Calcium in PDB 9eau: Rrv Dkta Vlp in Complex with Vldlr-Lbd-Fc

All present enzymatic activity of Rrv Dkta Vlp in Complex with Vldlr-Lbd-Fc:
3.4.21.90;

The binding sites of Calcium atom in the Rrv Dkta Vlp in Complex with Vldlr-Lbd-Fc (pdb code 9eau). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Rrv Dkta Vlp in Complex with Vldlr-Lbd-Fc, PDB code: 9eau:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Rrv Dkta Vlp in Complex with Vldlr-Lbd-Fc


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Rrv Dkta Vlp in Complex with Vldlr-Lbd-Fc within 5.0Å range: probe atom residue distance (Å) B Occ Y:Ca201 b:9.7 occ:1.00 O Y:TRP132 2.3 8.8 1.0 OD1 Y:ASP135 2.3 10.9 1.0 OD2 Y:ASP139 2.4 10.1 1.0 O Y:GLU137 2.4 9.7 1.0 OD2 Y:ASP145 2.4 9.1 1.0 OD2 Y:ASP135 2.4 10.5 1.0 CG Y:ASP135 2.6 10.7 1.0 CG Y:ASP145 3.1 9.0 1.0 CB Y:ASP145 3.4 9.1 1.0 C Y:TRP132 3.4 9.8 1.0 CG Y:ASP139 3.5 9.9 1.0 C Y:GLU137 3.6 9.7 1.0 CB Y:TRP132 3.6 9.7 1.0 CA Y:TRP132 3.9 9.7 1.0 CB Y:ASP135 3.9 9.5 1.0 OD1 Y:ASP145 4.1 9.7 1.0 NZ M:LYS345 4.1 91.8 1.0 N Y:ASP139 4.1 9.3 1.0 CB Y:ASP139 4.1 9.5 1.0 CG Y:GLU137 4.2 10.3 1.0 N Y:GLU137 4.3 9.6 1.0 N Y:ASP135 4.4 11.3 1.0 OD1 Y:ASP139 4.5 9.4 1.0 OE2 Y:GLU146 4.5 8.6 1.0 CA Y:GLU137 4.5 9.8 1.0 N Y:ARG133 4.5 11.1 1.0 N Y:ASN138 4.5 10.2 1.0 CA Y:ASN138 4.6 9.2 1.0 C Y:ASN138 4.6 9.7 1.0 CA Y:ASP145 4.6 8.7 1.0 CG Y:TRP132 4.7 9.3 1.0 CA Y:ASP139 4.7 9.2 1.0 CA Y:ASP135 4.7 9.7 1.0 CA Y:ARG133 4.9 9.8 1.0 CB Y:GLU137 5.0 10.7 1.0

Calcium binding site 2 out of 2 in the Rrv Dkta Vlp in Complex with Vldlr-Lbd-Fc


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Rrv Dkta Vlp in Complex with Vldlr-Lbd-Fc within 5.0Å range: probe atom residue distance (Å) B Occ Z:Ca201 b:4.7 occ:1.00 OD1 Z:ASP135 2.1 6.9 1.0 O Z:TRP132 2.2 9.0 1.0 OD2 Z:ASP139 2.3 9.0 1.0 OD1 Z:ASP139 2.4 0.0 1.0 O Z:GLU137 2.4 0.1 1.0 OE2 Z:GLU146 2.5 5.4 1.0 CG Z:ASP135 2.5 9.0 1.0 OD2 Z:ASP135 2.6 9.0 1.0 CG Z:ASP139 2.6 7.1 1.0 C Z:TRP132 3.3 9.0 1.0 C Z:GLU137 3.5 0.1 1.0 CD Z:GLU146 3.5 3.5 1.0 CB Z:ASP135 3.7 0.0 1.0 N Z:GLU137 3.9 0.6 1.0 N Z:ASP135 3.9 9.0 1.0 CB Z:GLU137 4.0 3.1 1.0 CA Z:GLU137 4.0 0.2 1.0 CA Z:TRP132 4.1 0.2 1.0 CB Z:ASP139 4.1 6.4 1.0 CB Z:TRP132 4.2 0.0 1.0 NZ I:LYS345 4.2 105.8 1.0 N Z:ARG133 4.3 1.1 1.0 CA Z:ASP135 4.3 9.0 1.0 N Z:ASP139 4.3 0.6 1.0 CG Z:GLU146 4.3 3.1 1.0 OE1 Z:GLU146 4.3 9.0 1.0 CA Z:ARG133 4.5 9.0 1.0 N Z:CYS134 4.5 9.0 1.0 C Z:ARG133 4.6 6.8 1.0 N Z:ASN138 4.6 9.0 1.0 N Z:GLY136 4.7 0.0 1.0 C Z:ASP135 4.7 9.0 1.0 CB Z:ASP145 4.7 5.8 1.0 CA Z:ASP139 4.7 0.2 1.0 C Z:ASN138 4.8 0.2 1.0 C Z:CYS134 5.0 0.0 1.0 CA Z:ASN138 5.0 9.0 1.0

S.Raju, S.Palakurty, A.Sariol, N.Wagoner, L.J.Adams, S.Hui, W.B.Klimstra, D.H.Fremont, M.S.Diamond. Structural Basis For Plasticity in Receptor Engagement By An Encephalitic Alphavirus. Cell 2025.
ISSN: ISSN 1097-4172
PubMed: 40187344
DOI: 10.1016/J.CELL.2025.02.036