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

Protein crystallography data

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

Other elements in 3wvu:

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

Ruthenium (Ru) 2 atoms

Cadmium Binding Sites:

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 3wvu

Go back to Cadmium Binding Sites List in 3wvu
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 3wvu

Go back to Cadmium Binding Sites List in 3wvu
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 3wvu

Go back to Cadmium Binding Sites List in 3wvu
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

Reference:

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
Page generated: Sun Jan 24 09:56:20 2021

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