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Gold 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:

Cadmium (Cd) 3 atoms

Gold Binding Sites:

The binding sites of Gold atom in the Apo-Fr with Au Ions (pdb code 3h7g). This binding sites where shown within 5.0 Angstroms radius around Gold atom.
In total 6 binding sites of Gold where determined in the Apo-Fr with Au Ions, PDB code: 3h7g:
Jump to Gold binding site number: 1; 2; 3; 4; 5; 6;

Gold binding site 1 out of 6 in 3h7g

Go back to Gold Binding Sites List in 3h7g
Gold binding site 1 out of 6 in the Apo-Fr with Au Ions


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 1 of Apo-Fr with Au Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au201

b:31.1
occ:1.00
ND1 A:HIS49 2.2 16.5 1.0
SG A:CYS48 2.2 10.5 1.0
AU A:AU3206 2.7 50.9 0.2
CE1 A:HIS49 2.9 19.4 1.0
N A:HIS49 3.0 7.9 1.0
CB A:CYS48 3.0 8.8 1.0
C A:CYS48 3.2 7.8 1.0
CG A:HIS49 3.4 13.6 1.0
CA A:HIS49 3.4 8.5 1.0
AU A:AU3202 3.5 32.4 1.0
O A:GLU45 3.6 8.0 1.0
CA A:CYS48 3.7 8.0 1.0
O A:CYS48 3.8 7.7 1.0
CB A:HIS49 3.9 9.3 1.0
NE2 A:HIS49 4.1 19.5 1.0
CZ A:ARG52 4.2 24.8 1.0
NE A:ARG52 4.3 22.3 1.0
O A:HOH1172 4.3 25.9 1.0
CD2 A:HIS49 4.4 17.4 1.0
NH2 A:ARG52 4.5 26.4 1.0
CG A:GLU45 4.5 13.5 1.0
C A:GLU45 4.6 7.6 1.0
NH1 A:ARG52 4.6 27.4 1.0
N A:CYS48 4.7 7.6 1.0
CD A:ARG52 4.7 14.6 1.0
C A:HIS49 4.8 7.4 1.0
CA A:GLU45 4.9 8.3 1.0
CB A:ARG52 5.0 9.5 1.0

Gold binding site 2 out of 6 in 3h7g

Go back to Gold Binding Sites List in 3h7g
Gold binding site 2 out of 6 in the Apo-Fr with Au Ions


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 2 of Apo-Fr with Au Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au202

b:32.4
occ:1.00
SG A:CYS48 2.0 10.5 1.0
O A:HOH1129 2.4 15.5 1.0
O A:GLY34 3.3 7.2 1.0
CB A:CYS48 3.3 8.8 1.0
O A:CYS48 3.4 7.7 1.0
C A:GLY34 3.4 6.6 1.0
AU A:AU3201 3.5 31.1 1.0
CA A:GLY34 3.5 6.6 1.0
C A:CYS48 3.6 7.8 1.0
CA A:CYS48 3.7 8.0 1.0
N A:PHE35 4.0 5.8 1.0
CB A:ARG52 4.0 9.5 1.0
AU A:AU3206 4.1 50.9 0.2
CD A:ARG52 4.5 14.6 1.0
CA A:PHE35 4.6 6.2 1.0
N A:HIS49 4.6 7.9 1.0
CG A:ARG52 4.7 13.9 1.0
CB A:ASP38 4.8 7.0 1.0
N A:ARG52 4.9 7.0 1.0
CA A:ARG52 4.9 9.5 1.0
CD1 A:PHE35 4.9 9.2 1.0
CG A:PHE35 4.9 5.7 1.0
N A:GLY34 4.9 5.9 1.0

Gold binding site 3 out of 6 in 3h7g

Go back to Gold Binding Sites List in 3h7g
Gold binding site 3 out of 6 in the Apo-Fr with Au Ions


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 3 of Apo-Fr with Au Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au203

b:36.8
occ:1.00
ND1 A:HIS114 2.1 16.3 1.0
SG A:CYS126 2.2 17.2 1.0
O A:HOH1114 2.6 35.1 1.0
CE1 A:HIS114 3.0 19.4 1.0
O A:HIS114 3.0 13.8 1.0
CB A:CYS126 3.1 14.4 1.0
CG A:HIS114 3.2 15.7 1.0
CA A:HIS114 3.6 12.8 1.0
C A:HIS114 3.6 13.0 1.0
CB A:HIS114 3.6 13.2 1.0
AU A:AU3204 3.7 42.5 1.0
CA A:CYS126 3.8 13.5 1.0
N A:SER118 4.1 13.7 1.0
NE2 A:HIS114 4.1 18.3 1.0
CB A:SER118 4.2 14.7 1.0
CD2 A:HIS114 4.2 18.2 1.0
OE2 A:GLU130 4.4 25.0 1.0
CA A:SER118 4.5 14.6 1.0
N A:CYS126 4.7 12.4 1.0
C A:GLY117 4.8 13.2 1.0
N A:ALA115 4.8 13.1 1.0
CA A:GLY117 4.9 13.1 1.0
C A:CYS126 5.0 13.9 1.0
N A:HIS114 5.0 11.0 1.0

