Cadmium in PDB 3wvv: Crystal Structure of Ruco/Apo-E45C_C48AFR

The structure of Crystal Structure of Ruco/Apo-E45C_C48AFR, PDB code: 3wvv 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)	25.44 / 1.82
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	181.672, 181.672, 181.672, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 19.1

The structure of Crystal Structure of Ruco/Apo-E45C_C48AFR also contains other interesting chemical elements:

Ruthenium

(Ru)

4 atoms

The binding sites of Cadmium atom in the Crystal Structure of Ruco/Apo-E45C_C48AFR (pdb code 3wvv). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Crystal Structure of Ruco/Apo-E45C_C48AFR, PDB code: 3wvv:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in the Crystal Structure of Ruco/Apo-E45C_C48AFR


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-E45C_C48AFR within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd201 b:63.8 occ:0.33 OD1 A:ASP127 3.6 32.2 1.0 OE1 A:GLU130 4.1 34.1 1.0 CG A:ASP127 4.7 31.7 1.0 CB A:GLU130 4.9 27.2 1.0

Cadmium binding site 2 out of 4 in the Crystal Structure of Ruco/Apo-E45C_C48AFR


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-E45C_C48AFR within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd202 b:30.8 occ:0.50 OD2 A:ASP80 2.1 34.0 1.0 OD1 A:ASP80 2.5 17.0 1.0 CG A:ASP80 2.8 22.6 1.0 CB A:ASP80 4.3 23.8 1.0 O A:HOH450 4.6 27.9 1.0

Cadmium binding site 3 out of 4 in the Crystal Structure of Ruco/Apo-E45C_C48AFR


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-E45C_C48AFR within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd203 b:42.9 occ:0.40 OE1 A:GLU130 2.8 34.1 1.0 OE2 A:GLU130 2.9 31.4 1.0 CD A:GLU130 3.1 35.1 1.0 RU A:RU213 3.7 41.2 0.5 N A:ASP127 4.1 24.3 1.0 CB A:CYS126 4.2 28.8 1.0 CA A:ASP127 4.2 23.9 1.0 C A:CYS126 4.3 23.6 1.0 CG A:GLU130 4.5 28.7 1.0 O A:CYS126 4.5 22.6 1.0 CB A:ASP127 4.6 26.9 1.0 CA A:CYS126 4.9 22.1 1.0 O A:PRO123 4.9 15.9 1.0 CB A:GLU130 5.0 27.2 1.0

Cadmium binding site 4 out of 4 in the Crystal Structure of Ruco/Apo-E45C_C48AFR


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Ruco/Apo-E45C_C48AFR within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd204 b:33.4 occ:0.20 OE2 A:GLU11 2.4 21.2 1.0 OE1 A:GLU11 2.6 29.3 1.0 CD A:GLU11 2.9 29.2 1.0 O A:HOH316 3.0 29.1 1.0 OG1 A:THR10 4.1 24.1 1.0 CG A:GLU11 4.4 24.0 1.0 OE1 A:GLN120 4.5 32.2 1.0 NE2 A:GLN120 4.5 32.9 1.0 CB A:SER9 4.6 18.4 1.0 N A:THR10 4.8 16.6 1.0 CD A:GLN120 4.9 33.0 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