Calcium in PDB 8r84: Pentameric Igmfc-Aim Complex Focused Refinement

The binding sites of Calcium atom in the Pentameric Igmfc-Aim Complex Focused Refinement (pdb code 8r84). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Pentameric Igmfc-Aim Complex Focused Refinement, PDB code: 8r84:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Pentameric Igmfc-Aim Complex Focused Refinement


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Pentameric Igmfc-Aim Complex Focused Refinement within 5.0Å range: probe atom residue distance (Å) B Occ N:Ca401 b:20.0 occ:1.00 OE1 N:GLU339 2.6 118.0 1.0 OD1 N:ASP271 2.8 121.2 1.0 OD1 N:ASP270 2.8 115.6 1.0 O J:ASN106 2.8 119.5 1.0 CD N:GLU339 3.2 119.0 1.0 CG N:ASP270 3.7 114.9 1.0 OE2 N:GLU339 3.8 117.1 1.0 CA N:ASP271 3.8 116.4 1.0 N N:ASP271 3.9 115.1 1.0 CG N:ASP271 3.9 119.7 1.0 CG N:GLU339 4.0 119.7 1.0 C J:ASN106 4.0 118.8 1.0 CB N:GLU339 4.1 119.1 1.0 C N:ASP270 4.1 113.8 1.0 OD2 N:ASP270 4.2 113.6 1.0 O N:ASP270 4.3 113.8 1.0 CB N:ASP271 4.5 118.2 1.0 CA J:ASN106 4.7 119.5 1.0 CB J:ASN106 4.7 121.4 1.0 NZ J:LYS107 4.8 121.0 1.0 CB N:ASP270 4.8 114.4 1.0 CA N:ASP270 4.9 114.0 1.0 C N:ASP271 4.9 116.1 1.0 OD2 N:ASP271 4.9 114.8 1.0 SG N:CYS269 5.0 96.4 1.0

Calcium binding site 2 out of 2 in the Pentameric Igmfc-Aim Complex Focused Refinement


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Pentameric Igmfc-Aim Complex Focused Refinement within 5.0Å range: probe atom residue distance (Å) B Occ N:Ca402 b:20.0 occ:1.00 OD1 N:ASN312 2.2 88.8 1.0 OD2 N:ASP271 2.7 114.8 1.0 OD1 N:ASP334 2.7 108.2 1.0 OD2 N:ASP311 2.8 96.8 1.0 OD1 N:ASP311 2.8 94.2 1.0 CG N:ASP311 3.1 93.1 1.0 CG N:ASN312 3.5 90.2 1.0 CG N:ASP334 3.5 107.4 1.0 OD2 N:ASP334 3.5 106.6 1.0 CG N:ASP271 3.6 119.7 1.0 CB N:ASP271 3.7 118.2 1.0 ND2 N:ASN312 4.3 88.4 1.0 N N:ASN312 4.4 82.3 1.0 CB N:ASN312 4.5 83.4 1.0 SG N:CYS335 4.5 116.8 1.0 CB N:ASP311 4.5 88.2 1.0 OD1 N:ASP271 4.7 121.2 1.0 CA N:ASN312 4.8 80.7 1.0 NH1 N:ARG328 4.9 94.3 1.0 CB N:ASP334 5.0 106.0 1.0

Q.Chen, K.Ishii, H.Mori, A.Nishijima, S.Arai, T.Miyazaki, P.B.Rosenthal. Cryo-Em Reveals Structural Basis For Human Aim/CD5L Recognition of Polymeric Immunoglobulin M Nat Commun V. 15 9387 2024.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-024-53615-5