Calcium in PDB 3qa3: Crystal Structure of A-Domain in Complex with Antibody

The structure of Crystal Structure of A-Domain in Complex with Antibody, PDB code: 3qa3 was solved by B.Mahalingam, J.P.Xiong, M.A.Arnaout, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.65 / 3.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	82.604, 158.346, 233.319, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 22.4

The binding sites of Calcium atom in the Crystal Structure of A-Domain in Complex with Antibody (pdb code 3qa3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of A-Domain in Complex with Antibody, PDB code: 3qa3:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of A-Domain in Complex with Antibody


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 A-Domain in Complex with Antibody within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca500 b:28.3 occ:1.00 O G:HOH1 2.2 36.8 1.0 OD2 G:ASP242 2.4 50.3 1.0 OG G:SER142 2.4 36.1 1.0 O D:HOH229 2.5 30.2 1.0 OD2 D:ASP107 2.5 44.8 1.0 OG G:SER144 2.5 38.0 1.0 OD1 D:ASP107 2.5 32.7 1.0 CG D:ASP107 2.9 33.1 1.0 CG G:ASP242 3.3 44.0 1.0 CB G:SER142 3.6 29.1 1.0 OD1 G:ASP242 3.7 47.7 1.0 CB G:SER144 3.7 28.3 1.0 OG1 G:THR209 3.7 36.1 1.0 OD2 G:ASP140 4.0 39.4 1.0 N G:SER144 4.4 27.3 1.0 OD1 G:ASP140 4.4 32.9 1.0 CB D:ASP107 4.4 24.8 1.0 O G:HOH55 4.4 46.2 1.0 N G:GLY243 4.5 24.0 1.0 CA G:SER144 4.5 26.9 1.0 OH C:TYR31 4.6 42.6 1.0 CG G:ASP140 4.6 34.5 1.0 CB G:ASP242 4.6 29.0 1.0 C G:SER142 4.6 29.6 1.0 C G:ASP242 4.7 30.1 1.0 CA G:SER142 4.7 26.1 1.0 O G:SER142 4.7 30.9 1.0 CA G:GLY243 4.7 23.1 1.0 CD1 G:ILE145 4.9 28.1 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of A-Domain in Complex with Antibody


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 A-Domain in Complex with Antibody within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca500 b:49.5 occ:1.00 O E:HOH67 2.2 58.8 1.0 OD1 E:ASP242 2.4 42.1 1.0 OG E:SER144 2.4 36.8 1.0 OG E:SER142 2.5 42.8 1.0 O B:HOH234 2.5 23.4 1.0 OD1 B:ASP107 2.5 53.1 1.0 OD2 B:ASP107 2.6 58.1 1.0 CG B:ASP107 2.9 50.8 1.0 CG E:ASP242 3.3 41.6 1.0 CB E:SER142 3.5 38.6 1.0 CB E:SER144 3.6 30.3 1.0 OG1 E:THR209 3.7 41.7 1.0 OD2 E:ASP242 3.7 45.3 1.0 OD2 E:ASP140 3.9 53.3 1.0 N E:SER144 4.3 29.1 1.0 CB B:ASP107 4.4 37.6 1.0 N E:GLY243 4.5 34.6 1.0 CA E:SER144 4.5 27.5 1.0 O E:HOH43 4.6 19.3 1.0 CB E:ASP242 4.6 35.9 1.0 OD1 E:ASP140 4.6 47.3 1.0 OH A:TYR31 4.6 40.0 1.0 C E:ASP242 4.6 37.8 1.0 CG E:ASP140 4.7 48.2 1.0 CA E:SER142 4.7 36.3 1.0 CA E:GLY243 4.7 34.2 1.0 C E:SER142 4.7 38.3 1.0 O E:SER142 4.9 37.9 1.0 N E:ILE145 5.0 24.9 1.0 O E:ASP242 5.0 37.6 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of A-Domain in Complex with Antibody


