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Cadmium in PDB 3wvw: Crystal Structure of Ruco/Apo-Wtfr

Protein crystallography data

The structure of Crystal Structure of Ruco/Apo-Wtfr, PDB code: 3wvw 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) 21.43 / 2.00
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 181.863, 181.863, 181.863, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 19.9

Other elements in 3wvw:

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

Ruthenium (Ru) 3 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Ruco/Apo-Wtfr (pdb code 3wvw). 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-Wtfr, PDB code: 3wvw:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in 3wvw

Go back to Cadmium Binding Sites List in 3wvw
Cadmium binding site 1 out of 3 in the Crystal Structure of Ruco/Apo-Wtfr


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-Wtfr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd201

b:48.1
occ:0.10
OE1 A:GLU130 2.5 36.1 1.0
CD A:GLU130 3.3 24.1 1.0
OE2 A:GLU130 3.3 21.1 1.0
CD A:CD202 4.3 78.6 0.3
RU A:RU213 4.3 46.1 0.4
OD1 A:ASP127 4.7 30.5 1.0
CG A:GLU130 4.8 21.8 1.0

Cadmium binding site 2 out of 3 in 3wvw

Go back to Cadmium Binding Sites List in 3wvw
Cadmium binding site 2 out of 3 in the Crystal Structure of Ruco/Apo-Wtfr


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-Wtfr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd202

b:78.6
occ:0.33
OD1 A:ASP127 2.7 30.5 1.0
OE1 A:GLU130 3.8 36.1 1.0
CG A:ASP127 3.9 28.8 1.0
CD A:CD201 4.3 48.1 0.1
OD2 A:ASP127 4.6 27.8 1.0
CB A:GLU130 4.8 20.6 1.0
CD A:GLU130 5.0 24.1 1.0

Cadmium binding site 3 out of 3 in 3wvw

Go back to Cadmium Binding Sites List in 3wvw
Cadmium binding site 3 out of 3 in the Crystal Structure of Ruco/Apo-Wtfr


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-Wtfr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:30.9
occ:0.50
OD2 A:ASP80 2.1 31.1 1.0
OD1 A:ASP80 2.7 23.2 1.0
CG A:ASP80 2.9 21.9 1.0
CB A:ASP80 4.3 24.5 1.0
O A:HOH405 4.6 28.7 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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