Sodium 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
Calcium	(Ca)	4 atoms

The binding sites of Sodium 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 Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of A-Domain in Complex with Antibody, PDB code: 3q3g:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of A-Domain in Complex with Antibody


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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 D:Na800 b:41.2 occ:1.00 O D:HOH1230 3.5 37.3 1.0 OG1 D:THR119 3.6 59.6 1.0 CG2 D:VAL95 4.2 26.9 1.0 O D:GLN116 4.3 40.2 1.0 O D:HOH1239 4.4 28.7 1.0 CG1 D:VAL95 4.4 26.6 1.0 O D:GLY117 4.5 38.0 1.0 C D:GLY117 4.6 38.7 1.0 N D:THR119 4.8 34.6 1.0 CA D:GLY117 4.8 36.2 1.0 CB D:THR119 5.0 46.7 1.0 N D:THR118 5.0 34.0 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of A-Domain in Complex with Antibody


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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 H:Na801 b:37.9 occ:1.00 N H:VAL132 3.1 37.0 1.0 O H:VAL132 3.3 37.1 1.0 CA H:VAL132 3.9 35.8 1.0 C H:VAL132 4.0 39.0 1.0 C H:SER131 4.1 41.5 1.0 CB H:VAL132 4.1 38.2 1.0 CA H:SER131 4.2 37.1 1.0 CG1 H:VAL217 4.5 31.1 1.0 NZ H:LYS219 4.7 62.6 1.0 CG2 H:VAL132 4.7 37.9 1.0 O H:PRO130 4.8 42.5 1.0 CB H:SER131 4.8 40.1 1.0

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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 H:Na802 b:58.3 occ:1.00 NZ H:LYS40 3.1 67.5 1.0 O H:HOH2244 3.2 40.8 1.0 NH1 H:ARG42 3.8 98.3 1.0 OE2 H:GLU48 4.2 72.6 1.0 CE H:LYS40 4.3 56.7 1.0 CE1 H:PHE66 4.3 60.1 1.0 CZ H:PHE66 4.6 58.9 1.0 O H:GLU91 4.8 52.9 1.0 CD H:LYS40 4.8 54.0 1.0 CB H:GLU91 5.0 55.0 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