Calcium in PDB 8yf9: Cryo-Em Structure of Dragon Grouper Nervous Necrosis Virion at PH6.5 (3.12A)

The binding sites of Calcium atom in the Cryo-Em Structure of Dragon Grouper Nervous Necrosis Virion at PH6.5 (3.12A) (pdb code 8yf9). 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 Virion at PH6.5 (3.12A), PDB code: 8yf9:
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 Virion at PH6.5 (3.12A)


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 Virion at PH6.5 (3.12A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:118.4 occ:1.00 OE1 B:GLN100 2.4 100.2 1.0 OE2 B:GLU213 2.4 118.1 1.0 NE2 B:GLN100 2.7 100.6 1.0 CG A:ASP130 2.7 95.9 1.0 CD B:GLN100 2.9 101.1 1.0 OD2 A:ASP130 3.0 94.7 1.0 OD1 A:ASP133 3.0 124.3 1.0 OD1 A:ASP130 3.0 98.8 1.0 CB A:ASP130 3.2 92.6 1.0 CB B:SER170 3.2 101.9 1.0 OD2 A:ASP133 3.5 120.4 1.0 CG A:ASP133 3.6 123.0 1.0 CD B:GLU213 3.6 120.8 1.0 OG B:SER170 3.9 106.0 1.0 OE1 B:GLU213 4.1 117.1 1.0 NH2 A:ARG176 4.3 84.4 1.0 CG B:GLN100 4.4 97.9 1.0 CA B:SER170 4.5 96.5 1.0 NH1 A:ARG176 4.6 79.6 1.0 CA A:ASP130 4.6 88.7 1.0 N B:SER170 4.7 94.8 1.0 CE3 B:TRP168 4.7 86.3 1.0 CG B:GLU213 4.8 117.0 1.0 OG1 A:THR132 4.9 102.1 1.0 CZ A:ARG176 4.9 85.6 1.0 CB A:ASP133 4.9 118.0 1.0

Calcium binding site 2 out of 3 in the Cryo-Em Structure of Dragon Grouper Nervous Necrosis Virion at PH6.5 (3.12A)


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 Virion at PH6.5 (3.12A) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:100.5 occ:1.00 OD2 B:ASP130 2.3 113.6 1.0 OE1 C:GLN100 2.4 90.5 1.0 OE1 C:GLU213 2.4 118.1 1.0 OE2 C:GLU213 2.4 114.1 1.0 CD C:GLU213 2.5 118.7 1.0 CG B:ASP130 3.1 108.1 1.0 OD1 B:ASP133 3.1 124.6 1.0 CB C:SER170 3.2 98.9 1.0 CD C:GLN100 3.3 94.0 1.0 NE2 C:GLN100 3.6 87.8 1.0 CB B:ASP130 3.6 101.7 1.0 CG C:GLU213 3.8 117.7 1.0 OD2 B:ASP133 3.9 120.1 1.0 CG B:ASP133 3.9 122.9 1.0 OD1 B:ASP130 4.0 103.8 1.0 OG C:SER170 4.0 100.9 1.0 N C:SER170 4.3 91.3 1.0 CA C:SER170 4.4 97.1 1.0 OG1 C:THR169 4.6 88.7 1.0 CG C:GLN100 4.6 91.4 1.0 CB C:GLU213 4.7 113.7 1.0 O C:GLN100 4.8 97.9 1.0 CA C:GLN100 4.8 84.9 1.0 CB C:GLN100 5.0 86.5 1.0 OG1 B:THR132 5.0 98.4 1.0 CE3 C:TRP168 5.0 85.7 1.0

Calcium binding site 3 out of 3 in the Cryo-Em Structure of Dragon Grouper Nervous Necrosis Virion at PH6.5 (3.12A)


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 Virion at PH6.5 (3.12A) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca402 b:94.9 occ:1.00 OE2 A:GLU213 2.3 91.0 1.0 OE1 A:GLN100 2.3 81.3 1.0 OD1 C:ASP133 2.3 128.8 1.0 OD2 C:ASP130 2.3 114.2 1.0 CB A:SER170 2.7 78.6 1.0 OD2 C:ASP133 2.9 127.7 1.0 CG C:ASP133 2.9 129.1 1.0 CG C:ASP130 3.0 114.3 1.0 OG A:SER170 3.3 80.3 1.0 CD A:GLN100 3.5 76.6 1.0 CD A:GLU213 3.5 88.7 1.0 CB C:ASP130 3.6 106.5 1.0 OD1 C:ASP130 3.7 115.5 1.0 CA A:SER170 4.1 77.8 1.0 N A:SER170 4.3 73.7 1.0 NE2 A:GLN100 4.3 64.7 1.0 CG A:GLU213 4.3 84.6 1.0 CB C:ASP133 4.3 124.2 1.0 OE1 A:GLU213 4.4 91.4 1.0 CG A:GLN100 4.5 74.9 1.0 OG1 C:THR132 4.8 109.9 1.0 CE3 A:TRP168 4.8 61.6 1.0 CA C:ASP133 4.9 126.2 1.0 OG1 A:THR169 4.9 71.2 1.0 N C:ASP133 5.0 127.8 1.0 C A:SER170 5.0 78.9 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