Calcium in PDB 8x0k: Cryo-Em Structure of Semliki Forest Virus in Complex with Its Receptor Vldlr(2-Fold)

The binding sites of Calcium atom in the Cryo-Em Structure of Semliki Forest Virus in Complex with Its Receptor Vldlr(2-Fold) (pdb code 8x0k). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Cryo-Em Structure of Semliki Forest Virus in Complex with Its Receptor Vldlr(2-Fold), PDB code: 8x0k:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Cryo-Em Structure of Semliki Forest Virus in Complex with Its Receptor Vldlr(2-Fold)


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 Semliki Forest Virus in Complex with Its Receptor Vldlr(2-Fold) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca400 b:129.9 occ:1.00 OD1 D:ASP105 2.2 127.4 1.0 O D:TRP102 2.2 114.1 1.0 OE2 D:GLU116 2.3 135.0 1.0 OD1 D:ASP109 2.3 125.5 1.0 OD2 D:ASP115 2.3 133.4 1.0 O D:GLU107 2.8 127.6 1.0 CG D:ASP105 2.8 127.4 1.0 OD2 D:ASP105 3.2 127.4 1.0 N D:ASP105 3.3 127.4 1.0 C D:TRP102 3.4 114.1 1.0 N D:CYS104 3.4 130.7 1.0 CG D:ASP115 3.4 133.4 1.0 CD D:GLU116 3.4 135.0 1.0 CG D:ASP109 3.5 125.5 1.0 CA D:ARG103 3.8 125.1 1.0 C D:ARG103 3.8 125.1 1.0 CB D:ASP105 3.9 127.4 1.0 C D:GLU107 3.9 127.6 1.0 N D:ARG103 4.0 125.1 1.0 CA D:ASP105 4.1 127.4 1.0 CG D:GLU116 4.1 135.0 1.0 CA D:CYS104 4.1 130.7 1.0 CB D:ASP115 4.1 133.4 1.0 N D:GLU107 4.2 127.6 1.0 C D:CYS104 4.2 130.7 1.0 OD1 D:ASP115 4.3 133.4 1.0 OD2 D:ASP109 4.3 125.5 1.0 CB D:ASP109 4.4 125.5 1.0 N D:ASP109 4.4 125.5 1.0 OE1 D:GLU116 4.4 135.0 1.0 N D:GLY106 4.4 126.9 1.0 CA D:TRP102 4.5 114.1 1.0 C D:ASP105 4.6 127.4 1.0 CA D:GLU107 4.6 127.6 1.0 O D:ARG103 4.7 125.1 1.0 CB D:TRP102 4.9 114.1 1.0 N D:ASN108 5.0 130.2 1.0

Calcium binding site 2 out of 4 in the Cryo-Em Structure of Semliki Forest Virus in Complex with Its Receptor Vldlr(2-Fold)


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 Semliki Forest Virus in Complex with Its Receptor Vldlr(2-Fold) within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca400 b:150.9 occ:1.00 OD2 H:ASP109 2.2 146.5 1.0 O H:GLU107 2.3 147.1 1.0 OD2 H:ASP115 2.3 152.2 1.0 OD1 H:ASP115 2.4 152.2 1.0 OD1 H:ASP105 2.4 146.0 1.0 CG H:ASP115 2.5 152.2 1.0 CG H:ASP109 2.9 146.5 1.0 N H:ASP109 3.0 146.5 1.0 O H:TRP102 3.1 131.7 1.0 C H:GLU107 3.2 147.1 1.0 CG H:ASP105 3.3 146.0 1.0 CB H:ASP109 3.4 146.5 1.0 OD1 H:ASP109 3.7 146.5 1.0 OD2 H:ASP105 3.7 146.0 1.0 CA H:ASP109 3.8 146.5 1.0 CB H:ASP115 3.8 152.2 1.0 OE2 H:GLU116 3.8 154.0 1.0 N H:ASN108 4.0 149.1 1.0 CA H:ASN108 4.0 149.1 1.0 C H:ASN108 4.0 149.1 1.0 CA H:GLU107 4.2 147.1 1.0 C H:TRP102 4.3 131.7 1.0 N H:GLU107 4.3 147.1 1.0 CB H:GLU107 4.5 147.1 1.0 CG H:GLU116 4.5 154.0 1.0 CB H:ASP105 4.6 146.0 1.0 CD H:GLU116 4.7 154.0 1.0 N H:CYS110 4.7 155.7 1.0 C H:ASP109 4.7 146.5 1.0 CB H:TRP102 4.7 131.7 1.0 N H:ASP105 4.8 146.0 1.0

