Calcium in PDB 7kpj: Crystal Structure of Ruminococcus Gnavus Immunoglobulin Binding Protein in Complex with 338E6 Fab

The structure of Crystal Structure of Ruminococcus Gnavus Immunoglobulin Binding Protein in Complex with 338E6 Fab, PDB code: 7kpj was solved by M.T.Borowska, E.J.Adams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	83.36 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	85.24, 102.191, 118.28, 90, 102.05, 90
R / Rfree (%)	22.9 / 26.6

The binding sites of Calcium atom in the Crystal Structure of Ruminococcus Gnavus Immunoglobulin Binding Protein in Complex with 338E6 Fab (pdb code 7kpj). 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 Ruminococcus Gnavus Immunoglobulin Binding Protein in Complex with 338E6 Fab, PDB code: 7kpj:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Ruminococcus Gnavus Immunoglobulin Binding Protein in Complex with 338E6 Fab


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 Ruminococcus Gnavus Immunoglobulin Binding Protein in Complex with 338E6 Fab within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca301 b:29.7 occ:1.00 OD1 E:ASP178 2.2 34.3 1.0 O E:ILE184 2.4 29.1 1.0 OD1 E:ASP182 2.5 33.5 1.0 OD1 E:ASP180 2.5 31.4 1.0 OD2 E:ASP180 2.6 33.8 1.0 CG E:ASP180 2.9 35.5 1.0 CG E:ASP182 3.3 35.5 1.0 CG E:ASP178 3.4 30.9 1.0 C E:ILE184 3.6 32.4 1.0 OD2 E:ASP182 3.7 36.6 1.0 CA E:ASP178 3.9 32.2 1.0 CB E:ASP178 4.0 29.9 1.0 N E:ILE184 4.1 29.6 1.0 N E:ASP182 4.3 33.4 1.0 CA E:ILE184 4.4 32.1 1.0 OD2 E:ASP178 4.4 30.3 1.0 CB E:ASP182 4.4 33.2 1.0 CB E:ASP180 4.4 32.6 1.0 N E:PHE185 4.6 26.4 1.0 CA E:PHE185 4.6 29.9 1.0 C E:ASP178 4.6 32.7 1.0 N E:GLY181 4.7 34.8 1.0 OE1 E:GLU189 4.7 31.5 1.0 CB E:ILE184 4.7 33.3 1.0 CA E:ASP182 4.8 34.8 1.0 N E:GLY183 4.8 38.5 1.0 N E:ASP180 4.9 28.9 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Ruminococcus Gnavus Immunoglobulin Binding Protein in Complex with 338E6 Fab


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 Ruminococcus Gnavus Immunoglobulin Binding Protein in Complex with 338E6 Fab within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca301 b:53.5 occ:1.00 OD1 F:ASP182 2.2 52.0 1.0 O F:ILE184 2.3 51.6 1.0 OD2 F:ASP180 2.5 52.4 1.0 OD2 F:ASP178 2.6 53.2 1.0 OD1 F:ASP180 3.0 57.0 1.0 CG F:ASP180 3.1 54.7 1.0 CG F:ASP182 3.2 53.0 1.0 C F:ILE184 3.5 50.2 1.0 CG F:ASP178 3.6 52.4 1.0 OD2 F:ASP182 3.6 57.4 1.0 CA F:ASP178 3.9 52.2 1.0 CB F:ASP178 4.1 50.1 1.0 CB F:ASP182 4.4 53.7 1.0 CA F:PHE185 4.4 49.3 1.0 N F:ILE184 4.4 51.6 1.0 N F:PHE185 4.4 49.3 1.0 CA F:ILE184 4.4 53.3 1.0 N F:ASP182 4.5 54.6 1.0 C F:ASP178 4.6 53.3 1.0 CB F:ASP180 4.6 54.0 1.0 OD1 F:ASP178 4.6 51.3 1.0 OE2 F:GLU189 4.7 53.6 1.0 CB F:ILE184 4.7 51.5 1.0 N F:ASP178 4.9 53.2 1.0 N F:ASP180 4.9 48.8 1.0 CA F:ASP182 4.9 55.8 1.0 N F:GLY181 5.0 50.5 1.0

M.T.Borowska, C.Drees, A.E.Yarawsky, M.Viswanathan, S.M.Ryan, J.J.Bunker, A.B.Herr, A.Bendelac, E.J.Adams. The Molecular Characterization of Antibody Binding to A Superantigen-Like Protein From A Commensal Microbe. Proc.Natl.Acad.Sci.Usa V. 118 2021.
ISSN: ESSN 1091-6490
PubMed: 34548394
DOI: 10.1073/PNAS.2023898118