Calcium in PDB 8zca: Crystal Structure of Human CD47 Ecd Bound to Fab of HU1C8

The structure of Crystal Structure of Human CD47 Ecd Bound to Fab of HU1C8, PDB code: 8zca was solved by Z.Chen, J.Ding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.52 / 2.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	45.224, 79.931, 92.751, 112.5, 96.61, 103.16
R / Rfree (%)	21.5 / 26.6

The binding sites of Calcium atom in the Crystal Structure of Human CD47 Ecd Bound to Fab of HU1C8 (pdb code 8zca). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Human CD47 Ecd Bound to Fab of HU1C8, PDB code: 8zca:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Human CD47 Ecd Bound to Fab of HU1C8


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Human CD47 Ecd Bound to Fab of HU1C8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:45.6 occ:1.00 OD1 D:ASP101 2.1 45.2 1.0 O A:TYR94 2.4 44.9 1.0 O F:HOH311 2.4 44.9 1.0 OD1 A:ASP93 2.5 44.7 1.0 OD2 A:ASP93 2.5 44.8 1.0 OD1 A:ASP97 2.5 45.2 1.0 O F:HOH305 2.6 44.5 1.0 CG A:ASP93 2.9 44.7 1.0 CG D:ASP101 3.1 45.0 1.0 C A:TYR94 3.5 44.9 1.0 CG A:ASP97 3.7 45.0 1.0 NZ F:LYS41 3.8 45.1 1.0 OD2 D:ASP101 3.8 45.3 1.0 N A:TYR94 3.9 44.8 1.0 CB D:ASP101 4.0 44.8 1.0 CA D:ASP101 4.2 44.3 1.0 OD2 A:ASP97 4.2 44.9 1.0 CA A:TYR94 4.4 44.5 1.0 CB A:ASP93 4.4 44.5 1.0 N A:SER95 4.4 45.1 1.0 CA A:SER95 4.4 45.2 1.0 C A:SER95 4.5 45.4 1.0 OD1 A:ASN100 4.6 45.0 1.0 OD1 F:ASP46 4.6 45.1 1.0 OD2 F:ASP46 4.6 45.3 1.0 NZ F:LYS39 4.6 45.5 1.0 O A:SER95 4.7 45.7 1.0 ND2 A:ASN100 4.7 45.1 1.0 N A:ASP97 4.8 45.7 1.0 C A:ASP93 4.8 44.8 1.0 CA A:ASP97 4.8 45.9 1.0 CB A:ASP97 4.9 45.4 1.0 N A:ASP96 5.0 45.4 1.0 CA A:ASP93 5.0 44.6 1.0 CG F:ASP46 5.0 45.3 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Human CD47 Ecd Bound to Fab of HU1C8


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Human CD47 Ecd Bound to Fab of HU1C8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:45.6 occ:1.00 OD1 C:ASP101 2.3 43.8 1.0 OD1 B:ASP97 2.3 44.4 1.0 O B:TYR94 2.4 44.6 1.0 OD1 B:ASP93 2.5 44.2 1.0 O E:HOH311 2.5 43.9 1.0 O E:HOH310 2.6 42.6 1.0 OD2 B:ASP93 2.8 44.0 1.0 CG B:ASP93 3.0 44.0 1.0 CG C:ASP101 3.2 43.7 1.0 C B:TYR94 3.5 44.6 1.0 CG B:ASP97 3.5 43.7 1.0 N B:TYR94 4.0 44.7 1.0 CB C:ASP101 4.0 43.3 1.0 OD2 C:ASP101 4.0 43.8 1.0 OD2 B:ASP97 4.1 43.2 1.0 CA C:ASP101 4.2 43.2 1.0 CA B:SER95 4.4 44.0 1.0 N B:SER95 4.4 44.4 1.0 CA B:TYR94 4.4 44.7 1.0 C B:SER95 4.4 44.0 1.0 CB B:ASP93 4.5 44.0 1.0 OD1 B:ASN100 4.5 44.5 1.0 OD1 E:ASP46 4.5 43.8 1.0 N B:ASP97 4.6 44.3 1.0 NZ E:LYS39 4.6 43.7 1.0 CA B:ASP97 4.6 44.5 1.0 NZ E:LYS41 4.6 42.8 1.0 O B:SER95 4.7 44.1 1.0 CB B:ASP97 4.7 43.9 1.0 OD2 E:ASP46 4.7 43.9 1.0 C B:ASP93 4.7 44.5 1.0 O E:GLY44 4.7 43.7 1.0 CE E:LYS41 4.8 43.0 1.0 N B:ASP96 4.8 43.9 1.0 C B:ASP96 4.9 44.5 1.0 ND2 B:ASN100 4.9 44.2 1.0 CA B:ASP93 5.0 44.0 1.0 CB B:TYR30 5.0 44.6 1.0 CG E:ASP46 5.0 43.8 1.0

X.Lu, B.Sun. The Humanized Antibody HU1C8 Binds to A Distinct Epitope of CD47 in A Novel Metal Ion-Dependent Manner to Induce Low Rbc Toxicity and Effective Antitumour Activity To Be Published.