Calcium in PDB 8yf7: Cryo-Em Structure of Dragon Grouper Nervous Necrosis Virus-Like Particle at PH6.5 (2.82A)

The binding sites of Calcium atom in the Cryo-Em Structure of Dragon Grouper Nervous Necrosis Virus-Like Particle at PH6.5 (2.82A) (pdb code 8yf7). 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 PH6.5 (2.82A), PDB code: 8yf7:
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 PH6.5 (2.82A)


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 PH6.5 (2.82A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:63.9 occ:1.00 OD2 C:ASP133 2.2 60.4 1.0 OG A:SER170 2.3 62.6 1.0 OD2 C:ASP130 2.3 58.6 1.0 OE2 A:GLU213 2.3 71.5 1.0 OE1 A:GLN100 2.3 60.1 1.0 CG C:ASP133 3.0 66.9 1.0 CB A:SER170 3.0 55.3 1.0 OD1 C:ASP133 3.0 67.1 1.0 CD A:GLU213 3.3 65.9 1.0 CG C:ASP130 3.4 50.1 1.0 CD A:GLN100 3.5 45.8 1.0 CB C:ASP130 3.8 48.4 1.0 N A:SER170 4.0 54.2 1.0 CG A:GLU213 4.0 62.5 1.0 NE2 A:GLN100 4.1 42.0 1.0 CA A:SER170 4.1 53.9 1.0 OE1 A:GLU213 4.1 64.7 1.0 OG1 A:THR169 4.2 49.2 1.0 NH2 C:ARG176 4.4 53.2 1.0 CB C:ASP133 4.4 62.9 1.0 OD1 C:ASP130 4.5 47.6 1.0 O A:GLN100 4.6 51.8 1.0 CA A:GLN100 4.6 42.3 1.0 CG A:GLN100 4.6 45.8 1.0 CB A:GLN100 4.8 42.2 1.0 CE3 A:TRP168 4.8 48.6 1.0 C A:SER170 5.0 56.6 1.0

Calcium binding site 2 out of 3 in the Cryo-Em Structure of Dragon Grouper Nervous Necrosis Virus-Like Particle at PH6.5 (2.82A)


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 PH6.5 (2.82A) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:65.0 occ:1.00 OE1 B:GLN100 2.3 49.5 1.0 OG B:SER170 2.4 47.8 1.0 OD2 A:ASP133 2.6 79.6 1.0 OD2 A:ASP130 2.6 64.6 1.0 OD1 A:ASP133 2.6 79.9 1.0 CG A:ASP133 2.9 79.4 1.0 CG A:ASP130 3.1 59.9 1.0 OE2 B:GLU213 3.1 63.5 1.0 CB B:SER170 3.1 49.9 1.0 CD B:GLN100 3.2 41.0 1.0 NE2 B:GLN100 3.4 38.5 1.0 CB A:ASP130 3.5 55.0 1.0 CD B:GLU213 3.8 59.9 1.0 OD1 A:ASP130 3.9 63.7 1.0 NH2 A:ARG176 4.1 56.5 1.0 CG B:GLU213 4.1 54.8 1.0 CB A:ASP133 4.3 70.5 1.0 CA B:SER170 4.3 43.9 1.0 N B:SER170 4.4 47.6 1.0 CG B:GLN100 4.6 31.6 1.0 OG1 B:THR169 4.6 49.5 1.0 OE1 B:GLU213 4.7 59.8 1.0 OG1 A:THR132 5.0 67.1 1.0

Calcium binding site 3 out of 3 in the Cryo-Em Structure of Dragon Grouper Nervous Necrosis Virus-Like Particle at PH6.5 (2.82A)


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 PH6.5 (2.82A) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:45.0 occ:1.00 OE1 C:GLN100 2.4 44.2 1.0 OG C:SER170 2.5 53.8 1.0 OE2 C:GLU213 2.6 65.0 1.0 OD1 B:ASP133 2.9 67.3 1.0 OD2 B:ASP133 2.9 71.0 1.0 OD2 B:ASP130 2.9 55.6 1.0 CD C:GLN100 3.0 39.5 1.0 NE2 C:GLN100 3.0 42.4 1.0 CD C:GLU213 3.2 60.7 1.0 CG B:ASP133 3.2 69.8 1.0 CB C:SER170 3.4 49.5 1.0 CG C:GLU213 3.4 57.2 1.0 CG B:ASP130 3.8 51.1 1.0 CB B:ASP130 4.0 46.1 1.0 OE1 C:GLU213 4.2 54.0 1.0 CG C:GLN100 4.4 32.0 1.0 OG1 C:THR169 4.5 46.1 1.0 N C:SER170 4.5 47.1 1.0 NH2 B:ARG176 4.5 49.0 1.0 CA C:SER170 4.6 46.0 1.0 CB C:GLU213 4.6 56.3 1.0 CA C:GLN100 4.7 32.2 1.0 CB B:ASP133 4.7 62.7 1.0 CB C:GLN100 4.8 28.8 1.0 O C:GLN100 4.9 38.3 1.0 OD1 B:ASP130 4.9 57.4 1.0 OG C:SER211 4.9 44.5 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