Calcium in PDB 7ffn: Cryo-Em Structure of Veev Vlp-LDLRAD3-D1 Complex at the 5-Fold Axes

All present enzymatic activity of Cryo-Em Structure of Veev Vlp-LDLRAD3-D1 Complex at the 5-Fold Axes:
3.4.21.90;

The binding sites of Calcium atom in the Cryo-Em Structure of Veev Vlp-LDLRAD3-D1 Complex at the 5-Fold Axes (pdb code 7ffn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Cryo-Em Structure of Veev Vlp-LDLRAD3-D1 Complex at the 5-Fold Axes, PDB code: 7ffn:

Calcium binding site 1 out of 1 in the Cryo-Em Structure of Veev Vlp-LDLRAD3-D1 Complex at the 5-Fold Axes


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 Veev Vlp-LDLRAD3-D1 Complex at the 5-Fold Axes within 5.0Å range: probe atom residue distance (Å) B Occ M:Ca100 b:64.9 occ:1.00 OD1 M:ASP50 2.5 59.0 1.0 OD2 M:ASP60 2.5 64.7 1.0 O M:LEU52 2.5 59.0 1.0 OD2 M:ASP54 2.6 59.0 1.0 O M:TRP47 2.9 44.5 1.0 OE2 M:GLU61 3.1 68.7 1.0 CG M:ASP60 3.2 64.7 1.0 CG M:ASP54 3.2 59.0 1.0 OD1 M:ASP60 3.5 64.7 1.0 CG M:ASP50 3.5 59.0 1.0 CB M:ASP54 3.5 59.0 1.0 N M:ASP54 3.7 59.0 1.0 C M:LEU52 3.7 59.0 1.0 CG M:GLU61 3.7 68.7 1.0 OD2 M:ASP50 3.8 59.0 1.0 CD M:GLU61 3.8 68.7 1.0 O M:GLN48 3.9 55.6 1.0 OD1 M:ASP54 4.1 59.0 1.0 C M:TRP47 4.1 44.5 1.0 CA M:ASP54 4.2 59.0 1.0 CB M:ASP60 4.4 64.7 1.0 CA M:PRO53 4.4 60.4 1.0 C M:PRO53 4.4 60.4 1.0 N M:LEU52 4.5 59.0 1.0 N M:PRO53 4.5 60.4 1.0 C M:GLN48 4.6 55.6 1.0 N M:ASP50 4.6 59.0 1.0 CA M:LEU52 4.7 59.0 1.0 CB M:ASP50 4.8 59.0 1.0 CB M:TRP47 4.9 44.5 1.0 CA M:TRP47 5.0 44.5 1.0 N M:GLY51 5.0 61.0 1.0

B.Ma, C.Huang, J.Ma, Y.Xiang, X.Zhang. Structure of Venezuelan Equine Encephalitis Virus with Its Receptor LDLRAD3 Nature 2021.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-021-03909-1