Calcium in PDB 5yl1: T=1 Subviral Particle of Penaeus Vannamei Nodavirus Capsid Protein Deletion Mutant (Delta 1-37 & 251-368)

The structure of T=1 Subviral Particle of Penaeus Vannamei Nodavirus Capsid Protein Deletion Mutant (Delta 1-37 & 251-368), PDB code: 5yl1 was solved by N.C.Chen, M.Yoshimura, C.C.Lin, H.H.Guan, P.Chuankhayan, C.J.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.62 / 3.12
Space group	P 21 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	196.981, 200.319, 419.290, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 22.1

The binding sites of Calcium atom in the T=1 Subviral Particle of Penaeus Vannamei Nodavirus Capsid Protein Deletion Mutant (Delta 1-37 & 251-368) (pdb code 5yl1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the T=1 Subviral Particle of Penaeus Vannamei Nodavirus Capsid Protein Deletion Mutant (Delta 1-37 & 251-368), PDB code: 5yl1:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the T=1 Subviral Particle of Penaeus Vannamei Nodavirus Capsid Protein Deletion Mutant (Delta 1-37 & 251-368)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of T=1 Subviral Particle of Penaeus Vannamei Nodavirus Capsid Protein Deletion Mutant (Delta 1-37 & 251-368) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:53.4 occ:1.00 OE1 A:GLU118 2.6 69.5 1.0 OD1 A:ASN250 3.2 63.9 1.0 ND2 A:ASN250 3.6 86.7 1.0 O A:THR196 3.6 66.5 1.0 CG A:ASN250 3.7 78.2 1.0 CD A:GLU118 3.8 73.6 1.0 OE1 A:GLN248 3.9 76.5 1.0 O A:GLU118 4.2 68.8 1.0 CG A:GLU118 4.5 71.5 1.0 OG1 A:THR196 4.6 72.8 1.0 C A:THR196 4.7 67.2 1.0 CD2 A:TYR195 4.8 60.6 1.0 CD A:GLN248 4.8 82.8 1.0 OE2 A:GLU118 4.8 80.6 1.0 CA A:GLU118 5.0 68.2 1.0 CB A:ASN250 5.0 77.6 1.0

Calcium binding site 2 out of 2 in the T=1 Subviral Particle of Penaeus Vannamei Nodavirus Capsid Protein Deletion Mutant (Delta 1-37 & 251-368)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of T=1 Subviral Particle of Penaeus Vannamei Nodavirus Capsid Protein Deletion Mutant (Delta 1-37 & 251-368) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:93.5 occ:1.00 OE1 A:GLN248 2.1 76.5 1.0 NE2 A:GLN248 2.3 80.7 1.0 CD A:GLN248 2.5 82.8 1.0 OE2 A:GLU118 2.8 80.6 1.0 CD A:GLU118 3.5 73.6 1.0 OE1 A:GLU118 3.5 69.5 1.0 CG A:GLN248 4.0 73.0 1.0 CB A:GLN248 4.8 70.5 1.0 CG A:GLU118 4.9 71.5 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