0 OE1 T:GLU131 3.0 191.8 1.0 OH U:TYR67 3.0 190.6 1.0 CZ U:TYR67 3.1 189.0 1.0 OE2 T:GLU131 3.1 192.3 1.0 CE1 U:TYR67 3.2 188.1 1.0 ND2 U:ASN48 3.3 184.3 1.0 CD T:GLU131 3.4 189.7 1.0 OD1 T:ASP127 3.4 177.7 1.0 CG T:ASP120 3.6 184.9 1.0 CE2 U:TYR67 3.8 188.0 1.0 CD1 U:TYR67 4.0 187.1 1.0 OD1 T:ASP120 4.1 185.9 1.0 CG T:ASP127 4.4 176.9 1.0 CG U:ASN48 4.4 183.6 1.0 CD2 U:TYR67 4.5 187.1 1.0 OD2 T:ASP127 4.6 179.3 1.0 CG U:TYR67 4.6 186.2 1.0 CB T:ASP120 4.7 181.1 1.0 CG T:GLU131 4.9 180.9 1.0 OD1 U:ASN48 5.0 184.5 1.0

Calcium binding site 7 out of 8 in the Pfcyrpa Bound to Fab Fragments From Monoclonal Antibodies Cy.003, Cy.004 and Cy.007


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Pfcyrpa Bound to Fab Fragments From Monoclonal Antibodies Cy.003, Cy.004 and Cy.007 within 5.0Å range: probe atom residue distance (Å) B Occ a:Ca401 b:241.7 occ:0.00 NZ V:LYS128 2.4 218.2 1.0 OD2 a:ASP120 3.1 195.8 1.0 ND1 a:HIS124 3.1 190.2 1.0 CE1 a:HIS124 3.2 190.8 1.0 OD2 a:ASP127 3.4 188.6 1.0 OD1 a:ASP121 3.5 191.5 1.0 CA a:CA402 3.7 178.4 0.0 CG a:ASP120 3.7 193.7 1.0 CE V:LYS128 3.9 216.0 1.0 OE2 V:GLU120 4.0 190.1 1.0 CG a:ASP127 4.3 186.6 1.0 OD1 a:ASP120 4.3 194.7 1.0 CG a:HIS124 4.3 188.2 1.0 OD1 a:ASP127 4.4 186.6 1.0 NE2 a:HIS124 4.4 190.6 1.0 CB a:ASP120 4.5 188.7 1.0 N a:GLY123 4.5 185.1 1.0 CA a:GLY123 4.5 185.1 1.0 CG a:ASP121 4.5 191.2 1.0 N a:HIS124 4.7 184.3 1.0 OD2 a:ASP121 4.8 193.1 1.0 CD V:LYS128 4.8 212.6 1.0 C a:GLY123 4.9 184.8 1.0 CD V:GLU120 5.0 188.9 1.0

Calcium binding site 8 out of 8 in the Pfcyrpa Bound to Fab Fragments From Monoclonal Antibodies Cy.003, Cy.004 and Cy.007


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Pfcyrpa Bound to Fab Fragments From Monoclonal Antibodies Cy.003, Cy.004 and Cy.007 within 5.0Å range: probe atom residue distance (Å) B Occ a:Ca402 b:178.4 occ:0.00 OD1 a:ASP127 2.1 186.6 1.0 OE2 a:GLU131 2.8 206.3 1.0 OD2 a:ASP120 2.9 195.8 1.0 ND2 b:ASN48 3.1 192.5 1.0 CG a:ASP127 3.1 186.6 1.0 ND1 a:HIS124 3.3 190.2 1.0 OD2 a:ASP127 3.5 188.6 1.0 CA a:CA401 3.7 241.7 0.0 CD a:GLU131 3.7 203.7 1.0 OE1 a:GLU131 3.9 205.6 1.0 CG a:ASP120 4.1 193.7 1.0 CE1 a:HIS124 4.1 190.8 1.0 CG a:HIS124 4.1 188.2 1.0 CB a:HIS124 4.3 185.4 1.0 CE1 b:TYR67 4.4 194.1 1.0 CG b:ASN48 4.4 191.8 1.0 CB a:ASP127 4.4 183.9 1.0 OG a:SER126 4.6 187.3 1.0 CB a:ASP120 4.6 188.7 1.0 CA a:ASP127 4.8 182.9 1.0 N a:ASP127 4.9 182.9 1.0 CD1 b:TYR67 4.9 193.1 1.0

R.J.Ragotte, D.Pulido, A.M.Lias, D.Quinkert, D.G.W.Alanine, A.Jamwal, H.Davies, A.Nacer, E.D.Lowe, G.W.Grime, J.J.Illingworth, R.F.Donat, E.F.Garman, P.W.Bowyer, M.K.Higgins, S.J.Draper. Heterotypic Interactions Drive Antibody Synergy Against A Malaria Vaccine Candidate. Nat Commun V. 13 933 2022.
ISSN: ESSN 2041-1723
PubMed: 35177602
DOI: 10.1038/S41467-022-28601-4