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:
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: Wed Jul 10 14:14:57 2024
|