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

Protein crystallography data

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

Cadmium Binding Sites:

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 5ykx

Go back to Cadmium Binding Sites List in 5ykx
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 5ykx

Go back to Cadmium Binding Sites List in 5ykx
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 5ykx

Go back to Cadmium Binding Sites List in 5ykx
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

Reference:

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
Page generated: Sat Dec 12 08:28:00 2020

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