Calcium in PDB 8wyr: Cryo-Em Structure of Human CD5L Bound to Igm-Fc/J

The binding sites of Calcium atom in the Cryo-Em Structure of Human CD5L Bound to Igm-Fc/J (pdb code 8wyr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Cryo-Em Structure of Human CD5L Bound to Igm-Fc/J, PDB code: 8wyr:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Cryo-Em Structure of Human CD5L Bound to Igm-Fc/J


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structure of Human CD5L Bound to Igm-Fc/J within 5.0Å range: probe atom residue distance (Å) B Occ M:Ca401 b:113.5 occ:1.00 OE2 M:GLU339 2.5 112.7 1.0 O J:ASN106 2.5 105.7 1.0 OE1 M:GLU339 2.6 112.7 1.0 OD1 M:ASP270 2.6 114.2 1.0 CD M:GLU339 2.6 112.7 1.0 OD1 M:ASP271 3.0 111.0 1.0 C J:ASN106 3.4 105.7 1.0 CG M:ASP270 3.5 114.2 1.0 O M:ASP270 3.7 114.2 1.0 CG M:GLU339 3.9 112.7 1.0 C M:ASP270 4.0 114.2 1.0 CB J:ASN106 4.0 105.7 1.0 OD2 M:ASP270 4.0 114.2 1.0 CA J:ASN106 4.1 105.7 1.0 CD J:LYS107 4.1 107.7 1.0 N M:ASP271 4.2 111.0 1.0 CG M:ASP271 4.2 111.0 1.0 CA M:ASP271 4.3 111.0 1.0 N J:LYS107 4.4 107.7 1.0 CB M:GLU339 4.4 112.7 1.0 CB M:ASP270 4.5 114.2 1.0 CA J:LYS107 4.6 107.7 1.0 CA M:ASP270 4.7 114.2 1.0 CE J:LYS107 4.8 107.7 1.0 N M:ASP270 4.9 114.2 1.0 CB M:ASP271 4.9 111.0 1.0

Calcium binding site 2 out of 2 in the Cryo-Em Structure of Human CD5L Bound to Igm-Fc/J


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structure of Human CD5L Bound to Igm-Fc/J within 5.0Å range: probe atom residue distance (Å) B Occ M:Ca402 b:88.1 occ:1.00 OD2 M:ASP271 2.4 111.0 1.0 OD2 M:ASP311 2.4 95.5 1.0 CG M:ASP271 3.2 111.0 1.0 CG M:ASP311 3.2 95.5 1.0 CB M:ASP271 3.2 111.0 1.0 OD1 M:ASP334 3.2 101.5 1.0 OD1 M:ASP311 3.3 95.5 1.0 OD2 M:ASP334 3.5 101.5 1.0 CG M:ASP334 3.7 101.5 1.0 CB M:ASN312 3.7 99.4 1.0 CG M:ASN312 4.2 99.4 1.0 N M:ASN312 4.3 99.4 1.0 OD1 M:ASP271 4.4 111.0 1.0 CA M:ASN312 4.4 99.4 1.0 ND2 M:ASN312 4.5 99.4 1.0 CB M:ASP311 4.6 95.5 1.0 CA M:ASP271 4.7 111.0 1.0 OD1 M:ASN312 4.7 99.4 1.0 CD M:ARG328 4.8 91.4 1.0 C M:ASP311 4.9 95.5 1.0 NH1 M:ARG328 4.9 91.4 1.0

Y.Wang, C.Su, C.Ji, J.Xiao. CD5L Associates with Igm Via the J Chain. Nat Commun V. 15 8397 2024.
ISSN: ESSN 2041-1723
PubMed: 39333069
DOI: 10.1038/S41467-024-52175-Y