Calcium in PDB 6ab6: Cryo-Em Structure of T=3 Penaeus Vannamei Nodavirus

The binding sites of Calcium atom in the Cryo-Em Structure of T=3 Penaeus Vannamei Nodavirus (pdb code 6ab6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Cryo-Em Structure of T=3 Penaeus Vannamei Nodavirus, PDB code: 6ab6:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Cryo-Em Structure of T=3 Penaeus Vannamei Nodavirus


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 T=3 Penaeus Vannamei Nodavirus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:69.3 occ:1.00 OD2 A:ASP148 2.3 43.0 1.0 OD2 A:ASP151 2.3 52.1 1.0 OE1 B:GLU118 2.5 35.4 1.0 ND2 B:ASN250 2.5 43.6 1.0 OD1 A:ASP151 2.6 52.1 1.0 CG A:ASP151 2.8 52.1 1.0 CG A:ASP148 3.3 43.0 1.0 CD B:GLU118 3.5 35.4 1.0 CB A:ASP148 3.7 43.0 1.0 CG B:ASN250 3.7 43.6 1.0 OE2 B:GLU118 3.8 35.4 1.0 O B:THR196 4.1 36.2 1.0 OD1 B:ASN250 4.1 43.6 1.0 CB A:ASP151 4.3 52.1 1.0 OD1 A:ASP148 4.4 43.0 1.0 CA A:CA402 4.4 72.8 1.0 C B:THR196 4.8 36.2 1.0 CE B:LYS200 4.8 49.4 1.0 OE1 B:GLN248 4.8 38.0 1.0 OG1 B:THR196 4.8 36.2 1.0 CG B:GLU118 4.9 35.4 1.0 CB B:ASN250 4.9 43.6 1.0 NE2 B:GLN248 5.0 38.0 1.0 NH2 A:ARG204 5.0 37.9 1.0

Calcium binding site 2 out of 6 in the Cryo-Em Structure of T=3 Penaeus Vannamei Nodavirus


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 T=3 Penaeus Vannamei Nodavirus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:72.8 occ:1.00 OE2 B:GLU118 2.3 35.4 1.0 OD2 A:ASP151 2.3 52.1 1.0 OD1 A:ASP146 2.5 46.3 1.0 OE1 B:GLN248 3.0 38.0 1.0 OD2 A:ASP146 3.0 46.3 1.0 CG A:ASP151 3.1 52.1 1.0 CG A:ASP146 3.1 46.3 1.0 CB A:ASP151 3.2 52.1 1.0 CD B:GLU118 3.4 35.4 1.0 CD B:GLN248 3.8 38.0 1.0 OE1 B:GLU118 4.0 35.4 1.0 OD1 A:ASP151 4.2 52.1 1.0 CB A:ASP148 4.2 43.0 1.0 CG B:GLN248 4.2 38.0 1.0 CB B:GLN248 4.3 38.0 1.0 CA A:CA401 4.4 69.3 1.0 NE2 A:GLN165 4.4 51.0 1.0 NE2 A:GLN169 4.5 45.1 1.0 CG B:GLU118 4.6 35.4 1.0 CB A:ASP146 4.6 46.3 1.0 ND2 B:ASN250 4.7 43.6 1.0 N B:ASN250 4.7 43.6 1.0 CA A:ASP151 4.7 52.1 1.0 CD B:PRO251 4.8 50.6 1.0 NE2 B:GLN248 4.8 38.0 1.0 CA B:ASN250 4.9 43.6 1.0 O A:ASP148 4.9 43.0 1.0 N A:ASP148 4.9 43.0 1.0

Calcium binding site 3 out of 6 in the Cryo-Em Structure of T=3 Penaeus Vannamei Nodavirus


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 T=3 Penaeus Vannamei Nodavirus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:0.5 occ:1.00 OD2 C:ASP151 2.2 49.2 1.0 OE2 A:GLU118 2.3 34.3 1.0 OD2 C:ASP146 2.5 44.1 1.0 OD1 C:ASP146 2.5 44.1 1.0 NE2 A:GLN248 2.5 37.4 1.0 OE1 A:GLN248 2.6 37.4 1.0 CD A:GLN248 2.7 37.4 1.0 CG C:ASP146 2.8 44.1 1.0 CB C:ASP148 2.9 43.8 1.0 CG C:ASP151 3.1 49.2 1.0 CB C:ASP151 3.2 49.2 1.0 CD A:GLU118 3.2 34.3 1.0 OE1 A:GLU118 3.4 34.3 1.0 N C:ASP148 3.6 43.8 1.0 CA C:ASP148 3.7 43.8 1.0 O C:ASP148 3.9 43.8 1.0 CA C:CA401 4.0 95.2 1.0 CG C:ASP148 4.0 43.8 1.0 CG A:GLN248 4.1 37.4 1.0 OD2 C:ASP148 4.1 43.8 1.0 CB C:ASP146 4.2 44.1 1.0 OD1 C:ASP151 4.3 49.2 1.0 C C:ASP148 4.3 43.8 1.0 CA C:ASP151 4.6 49.2 1.0 N C:THR147 4.6 43.0 1.0 CG A:GLU118 4.6 34.3 1.0 NE2 C:GLN169 4.7 46.5 1.0 C C:THR147 4.8 43.0 1.0 N C:ASP151 4.8 49.2 1.0 CB A:GLN248 4.9 37.4 1.0 CA C:ASP146 5.0 44.1 1.0 C C:ASP146 5.0 44.1 1.0

