Calcium in PDB 3q3g: Crystal Structure of A-Domain in Complex with Antibody

The structure of Crystal Structure of A-Domain in Complex with Antibody, PDB code: 3q3g 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)	47.76 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	81.939, 157.218, 232.128, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 24.4

The structure of Crystal Structure of A-Domain in Complex with Antibody also contains other interesting chemical elements:

Chlorine	(Cl)	5 atoms
Sodium	(Na)	3 atoms

The binding sites of Calcium atom in the Crystal Structure of A-Domain in Complex with Antibody (pdb code 3q3g). 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: 3q3g:
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:27.5 occ:1.00 OD2 G:ASP242 2.3 46.0 1.0 OG G:SER144 2.4 34.4 1.0 O G:HOH1009 2.4 28.1 1.0 OG G:SER142 2.5 33.8 1.0 OD1 D:ASP107 2.5 29.6 1.0 O G:HOH1008 2.6 17.6 1.0 OD2 D:ASP107 2.6 31.7 1.0 CG D:ASP107 2.9 29.3 1.0 CG G:ASP242 3.4 41.1 1.0 CB G:SER142 3.5 28.1 1.0 CB G:SER144 3.6 26.4 1.0 OG1 G:THR209 3.7 36.4 1.0 OD1 G:ASP242 3.8 42.7 1.0 OD2 G:ASP140 4.1 42.6 1.0 O1 G:EDO620 4.3 38.0 1.0 CB D:ASP107 4.4 24.3 1.0 N G:GLY243 4.4 30.6 1.0 N G:SER144 4.4 26.6 1.0 OD1 G:ASP140 4.5 48.2 1.0 OH C:TYR31 4.5 32.8 1.0 C G:ASP242 4.6 36.1 1.0 CA G:SER144 4.6 25.2 1.0 CA G:GLY243 4.6 30.1 1.0 C1 G:EDO620 4.7 38.8 1.0 CA G:SER142 4.7 27.0 1.0 CG G:ASP140 4.7 45.7 1.0 CB G:ASP242 4.7 33.8 1.0 CD1 G:ILE145 4.7 34.9 1.0 C G:SER142 4.7 31.6 1.0 O G:ASP242 4.9 37.7 1.0 O G:SER142 4.9 32.4 1.0 CB G:THR209 4.9 33.0 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:40.9 occ:1.00 OD2 E:ASP242 2.3 51.8 1.0 OG E:SER144 2.3 31.5 1.0 O E:HOH1009 2.4 57.6 1.0 OG E:SER142 2.5 38.8 1.0 OD2 B:ASP107 2.6 41.8 1.0 OD1 B:ASP107 2.6 36.1 1.0 O A:HOH1008 2.6 53.8 1.0 CG B:ASP107 2.9 34.8 1.0 CG E:ASP242 3.3 47.2 1.0 CB E:SER142 3.4 33.7 1.0 OG1 E:THR209 3.6 31.5 1.0 CB E:SER144 3.7 31.1 1.0 OD1 E:ASP242 3.7 47.6 1.0 OD2 E:ASP140 4.1 35.6 1.0 OD1 E:ASP140 4.4 30.6 1.0 N E:GLY243 4.4 34.5 1.0 CB B:ASP107 4.4 28.9 1.0 N E:SER144 4.5 31.2 1.0 OH A:TYR31 4.5 36.9 1.0 C E:ASP242 4.5 40.7 1.0 O A:HOH1248 4.6 31.2 1.0 CA E:GLY243 4.6 34.0 1.0 CA E:SER144 4.6 29.8 1.0 CB E:ASP242 4.6 38.4 1.0 CG E:ASP140 4.6 33.2 1.0 CA E:SER142 4.7 31.1 1.0 CD1 E:ILE145 4.7 36.5 1.0 C E:SER142 4.8 36.4 1.0 O E:ASP242 4.8 42.0 1.0 O E:SER142 4.9 36.1 1.0 CB E:THR209 4.9 29.6 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:57.7 occ:1.00 OG I:SER144 2.3 43.9 1.0 OD2 I:ASP242 2.3 76.4 1.0 O I:HOH1009 2.4 51.2 1.0 O F:HOH1008 2.5 38.5 1.0 OD1 H:ASP107 2.6 61.9 1.0 OG I:SER142 2.6 57.1 1.0 OD2 H:ASP107 2.6 67.3 1.0 CG H:ASP107 2.9 61.0 1.0 CG I:ASP242 3.4 69.0 1.0 CB I:SER142 3.6 45.6 1.0 CB I:SER144 3.6 41.6 1.0 OG1 I:THR209 3.7 69.9 1.0 OD1 I:ASP242 3.7 68.0 1.0 OD2 I:ASP140 3.8 68.1 1.0 N I:GLY243 4.4 58.0 1.0 N I:SER144 4.4 40.0 1.0 CB H:ASP107 4.4 52.3 1.0 O1 F:EDO621 4.5 58.3 1.0 OH F:TYR31 4.5 71.4 1.0 CA I:SER144 4.6 39.4 1.0 C I:ASP242 4.6 61.5 1.0 CA I:GLY243 4.6 57.9 1.0 CB I:ASP242 4.7 60.1 1.0 CG I:ASP140 4.7 64.7 1.0 CD1 I:ILE145 4.7 59.5 1.0 OD1 I:ASP140 4.8 67.0 1.0 CA I:SER142 4.8 42.0 1.0 O I:ASP242 4.9 60.2 1.0 C I:SER142 4.9 46.0 1.0 CB I:THR209 4.9 73.9 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:40.5 occ:1.00 OD2 L:ASP242 2.3 64.4 1.0 OG L:SER144 2.3 47.6 1.0 O L:HOH1009 2.4 46.9 1.0 O J:HOH1008 2.6 34.9 1.0 OD2 K:ASP107 2.6 63.6 1.0 OG L:SER142 2.6 50.5 1.0 OD1 K:ASP107 2.6 55.2 1.0 CG K:ASP107 3.0 54.7 1.0 CG L:ASP242 3.4 59.6 1.0 CB L:SER142 3.5 45.4 1.0 CB L:SER144 3.6 41.3 1.0 OG1 L:THR209 3.7 46.1 1.0 OD1 L:ASP242 3.8 60.2 1.0 OD2 L:ASP140 4.3 58.9 1.0 N L:GLY243 4.4 47.9 1.0 CB K:ASP107 4.4 41.4 1.0 OD1 L:ASP140 4.4 52.8 1.0 N L:SER144 4.5 40.0 1.0 OH J:TYR31 4.5 41.5 1.0 O J:HOH1251 4.5 47.9 1.0 C L:ASP242 4.5 53.4 1.0 CA L:GLY243 4.6 46.8 1.0 CA L:SER144 4.6 39.9 1.0 CB L:ASP242 4.7 52.2 1.0 CA L:SER142 4.7 43.6 1.0 CG L:ASP140 4.8 55.1 1.0 CD1 L:ILE145 4.8 47.5 1.0 O L:ASP242 4.8 54.4 1.0 C L:SER142 4.8 47.5 1.0 CB L:THR209 4.9 43.9 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