Calcium in PDB 5aze: Fab Fragment of Calcium-Dependent Antigen Binding Antibody, 6RL#9

The structure of Fab Fragment of Calcium-Dependent Antigen Binding Antibody, 6RL#9, PDB code: 5aze was solved by S.Kadono, N.Hironiwa, S.Ishii, T.Igawa, K.Hattori, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.470, 79.860, 116.250, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 27.2

The binding sites of Calcium atom in the Fab Fragment of Calcium-Dependent Antigen Binding Antibody, 6RL#9 (pdb code 5aze). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Fab Fragment of Calcium-Dependent Antigen Binding Antibody, 6RL#9, PDB code: 5aze:

Calcium binding site 1 out of 1 in the Fab Fragment of Calcium-Dependent Antigen Binding Antibody, 6RL#9


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Fab Fragment of Calcium-Dependent Antigen Binding Antibody, 6RL#9 within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca301 b:47.7 occ:1.00 O H:ASP100 2.2 42.4 1.0 O H:GLU105 2.4 46.2 1.0 OD2 H:ASP99 2.7 31.3 1.0 C H:GLU105 3.5 45.1 1.0 C H:ASP100 3.5 43.6 1.0 CG H:ASP99 3.6 31.3 1.0 O H:GLY102 3.8 52.2 1.0 OD1 H:ASP99 3.8 32.0 1.0 N H:GLU105 4.1 49.9 1.0 N H:GLY104 4.2 56.3 1.0 C H:GLY104 4.2 52.8 1.0 CA H:GLU105 4.3 48.1 1.0 N H:TYR106 4.3 40.3 1.0 C H:PRO101 4.4 48.9 1.0 N H:PRO101 4.4 45.8 1.0 N H:ASP100 4.4 37.7 1.0 CA H:ASP100 4.4 41.0 1.0 CA H:PRO101 4.4 47.4 1.0 CA H:TYR106 4.4 36.8 1.0 C H:GLY102 4.5 53.1 1.0 O H:GLY104 4.6 54.5 1.0 CA H:GLY104 4.6 54.4 1.0 CE2 H:TYR107 4.6 30.0 1.0 O H:PRO101 4.6 49.2 1.0 N H:TYR107 4.6 31.2 1.0 N H:GLY102 4.6 50.4 1.0 CD2 H:TYR107 4.7 29.4 1.0 O H:HOH417 4.7 32.3 1.0 CB H:ASP100 4.7 42.0 1.0 C H:ASP99 4.8 33.7 1.0 CB H:GLU105 4.9 49.5 1.0 CD2 H:TYR106 4.9 38.3 1.0 O H:TYR107 5.0 27.7 1.0

N.Hironiwa, S.Ishii, S.Kadono, Y.Iwayanagi, F.Mimoto, K.Habu, T.Igawa, K.Hattori. Calcium-Dependent Antigen Binding As A Novel Modality For Antibody Recycling By Endosomal Antigen Dissociation Mabs V. 8 65 2016.
ISSN: ESSN 1942-0870
PubMed: 26496237
DOI: 10.1080/19420862.2015.1110660