Calcium binding site 4 out of 6 in the Cryo-Em Structure of T=3 Penaeus Vannamei Nodavirus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cryo-Em Structure of T=3 Penaeus Vannamei Nodavirus within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:0.1 occ:1.00 OD2 B:ASP151 2.2 51.1 1.0 OE2 C:GLU118 2.3 37.1 1.0 OE1 C:GLN248 2.5 40.8 1.0 OD1 B:ASP146 2.6 46.5 1.0 NE2 C:GLN248 2.6 40.8 1.0 CD C:GLN248 2.7 40.8 1.0 CB B:ASP148 2.9 45.6 1.0 CD C:GLU118 3.0 37.1 1.0 CG B:ASP151 3.1 51.1 1.0 OE1 C:GLU118 3.3 37.1 1.0 CB B:ASP151 3.3 51.1 1.0 CG B:ASP146 3.5 46.5 1.0 OD2 B:ASP146 3.7 46.5 1.0 N B:ASP148 3.7 45.6 1.0 CA B:ASP148 3.8 45.6 1.0 CG C:GLN248 3.9 40.8 1.0 CG B:ASP148 3.9 45.6 1.0 OD2 B:ASP148 4.0 45.6 1.0 CA B:CA402 4.1 0.3 1.0 O B:ASP148 4.1 45.6 1.0 CG C:GLU118 4.2 37.1 1.0 OD1 B:ASP151 4.3 51.1 1.0 C B:ASP148 4.5 45.6 1.0 CB C:GLN248 4.6 40.8 1.0 CA B:ASP151 4.7 51.1 1.0 N B:THR147 4.9 44.0 1.0 CB B:ASP146 4.9 46.5 1.0 NE2 B:GLN169 4.9 48.3 1.0 N B:ASP151 4.9 51.1 1.0 C B:THR147 5.0 44.0 1.0

Calcium binding site 5 out of 6 in the Cryo-Em Structure of T=3 Penaeus Vannamei Nodavirus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Cryo-Em Structure of T=3 Penaeus Vannamei Nodavirus within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:0.3 occ:1.00 OD2 B:ASP151 2.3 51.1 1.0 OD2 B:ASP148 2.7 45.6 1.0 ND2 C:ASN250 2.8 49.9 1.0 OD1 B:ASP151 2.9 51.1 1.0 CG B:ASP151 3.0 51.1 1.0 CG C:ASN250 3.5 49.9 1.0 OD1 C:ASN250 3.5 49.9 1.0 CG B:ASP148 3.8 45.6 1.0 OE2 C:GLU118 3.9 37.1 1.0 OE1 C:GLU118 3.9 37.1 1.0 CA B:CA401 4.1 0.1 1.0 O C:THR196 4.1 38.1 1.0 CB B:ASP148 4.2 45.6 1.0 CD C:GLU118 4.3 37.1 1.0 NH2 B:ARG204 4.4 40.0 1.0 CB B:ASP151 4.4 51.1 1.0 OG1 C:THR196 4.5 38.1 1.0 C C:THR196 4.7 38.1 1.0 CB C:ASN250 4.8 49.9 1.0 OD1 B:ASP148 4.8 45.6 1.0

Calcium binding site 6 out of 6 in the Cryo-Em Structure of T=3 Penaeus Vannamei Nodavirus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Cryo-Em Structure of T=3 Penaeus Vannamei Nodavirus within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:95.2 occ:1.00 OD2 C:ASP151 2.2 49.2 1.0 OD2 C:ASP148 2.6 43.8 1.0 OD1 C:ASP151 2.8 49.2 1.0 CG C:ASP151 2.9 49.2 1.0 ND2 A:ASN250 3.1 42.9 1.0 CG C:ASP148 3.7 43.8 1.0 CG A:ASN250 3.8 42.9 1.0 OD1 A:ASN250 3.8 42.9 1.0 OE1 A:GLN248 3.8 37.4 1.0 OE1 A:GLU118 3.9 34.3 1.0 O A:THR196 3.9 33.5 1.0 CA A:CA403 4.0 0.5 1.0 CB C:ASP148 4.0 43.8 1.0 CB C:ASP151 4.3 49.2 1.0 NH2 C:ARG204 4.5 41.6 1.0 C A:THR196 4.6 33.5 1.0 CD A:GLU118 4.6 34.3 1.0 OG1 A:THR196 4.7 33.5 1.0 OE2 A:GLU118 4.8 34.3 1.0 OD1 C:ASP148 4.8 43.8 1.0 CD A:GLN248 4.8 37.4 1.0 O A:GLU118 4.9 34.3 1.0 NZ A:LYS200 4.9 49.5 1.0 CA A:GLY197 5.0 40.1 1.0

N.C.Chen, M.Yoshimura, N.Miyazaki, H.H.Guan, P.Chuankhayan, C.C.Lin, S.K.Chen, P.J.Lin, Y.C.Huang, K.Iwasaki, A.Nakagawa, S.I.Chan, C.J.Chen. The Atomic Structures of Shrimp Nodaviruses Reveal New Dimeric Spike Structures and Particle Polymorphism. Commun Biol V. 2 72 2019.
ISSN: ESSN 2399-3642
PubMed: 30820467
DOI: 10.1038/S42003-019-0311-Z