Cadmium in PDB 3wvu: Crystal Structure of Ruco/Apo-R52CFR

The structure of Crystal Structure of Ruco/Apo-R52CFR, PDB code: 3wvu was solved by K.Fujita, Y.Tanaka, S.Abe, T.Hikage, T.Kuchimaru, S.Kizaka-Kondoh, T.Ueno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.26 / 1.92
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	181.575, 181.575, 181.575, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 19.3

The structure of Crystal Structure of Ruco/Apo-R52CFR also contains other interesting chemical elements:

Ruthenium

(Ru)

2 atoms

The binding sites of Cadmium atom in the Crystal Structure of Ruco/Apo-R52CFR (pdb code 3wvu). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Crystal Structure of Ruco/Apo-R52CFR, PDB code: 3wvu:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in the Crystal Structure of Ruco/Apo-R52CFR


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Ruco/Apo-R52CFR within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd201 b:55.1 occ:0.20 OE1 A:GLU130 2.7 25.6 1.0 OE2 A:GLU130 3.3 16.2 1.0 CD A:GLU130 3.3 17.7 1.0 O A:HOH381 4.2 30.1 1.0 CD A:CD202 4.6 40.0 0.2 CG A:GLU130 4.8 16.3 1.0

Cadmium binding site 2 out of 3 in the Crystal Structure of Ruco/Apo-R52CFR


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Ruco/Apo-R52CFR within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd202 b:40.0 occ:0.20 O A:HOH404 2.5 31.8 1.0 OD1 A:ASP127 3.4 26.0 1.0 OG A:SER131 4.0 19.7 0.5 OE1 A:GLU130 4.1 25.6 1.0 CG A:ASP127 4.6 23.9 1.0 CD A:CD201 4.6 55.1 0.2 CB A:GLU130 4.9 16.1 1.0

Cadmium binding site 3 out of 3 in the Crystal Structure of Ruco/Apo-R52CFR


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Ruco/Apo-R52CFR within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd203 b:28.1 occ:0.50 OD2 A:ASP80 2.0 26.1 1.0 OD1 A:ASP80 2.6 12.7 1.0 CG A:ASP80 2.7 16.4 1.0 CB A:ASP80 4.1 19.0 1.0 O A:HOH353 4.6 24.1 1.0

K.Fujita, Y.Tanaka, T.Sho, S.Ozeki, S.Abe, T.Hikage, T.Kuchimaru, S.Kizaka-Kondoh, T.Ueno. Intracellular Co Release From Composite of Ferritin and Ruthenium Carbonyl Complexes. J.Am.Chem.Soc. V. 136 16902 2014.
ISSN: ISSN 0002-7863
PubMed: 25352251
DOI: 10.1021/JA508938F