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Cadmium in PDB 3h7g: Apo-Fr with Au Ions

Protein crystallography data

The structure of Apo-Fr with Au Ions, PDB code: 3h7g was solved by M.Abe, T.Ueno, S.Abe, M.Suzuki, T.Goto, Y.Toda, T.Akita, Y.Yamada, Y.Watanabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.28 / 1.65
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 181.632, 181.632, 181.632, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 23.6

Other elements in 3h7g:

The structure of Apo-Fr with Au Ions also contains other interesting chemical elements:

Gold (Au) 6 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Apo-Fr with Au Ions (pdb code 3h7g). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Apo-Fr with Au Ions, PDB code: 3h7g:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in 3h7g

Go back to Cadmium Binding Sites List in 3h7g
Cadmium binding site 1 out of 3 in the Apo-Fr with Au Ions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Apo-Fr with Au Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd207

b:22.4
occ:0.50
OD2 A:ASP80 2.5 16.0 1.0
OD1 A:ASP80 2.5 11.8 1.0
CG A:ASP80 2.8 12.1 1.0
CB A:ASP80 4.2 10.8 1.0
O A:HOH1042 4.4 15.0 1.0

Cadmium binding site 2 out of 3 in 3h7g

Go back to Cadmium Binding Sites List in 3h7g
Cadmium binding site 2 out of 3 in the Apo-Fr with Au Ions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Apo-Fr with Au Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd208

b:27.6
occ:0.33
OE1 A:GLU130 2.3 22.8 1.0
CD A:GLU130 3.3 20.6 1.0
OE2 A:GLU130 3.7 25.0 1.0
CD A:CD209 4.2 36.3 0.3
CG A:GLU130 4.7 19.6 1.0
CB A:GLU130 5.0 18.0 1.0

Cadmium binding site 3 out of 3 in 3h7g

Go back to Cadmium Binding Sites List in 3h7g
Cadmium binding site 3 out of 3 in the Apo-Fr with Au Ions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Apo-Fr with Au Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd209

b:36.3
occ:0.33
OD1 A:ASP127 3.8 17.9 1.0
CD A:CD208 4.2 27.6 0.3
OG A:SER131 4.3 22.8 1.0
OE1 A:GLU130 4.4 22.8 1.0
CG A:ASP127 5.0 17.4 1.0
CB A:GLU130 5.0 18.0 1.0

Reference:

M.Suzuki, M.Abe, T.Ueno, S.Abe, T.Goto, Y.Toda, T.Akita, Y.Yamada, Y.Watanabe. Preparation and Catalytic Reaction of Au/Pd Bimetallic Nanoparticles in Apo-Ferritin Chem.Commun.(Camb.) V. 32 4871 2009.
ISSN: ISSN 1359-7345
PubMed: 19652809
DOI: 10.1039/B908742G
Page generated: Sat Dec 12 08:21:52 2020

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