Cadmium in PDB 5ykx: The Crystal Structure of Macrobrachium Rosenbergii Nodavirus P-Domain with Cd Ion

The structure of The Crystal Structure of Macrobrachium Rosenbergii Nodavirus P-Domain with Cd Ion, PDB code: 5ykx 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)	29.30 / 2.00
Space group	P 43 3 2
Cell size a, b, c (Å), α, β, γ (°)	134.175, 134.175, 134.175, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 19.5

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

Cadmium binding site 1 out of 3 in the The Crystal Structure of Macrobrachium Rosenbergii Nodavirus P-Domain with Cd Ion


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of The Crystal Structure of Macrobrachium Rosenbergii Nodavirus P-Domain with Cd Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd201 b:26.0 occ:0.27 OE2 A:GLU55 2.3 35.1 1.0 OE1 A:GLU55 2.4 41.9 1.0 CD A:GLU55 2.8 35.2 1.0 O A:HOH334 3.8 87.2 0.3 O A:HOH419 4.3 48.4 1.0 CG A:GLU55 4.3 35.4 1.0 O A:HOH389 4.4 57.7 1.0

Cadmium binding site 2 out of 3 in the The Crystal Structure of Macrobrachium Rosenbergii Nodavirus P-Domain with Cd Ion


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of The Crystal Structure of Macrobrachium Rosenbergii Nodavirus P-Domain with Cd Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd201 b:27.8 occ:0.27 OE1 B:GLU55 2.3 41.6 1.0 OE2 B:GLU55 2.5 40.5 1.0 CD B:GLU55 2.7 36.8 1.0 CG B:GLU55 4.3 31.8 1.0 CB B:GLU55 5.0 26.6 1.0

Cadmium binding site 3 out of 3 in the The Crystal Structure of Macrobrachium Rosenbergii Nodavirus P-Domain with Cd Ion


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of The Crystal Structure of Macrobrachium Rosenbergii Nodavirus P-Domain with Cd Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd202 b:22.9 occ:0.81 O1 B:SO4204 1.7 34.8 1.0 O B:HOH382 2.2 42.6 1.0 SG B:CYS64 2.3 28.0 1.0 O B:THR98 2.4 23.8 1.0 O B:HOH344 2.5 36.8 1.0 S B:SO4204 2.8 54.6 1.0 O2 B:SO4204 3.1 81.4 1.0 O4 B:SO4204 3.2 30.4 1.0 C B:THR98 3.3 23.9 1.0 CB B:CYS64 3.4 26.9 1.0 O B:HOH303 3.7 45.3 1.0 CA B:CYS64 3.9 24.7 1.0 CA B:THR98 4.0 24.7 1.0 CB B:THR98 4.0 28.8 1.0 N B:THR98 4.0 23.4 1.0 CG B:GLU66 4.1 40.2 1.0 N B:ASN65 4.1 24.4 1.0 O8 B:EPE203 4.2 52.1 1.0 O B:HOH428 4.2 38.7 1.0 O B:HOH432 4.2 19.9 1.0 O3 B:SO4204 4.3 42.1 1.0 C B:CYS64 4.3 23.1 1.0 OD1 B:ASN65 4.3 26.9 1.0 N B:PHE99 4.3 25.4 1.0 N B:GLU66 4.6 29.2 1.0 CA B:PHE99 4.7 22.3 1.0 CG2 B:THR98 4.7 33.8 1.0 OE1 B:GLU66 4.8 54.5 1.0 CD B:GLU66 4.9 60.3 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