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of A-Domain in Complex with Antibody within 5.0Å range: probe atom residue distance (Å) B Occ I:Ca500 b:49.8 occ:1.00 O I:HOH1 2.2 68.5 1.0 OG I:SER142 2.4 48.6 1.0 OD2 I:ASP242 2.4 76.5 1.0 O H:HOH2 2.5 52.7 1.0 OG I:SER144 2.5 35.2 1.0 OD2 H:ASP107 2.5 62.7 1.0 OD1 H:ASP107 2.6 54.5 1.0 CG H:ASP107 2.8 54.6 1.0 CG I:ASP242 3.3 67.4 1.0 CB I:SER142 3.5 41.6 1.0 OD1 I:ASP242 3.6 69.3 1.0 CB I:SER144 3.6 35.4 1.0 OG1 I:THR209 3.7 45.3 1.0 OD2 I:ASP140 4.1 44.5 1.0 CB H:ASP107 4.3 43.9 1.0 N I:SER144 4.4 35.9 1.0 OD1 I:ASP140 4.4 38.8 1.0 O I:HOH6 4.5 25.6 1.0 N I:GLY243 4.5 46.8 1.0 CA I:SER144 4.5 35.5 1.0 CD1 I:ILE145 4.6 42.5 1.0 CB I:ASP242 4.6 50.9 1.0 OH F:TYR31 4.6 51.7 1.0 C I:ASP242 4.6 52.4 1.0 CG I:ASP140 4.6 40.3 1.0 CA I:GLY243 4.7 46.0 1.0 CA I:SER142 4.7 39.7 1.0 C I:SER142 4.9 46.1 1.0 O I:ASP242 5.0 53.2 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of A-Domain in Complex with Antibody


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of A-Domain in Complex with Antibody within 5.0Å range: probe atom residue distance (Å) B Occ L:Ca500 b:49.7 occ:1.00 O L:HOH1 2.2 40.4 1.0 OD1 L:ASP242 2.4 60.4 1.0 OG L:SER144 2.5 34.9 1.0 OD1 K:ASP107 2.5 45.1 1.0 O K:HOH2 2.5 54.8 1.0 OG L:SER142 2.5 40.9 1.0 OD2 K:ASP107 2.6 49.9 1.0 CG K:ASP107 2.9 43.6 1.0 CG L:ASP242 3.3 58.2 1.0 CB L:SER142 3.6 35.4 1.0 CB L:SER144 3.6 30.2 1.0 OG1 L:THR209 3.7 44.2 1.0 OD2 L:ASP242 3.7 65.0 1.0 OD2 L:ASP140 4.2 38.9 1.0 OD1 L:ASP140 4.2 46.5 1.0 CB K:ASP107 4.4 29.4 1.0 N L:SER144 4.4 30.8 1.0 N L:GLY243 4.5 39.8 1.0 CA L:SER144 4.5 30.2 1.0 CB L:ASP242 4.6 44.6 1.0 OH J:TYR31 4.6 39.4 1.0 C L:ASP242 4.6 46.2 1.0 CG L:ASP140 4.7 43.0 1.0 CA L:GLY243 4.7 38.8 1.0 CA L:SER142 4.8 34.4 1.0 CD1 L:ILE145 4.8 40.0 1.0 C L:SER142 4.9 39.0 1.0 N L:ILE145 5.0 34.9 1.0 O L:ASP242 5.0 47.3 1.0

B.Mahalingam, K.Ajroud, J.L.Alonso, S.Anand, B.D.Adair, A.L.Horenstein, F.Malavasi, J.P.Xiong, M.A.Arnaout. Stable Coordination of the Inhibitory CA2+ Ion at the Metal Ion-Dependent Adhesion Site in Integrin CD11B/CD18 By An Antibody-Derived Ligand Aspartate: Implications For Integrin Regulation and Structure-Based Drug Design. J.Immunol. V. 187 6393 2011.
ISSN: ISSN 0022-1767
PubMed: 22095715
DOI: 10.4049/JIMMUNOL.1102394