Gold binding site 4 out of 6 in 3h7g

Go back to Gold Binding Sites List in 3h7g
Gold binding site 4 out of 6 in the Apo-Fr with Au Ions


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 4 of Apo-Fr with Au Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au204

b:42.5
occ:1.00
SG A:CYS126 2.2 17.2 1.0
CB A:CYS126 3.2 14.4 1.0
O A:ASP122 3.5 10.1 1.0
CA A:SER118 3.7 14.6 1.0
AU A:AU3203 3.7 36.8 1.0
C A:ASP122 3.8 10.5 1.0
N A:SER118 3.8 13.7 1.0
CA A:PRO123 3.8 10.3 1.0
C A:GLY117 3.9 13.2 1.0
O A:GLY117 3.9 13.4 1.0
N A:PRO123 4.0 10.1 1.0
N A:ASP122 4.2 11.2 1.0
CB A:SER118 4.3 14.7 1.0
CA A:CYS126 4.5 13.5 1.0
N A:CYS126 4.6 12.4 1.0
CA A:ASP122 4.6 10.7 1.0
CB A:PRO123 4.7 10.8 1.0
CA A:GLY117 4.7 13.1 1.0
OG A:SER118 4.8 18.0 1.0
C A:PRO123 4.8 10.2 1.0
C A:SER118 4.9 14.7 1.0
CD A:PRO123 5.0 11.1 1.0
C A:ALA121 5.0 12.5 1.0
O A:PRO123 5.0 10.7 1.0

Gold binding site 5 out of 6 in 3h7g

Go back to Gold Binding Sites List in 3h7g
Gold binding site 5 out of 6 in the Apo-Fr with Au Ions


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 5 of Apo-Fr with Au Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au205

b:55.5
occ:0.40
CE A:MET96 1.9 10.6 1.0
SD A:MET96 2.6 13.4 1.0
ND1 A:HIS147 2.8 11.5 1.0
CB A:HIS147 3.3 8.5 1.0
CG A:HIS147 3.3 9.2 1.0
CG A:MET96 3.7 10.1 1.0
CE2 A:PHE50 3.7 9.3 1.0
CE1 A:HIS147 3.8 8.6 1.0
CZ A:PHE50 3.9 9.1 1.0
CD2 A:PHE50 4.0 8.5 1.0
CE2 A:PHE166 4.1 10.2 1.0
CZ A:PHE166 4.2 10.8 1.0
CD1 A:ILE151 4.3 16.9 1.0
CD2 A:LEU171 4.4 11.3 1.0
CB A:MET96 4.4 8.5 1.0
CE1 A:PHE50 4.4 10.2 1.0
CD2 A:HIS147 4.5 7.3 1.0
CG A:PHE50 4.5 7.0 1.0
CA A:HIS147 4.7 8.4 1.0
CD1 A:PHE50 4.7 10.3 1.0
NE2 A:HIS147 4.7 12.2 1.0
CD1 A:LEU171 5.0 11.2 1.0

Gold binding site 6 out of 6 in 3h7g

Go back to Gold Binding Sites List in 3h7g
Gold binding site 6 out of 6 in the Apo-Fr with Au Ions


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 6 of Apo-Fr with Au Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au206

b:50.9
occ:0.20
O A:HOH1172 1.8 25.9 1.0
SG A:CYS48 2.4 10.5 1.0
AU A:AU3201 2.7 31.1 1.0
CB A:CYS48 3.2 8.8 1.0
OD1 A:ASP38 3.2 11.5 1.0
O A:HOH1171 3.7 19.4 1.0
CB A:ASP38 3.8 7.0 1.0
CG A:ASP38 3.8 7.9 1.0
AU A:AU3202 4.1 32.4 1.0
CG A:GLU45 4.3 13.5 1.0
CA A:ASP38 4.3 6.5 1.0
ND1 A:HIS49 4.4 16.5 1.0
CA A:GLU45 4.5 8.3 1.0
CE1 A:HIS49 4.5 19.4 1.0
O A:GLU45 4.6 8.0 1.0
CA A:CYS48 4.6 8.0 1.0
CB A:GLU45 4.8 9.6 1.0
OD2 A:ASP38 4.9 9.6 1.0
N A:ASP38 5.0 6.1 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 01:53:32 2020

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