Calcium in PDB 6mrl: Cucumber Leaf Spot Virus

The binding sites of Calcium atom in the Cucumber Leaf Spot Virus (pdb code 6mrl). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Cucumber Leaf Spot Virus, PDB code: 6mrl:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Cucumber Leaf Spot Virus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cucumber Leaf Spot Virus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:0.4 occ:1.00 OD2 D:ASP179 2.4 0.3 1.0 OD1 D:ASP174 2.4 0.8 1.0 OD2 D:ASP174 2.5 0.8 1.0 OD2 A:ASP146 2.7 0.5 1.0 CG D:ASP174 2.8 0.8 1.0 CG A:GLN260 2.8 0.2 1.0 NE2 A:GLN260 3.1 0.2 1.0 CD A:GLN260 3.3 0.2 1.0 CG D:ASP179 3.5 0.3 1.0 CG A:ASP146 3.6 0.5 1.0 OD1 D:ASP176 3.7 0.2 1.0 OD1 A:ASP146 3.8 0.5 1.0 CB A:GLN260 3.8 0.2 1.0 CB D:ASP174 4.2 0.8 1.0 CA A:GLN260 4.2 0.2 1.0 CE1 D:TYR191 4.2 0.3 1.0 CB D:ASP179 4.2 0.3 1.0 OE1 A:GLN260 4.4 0.2 1.0 OD1 D:ASP179 4.5 0.3 1.0 CG D:ASP176 4.5 0.2 1.0 CD A:PRO261 4.6 0.0 1.0 OD2 D:ASP176 4.6 0.2 1.0 CD1 D:TYR191 4.7 0.3 1.0 CA D:ASP174 4.9 0.8 1.0 N D:LYS175 4.9 1.0 1.0 N A:GLN260 5.0 0.2 1.0

Calcium binding site 2 out of 3 in the Cucumber Leaf Spot Virus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cucumber Leaf Spot Virus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:0.3 occ:1.00 OD2 A:ASP179 2.5 0.8 1.0 OD1 A:ASP174 2.5 0.1 1.0 OE1 B:GLN260 2.5 0.8 1.0 OD2 B:ASP146 2.5 0.8 1.0 OD2 A:ASP174 2.6 0.1 1.0 CG A:ASP174 2.9 0.1 1.0 CB B:GLN260 2.9 0.8 1.0 OD1 B:ASP146 3.0 0.8 1.0 CG B:ASP146 3.1 0.8 1.0 OD1 A:ASP176 3.4 0.8 1.0 CD B:GLN260 3.4 0.8 1.0 CG A:ASP179 3.7 0.8 1.0 CG B:GLN260 3.7 0.8 1.0 CA B:GLN260 4.1 0.8 1.0 CG A:ASP176 4.2 0.8 1.0 OD2 A:ASP176 4.2 0.8 1.0 CB A:ASP174 4.3 0.1 1.0 CB A:ASP179 4.3 0.8 1.0 CB B:ASP146 4.6 0.8 1.0 NE2 B:GLN260 4.6 0.8 1.0 OD1 A:ASP179 4.7 0.8 1.0 N B:GLN260 4.9 0.8 1.0

Calcium binding site 3 out of 3 in the Cucumber Leaf Spot Virus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cucumber Leaf Spot Virus within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:0.7 occ:1.00 OD2 B:ASP176 2.4 0.8 1.0 OD2 D:ASP218 2.4 0.8 1.0 OD1 D:ASP146 2.5 0.3 1.0 OD1 B:ASP179 2.5 0.0 1.0 CG D:ASP218 2.9 0.8 1.0 CB D:ASP218 2.9 0.8 1.0 OD2 B:ASP179 3.0 0.0 1.0 CG B:ASP179 3.1 0.0 1.0 CG D:ASP146 3.6 0.3 1.0 CG B:ASP176 3.6 0.8 1.0 N D:ASP218 3.9 0.8 1.0 NE2 D:GLN260 3.9 0.9 1.0 CA D:ASP218 4.0 0.8 1.0 OD1 D:ASP218 4.0 0.8 1.0 OD1 B:ASP176 4.2 0.8 1.0 OD2 D:ASP146 4.2 0.3 1.0 CB D:ASP146 4.5 0.3 1.0 OE1 D:GLN260 4.6 0.9 1.0 CB B:ASP179 4.6 0.0 1.0 CD D:GLN260 4.7 0.9 1.0 CB B:ASP176 4.8 0.8 1.0 C D:ASP218 4.8 0.8 1.0 CA D:ASP146 4.8 0.3 1.0 N D:THR217 5.0 0.3 1.0

M.B.Sherman, R.Guenther, R.Reade, D.Rochon, T.Sit, T.J.Smith. Near Atomic Resolution Cryo-Electron Microscopy Structures of Cucumber Leaf Spot Virus and Red Clover Necrotic Mosaic Virus; Evolutionary Divergence at the Icosahedral Three-Fold Axes. J.Virol. 2019.
ISSN: ESSN 1098-5514
PubMed: 31694952
DOI: 10.1128/JVI.01439-19