Calcium in PDB 8yf8: Cryo-Em Structure of Dragon Grouper Nervous Necrosis Virus-Like Particle at PH5.0 (3.52A)

The binding sites of Calcium atom in the Cryo-Em Structure of Dragon Grouper Nervous Necrosis Virus-Like Particle at PH5.0 (3.52A) (pdb code 8yf8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Cryo-Em Structure of Dragon Grouper Nervous Necrosis Virus-Like Particle at PH5.0 (3.52A), PDB code: 8yf8:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Cryo-Em Structure of Dragon Grouper Nervous Necrosis Virus-Like Particle at PH5.0 (3.52A)


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 Dragon Grouper Nervous Necrosis Virus-Like Particle at PH5.0 (3.52A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:69.6 occ:1.00 OD2 C:ASP133 2.3 75.3 1.0 OE1 A:GLN100 2.4 59.3 1.0 OD1 C:ASP133 2.4 75.3 1.0 OE2 A:GLU213 2.4 70.9 1.0 OD2 C:ASP130 2.4 61.0 1.0 OG A:SER170 2.4 70.0 1.0 OE1 A:GLU213 2.6 70.9 1.0 CG C:ASP133 2.7 75.3 1.0 CD A:GLU213 2.7 70.9 1.0 CB A:SER170 2.8 70.0 1.0 CD A:GLN100 3.1 59.3 1.0 NE2 A:GLN100 3.2 59.3 1.0 CG C:ASP130 3.4 61.0 1.0 CB C:ASP130 3.8 61.0 1.0 CG A:GLU213 4.0 70.9 1.0 CA A:SER170 4.1 70.0 1.0 CB C:ASP133 4.2 75.3 1.0 N A:SER170 4.3 70.0 1.0 OG1 A:THR169 4.5 60.0 1.0 CG A:GLN100 4.5 59.3 1.0 OD1 C:ASP130 4.5 61.0 1.0 NH2 C:ARG176 4.6 65.8 1.0 CG A:GLU217 4.9 105.6 1.0 C A:THR169 4.9 60.0 1.0 CA A:GLN100 5.0 59.3 1.0

Calcium binding site 2 out of 3 in the Cryo-Em Structure of Dragon Grouper Nervous Necrosis Virus-Like Particle at PH5.0 (3.52A)


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 Dragon Grouper Nervous Necrosis Virus-Like Particle at PH5.0 (3.52A) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:88.8 occ:1.00 OG B:SER170 2.4 71.6 1.0 NE2 B:GLN100 2.4 61.9 1.0 OE1 B:GLN100 2.4 61.9 1.0 OD2 A:ASP130 2.5 69.0 1.0 CD B:GLN100 2.8 61.9 1.0 CG A:ASP130 3.0 69.0 1.0 CB B:SER170 3.0 71.6 1.0 CB A:ASP130 3.0 69.0 1.0 OE2 B:GLU213 3.7 78.0 1.0 OD1 A:ASP130 4.0 69.0 1.0 OD2 A:ASP133 4.1 89.8 1.0 CD B:GLU213 4.3 78.0 1.0 CG B:GLN100 4.3 61.9 1.0 CG B:GLU213 4.3 78.0 1.0 CG A:ASP133 4.3 89.8 1.0 CA B:SER170 4.4 71.6 1.0 CB A:ASP133 4.4 89.8 1.0 NH2 A:ARG176 4.4 68.3 1.0 CA A:ASP130 4.5 69.0 1.0 N B:SER170 4.6 71.6 1.0 CE3 B:TRP168 4.7 56.2 1.0 CZ3 B:TRP168 5.0 56.2 1.0

Calcium binding site 3 out of 3 in the Cryo-Em Structure of Dragon Grouper Nervous Necrosis Virus-Like Particle at PH5.0 (3.52A)


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 Dragon Grouper Nervous Necrosis Virus-Like Particle at PH5.0 (3.52A) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:88.8 occ:1.00 OE2 C:GLU213 2.2 83.9 1.0 OD1 B:ASP133 2.2 78.8 1.0 OG C:SER170 2.2 75.8 1.0 OD2 B:ASP130 2.3 65.6 1.0 OE1 C:GLU213 2.4 83.9 1.0 CD C:GLU213 2.6 83.9 1.0 CB C:SER170 2.8 75.8 1.0 CG B:ASP133 2.9 78.8 1.0 OD2 B:ASP133 3.1 78.8 1.0 CG B:ASP130 3.3 65.6 1.0 CB B:ASP130 3.7 65.6 1.0 CG C:GLU213 4.2 83.9 1.0 CA C:SER170 4.2 75.8 1.0 CB B:ASP133 4.3 78.8 1.0 OD1 B:ASP130 4.3 65.6 1.0 OG1 B:THR132 4.3 72.3 1.0 OE1 C:GLN100 4.4 65.9 1.0 N C:SER170 4.6 75.8 1.0 CD C:GLN100 4.7 65.9 1.0 N B:ASP133 4.7 78.8 1.0 CG C:GLN100 4.7 65.9 1.0 CA B:ASP133 4.7 78.8 1.0 NH1 B:ARG176 5.0 65.1 1.0

P.Sterbova, C.H.Wang, K.J.D.Carillo, Y.C.Lou, T.Kato, K.Namba, D.M.Tzou, W.H.Chang. Molecular Mechanism of pH-Induced Protrusion Configuration Switching in Piscine Betanodavirus Implies A Novel Antiviral Strategy. Acs Infect Dis. 2024.
ISSN: ESSN 2373-8227
PubMed: 39087906
DOI: 10.1021/ACSINFECDIS.4C00407