Zinc in PDB 5yku: The Crystal Structure of Macrobrachium Rosenbergii Nodavirus P-Domain with Zn Ions

The structure of The Crystal Structure of Macrobrachium Rosenbergii Nodavirus P-Domain with Zn Ions, PDB code: 5yku 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)	23.87 / 1.39
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	72.874, 72.874, 47.041, 90.00, 90.00, 120.00
R / Rfree (%)	14.2 / 15.1

The binding sites of Zinc atom in the The Crystal Structure of Macrobrachium Rosenbergii Nodavirus P-Domain with Zn Ions (pdb code 5yku). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the The Crystal Structure of Macrobrachium Rosenbergii Nodavirus P-Domain with Zn Ions, PDB code: 5yku:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the The Crystal Structure of Macrobrachium Rosenbergii Nodavirus P-Domain with Zn Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of Macrobrachium Rosenbergii Nodavirus P-Domain with Zn Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:12.2 occ:0.43 O A:HOH311 2.0 17.3 1.0 OE2 A:GLU96 2.0 14.3 1.0 CD A:GLU96 2.6 15.4 1.0 OE1 A:GLU96 2.6 18.0 1.0 CG A:GLU96 4.1 13.5 1.0 OG1 A:THR35 4.2 19.2 1.0 O A:HOH397 4.2 17.1 1.0 OD2 A:ASP33 4.3 15.7 1.0 CB A:THR35 4.6 15.5 1.0 CB A:ASP33 4.7 12.0 1.0 O A:HOH556 4.9 17.6 0.5 CG A:ASP33 5.0 12.7 1.0

Zinc binding site 2 out of 3 in the The Crystal Structure of Macrobrachium Rosenbergii Nodavirus P-Domain with Zn Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of Macrobrachium Rosenbergii Nodavirus P-Domain with Zn Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:9.4 occ:0.50 OD2 A:ASP68 2.1 10.9 1.0 CG A:ASP68 2.5 10.2 1.0 OD1 A:ASP68 2.5 12.7 1.0 CB A:ASP68 4.0 11.2 1.0 O A:HOH365 4.4 26.9 1.0 O A:HOH396 4.5 28.0 1.0 CA A:ASP68 5.0 10.2 1.0

Zinc binding site 3 out of 3 in the The Crystal Structure of Macrobrachium Rosenbergii Nodavirus P-Domain with Zn Ions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Crystal Structure of Macrobrachium Rosenbergii Nodavirus P-Domain with Zn Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:11.2 occ:0.42 OD1 A:ASP110 2.1 14.6 1.0 CG A:ASP110 2.7 13.5 1.0 OD2 A:ASP110 2.9 16.0 1.0 O A:HOH393 4.1 26.6 1.0 CB A:ASP110 4.2 12.5 1.0 O A:HOH454 4.7 28.0 1.0 CA A:ASP110 4.8 11.3 1.0 N A:ASP110 5.0 12.5 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