Calcium in PDB 8yf6: Cryo-Em Structure of Dragon Grouper Nervous Necrosis Virus-Like Particle at PH8.0 (3.23A)

The binding sites of Calcium atom in the Cryo-Em Structure of Dragon Grouper Nervous Necrosis Virus-Like Particle at PH8.0 (3.23A) (pdb code 8yf6). 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 PH8.0 (3.23A), PDB code: 8yf6:
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 PH8.0 (3.23A)


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 PH8.0 (3.23A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:86.7 occ:1.00 OD2 A:ASP133 2.2 79.0 1.0 OG B:SER170 2.3 61.4 1.0 OE2 B:GLU213 2.3 65.5 1.0 OD2 A:ASP130 2.3 68.2 1.0 OE1 B:GLN100 2.3 58.7 1.0 CB B:SER170 2.8 62.7 1.0 CG A:ASP133 3.0 82.2 1.0 OD1 A:ASP133 3.2 81.8 1.0 CG A:ASP130 3.3 66.0 1.0 CD B:GLN100 3.4 56.1 1.0 CD B:GLU213 3.5 70.0 1.0 N B:SER170 3.7 53.3 1.0 CB A:ASP130 3.8 59.8 1.0 CA B:SER170 3.8 55.5 1.0 NE2 B:GLN100 3.9 51.0 1.0 OG1 B:THR169 4.1 50.8 1.0 NH2 A:ARG176 4.3 58.3 1.0 O B:GLN100 4.3 61.6 1.0 OE1 B:GLU213 4.4 67.2 1.0 OD1 A:ASP130 4.4 71.2 1.0 CG B:GLU213 4.4 70.6 1.0 CB A:ASP133 4.4 76.5 1.0 CE3 B:TRP168 4.5 47.8 1.0 CA B:GLN100 4.6 42.5 1.0 CG B:GLN100 4.6 47.8 1.0 CB B:GLN100 4.7 43.5 1.0 C B:THR169 4.9 47.1 1.0 C B:GLN100 4.9 48.2 1.0 C B:SER170 4.9 58.2 1.0 CZ3 B:TRP168 5.0 45.8 1.0

Calcium binding site 2 out of 3 in the Cryo-Em Structure of Dragon Grouper Nervous Necrosis Virus-Like Particle at PH8.0 (3.23A)


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 PH8.0 (3.23A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:54.2 occ:1.00 OE2 A:GLU213 2.3 71.5 1.0 OG A:SER170 2.3 67.6 1.0 OD2 C:ASP130 2.3 70.0 1.0 OD2 C:ASP133 2.3 84.4 1.0 OD1 C:ASP133 2.4 89.5 1.0 OE1 A:GLN100 2.5 45.1 1.0 CG C:ASP133 2.6 90.2 1.0 CB A:SER170 2.9 58.0 1.0 CD A:GLU213 3.2 70.7 1.0 CG C:ASP130 3.3 70.8 1.0 CB C:ASP130 3.6 65.7 1.0 CD A:GLN100 3.6 53.1 1.0 OE1 A:GLU213 3.8 72.4 1.0 CB C:ASP133 4.0 85.7 1.0 CG A:GLU213 4.1 68.0 1.0 CA A:SER170 4.2 56.8 1.0 N A:SER170 4.3 57.9 1.0 CG A:GLN100 4.4 53.7 1.0 OD1 C:ASP130 4.4 73.0 1.0 NH2 C:ARG176 4.5 65.3 1.0 NE2 A:GLN100 4.6 54.2 1.0 OG1 A:THR169 4.8 48.6 1.0 CA C:ASP133 4.8 83.5 1.0

Calcium binding site 3 out of 3 in the Cryo-Em Structure of Dragon Grouper Nervous Necrosis Virus-Like Particle at PH8.0 (3.23A)


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 PH8.0 (3.23A) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:60.2 occ:1.00 OE1 C:GLU213 2.3 89.3 1.0 OD2 B:ASP130 2.3 70.3 1.0 OE2 C:GLU213 2.4 88.9 1.0 OG C:SER170 2.5 73.5 1.0 CD C:GLU213 2.6 91.3 1.0 OE1 C:GLN100 2.7 66.6 1.0 OD1 B:ASP133 2.7 86.0 1.0 OD2 B:ASP133 2.9 86.0 1.0 CB C:SER170 3.1 71.1 1.0 CG B:ASP133 3.2 85.3 1.0 CG B:ASP130 3.4 67.9 1.0 CD C:GLN100 3.7 62.0 1.0 CB B:ASP130 3.8 64.3 1.0 CG C:GLU213 4.0 82.8 1.0 NE2 C:GLN100 4.1 55.0 1.0 N C:SER170 4.2 70.6 1.0 CA C:SER170 4.3 69.2 1.0 NH2 B:ARG176 4.3 58.8 1.0 OD1 B:ASP130 4.5 70.7 1.0 OG1 C:THR169 4.5 61.0 1.0 CB B:ASP133 4.6 77.0 1.0 O C:GLN100 4.7 66.4 1.0 CA C:GLN100 4.8 51.2 1.0 CG C:GLN100 4.9 52.5 1.0 CB C:GLU213 5.0 81.8 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