Calcium in PDB 5vyf: Structure of Single Chain Fel D 1 Bound to A Neutralizing Antibody

The structure of Structure of Single Chain Fel D 1 Bound to A Neutralizing Antibody, PDB code: 5vyf was solved by M.C.Franklin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	98.40 / 2.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.985, 131.480, 148.357, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 25.9

The binding sites of Calcium atom in the Structure of Single Chain Fel D 1 Bound to A Neutralizing Antibody (pdb code 5vyf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of Single Chain Fel D 1 Bound to A Neutralizing Antibody, PDB code: 5vyf:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Single Chain Fel D 1 Bound to A Neutralizing Antibody


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Single Chain Fel D 1 Bound to A Neutralizing Antibody within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca201 b:35.5 occ:1.00 OD1 F:ASP60 3.1 59.7 1.0 OH F:TYR113 3.3 47.1 1.0 OD2 F:ASP101 3.3 57.7 1.0 OD2 F:ASP60 3.7 56.7 1.0 CG F:ASP60 3.8 56.0 1.0 OH F:TYR49 4.2 44.3 1.0 CE F:MET64 4.2 62.8 1.0 CZ F:TYR113 4.3 48.2 1.0 CG F:ASP101 4.3 58.7 1.0 CG F:PHE105 4.4 45.8 1.0 CE1 F:TYR113 4.5 50.0 1.0 CD2 F:PHE105 4.6 44.5 1.0 CB F:PHE105 4.6 47.3 1.0 OD1 F:ASP101 4.6 59.6 1.0 CD1 F:PHE105 4.6 45.8 1.0 CE1 F:PHE14 4.8 53.8 1.0

Calcium binding site 2 out of 2 in the Structure of Single Chain Fel D 1 Bound to A Neutralizing Antibody


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Single Chain Fel D 1 Bound to A Neutralizing Antibody within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:42.0 occ:1.00 OD1 C:ASP60 3.0 57.9 1.0 OH C:TYR113 3.2 53.3 1.0 OD2 C:ASP101 3.2 70.3 1.0 OD2 C:ASP60 3.6 56.9 1.0 CG C:ASP60 3.7 56.2 1.0 CE C:MET64 4.2 67.0 1.0 CG C:ASP101 4.2 71.6 1.0 CZ C:TYR113 4.3 55.8 1.0 OH C:TYR49 4.3 47.3 1.0 OD1 C:ASP101 4.5 72.3 1.0 CE1 C:TYR113 4.5 58.1 1.0 CG C:PHE105 4.5 59.5 1.0 CB C:PHE105 4.7 60.9 1.0 CD2 C:PHE105 4.8 59.0 1.0 CD1 C:PHE105 4.8 59.1 1.0 CE1 C:PHE14 4.9 57.2 1.0

J.M.Orengo, A.R.Radin, V.Kamat, A.Badithe, L.H.Ben, B.L.Bennett, S.Zhong, D.Birchard, A.Limnander, A.Rafique, J.Bautista, A.Kostic, D.Newell, X.Duan, M.C.Franklin, W.Olson, T.Huang, N.A.Gandhi, L.Lipsich, N.Stahl, N.J.Papadopoulos, A.J.Murphy, G.D.Yancopoulos. Treating Cat Allergy with Monoclonal Igg Antibodies That Bind Allergen and Prevent Ige Engagement. Nat Commun V. 9 1421 2018.
ISSN: ESSN 2041-1723
PubMed: 29650949
DOI: 10.1038/S41467-018-03636-8