Calcium binding site 3 out of 4 in the Cryo-Em Structure of Semliki Forest Virus in Complex with Its Receptor Vldlr(2-Fold)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cryo-Em Structure of Semliki Forest Virus in Complex with Its Receptor Vldlr(2-Fold) within 5.0Å range: probe atom residue distance (Å) B Occ L:Ca400 b:155.3 occ:1.00 OD2 L:ASP115 2.1 157.5 1.0 OD1 L:ASP105 2.2 151.1 1.0 OD2 L:ASP109 2.2 150.8 1.0 O L:GLU107 2.3 153.8 1.0 O L:TRP102 2.6 137.3 1.0 OE2 L:GLU116 2.8 158.8 1.0 CG L:ASP109 3.2 150.8 1.0 CG L:ASP115 3.2 157.5 1.0 CG L:ASP105 3.3 151.1 1.0 C L:GLU107 3.5 153.8 1.0 C L:TRP102 3.7 137.3 1.0 OD1 L:ASP115 3.8 157.5 1.0 CD L:GLU116 3.9 158.8 1.0 N L:ASP109 3.9 150.8 1.0 CB L:ASP109 4.0 150.8 1.0 N L:GLU107 4.0 153.8 1.0 OD2 L:ASP105 4.0 151.1 1.0 OD1 L:ASP109 4.0 150.8 1.0 N L:ASP105 4.1 151.1 1.0 CB L:ASP105 4.2 151.1 1.0 CA L:GLU107 4.2 153.8 1.0 CB L:ASP115 4.4 157.5 1.0 CG L:GLU116 4.4 158.8 1.0 CB L:TRP102 4.5 137.3 1.0 N L:CYS104 4.5 154.3 1.0 CB L:GLU107 4.5 153.8 1.0 N L:ASN108 4.5 154.5 1.0 CA L:TRP102 4.6 137.3 1.0 CA L:ASP105 4.6 151.1 1.0 CA L:ASP109 4.6 150.8 1.0 N L:ARG103 4.6 149.9 1.0 CA L:ARG103 4.6 149.9 1.0 N L:GLY106 4.7 152.6 1.0 CA L:ASN108 4.8 154.5 1.0 C L:ARG103 4.8 149.9 1.0 C L:ASP105 4.9 151.1 1.0 C L:ASN108 4.9 154.5 1.0 OE1 L:GLU116 4.9 158.8 1.0 CD1 L:ILE98 5.0 146.5 1.0

Calcium binding site 4 out of 4 in the Cryo-Em Structure of Semliki Forest Virus in Complex with Its Receptor Vldlr(2-Fold)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cryo-Em Structure of Semliki Forest Virus in Complex with Its Receptor Vldlr(2-Fold) within 5.0Å range: probe atom residue distance (Å) B Occ P:Ca400 b:147.0 occ:1.00 OD1 P:ASP109 2.3 142.6 1.0 OD1 P:ASP105 2.3 142.7 1.0 O P:GLU107 2.3 141.2 1.0 O P:TRP102 2.3 129.9 1.0 OD2 P:ASP115 2.3 149.6 1.0 OE2 P:GLU116 2.3 150.0 1.0 CG P:ASP105 3.1 142.7 1.0 CD P:GLU116 3.3 150.0 1.0 C P:GLU107 3.4 141.2 1.0 OD2 P:ASP105 3.4 142.7 1.0 CG P:ASP109 3.5 142.6 1.0 C P:TRP102 3.5 129.9 1.0 CG P:ASP115 3.5 149.6 1.0 N P:GLU107 3.9 141.2 1.0 CG P:GLU116 3.9 150.0 1.0 CA P:GLU107 4.0 141.2 1.0 CB P:GLU107 4.1 141.2 1.0 N P:ASP109 4.2 142.6 1.0 N P:ASP105 4.2 142.7 1.0 OE1 P:GLU116 4.2 150.0 1.0 CA P:ARG103 4.3 141.0 1.0 N P:CYS104 4.3 146.2 1.0 CB P:ASP115 4.3 149.6 1.0 CB P:ASP109 4.3 142.6 1.0 N P:ARG103 4.3 141.0 1.0 OD2 P:ASP109 4.4 142.6 1.0 OD1 P:ASP115 4.5 149.6 1.0 CB P:ASP105 4.5 142.7 1.0 CA P:TRP102 4.5 129.9 1.0 N P:ASN108 4.5 143.7 1.0 C P:ARG103 4.5 141.0 1.0 CB P:TRP102 4.6 129.9 1.0 CA P:ASP105 4.7 142.7 1.0 N P:GLY106 4.7 140.6 1.0 CA P:ASN108 4.8 143.7 1.0 CA P:ASP109 4.9 142.6 1.0 C P:ASP105 5.0 142.7 1.0

F.G.Gao, S.Liu. Cryo-Em Structure of Semliki Forest Virus in Complex with Its Receptor Vldlr(2-Fold) To Be Published.