Cadmium in PDB 5ix6: X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin
Protein crystallography data
The structure of X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin, PDB code: 5ix6
was solved by
G.Ferraro,
N.Pontillo,
A.Merlino,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
104.30 /
1.85
|
Space group
|
F 4 3 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
180.645,
180.645,
180.645,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18 /
22.6
|
Other elements in 5ix6:
The structure of X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin also contains other interesting chemical elements:
Cadmium Binding Sites:
The binding sites of Cadmium atom in the X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin
(pdb code 5ix6). This binding sites where shown within
5.0 Angstroms radius around Cadmium atom.
In total 9 binding sites of Cadmium where determined in the
X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin, PDB code: 5ix6:
Jump to Cadmium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Cadmium binding site 1 out
of 9 in 5ix6
Go back to
Cadmium Binding Sites List in 5ix6
Cadmium binding site 1 out
of 9 in the X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin
 Mono view
 Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 1 of X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd208
b:40.5
occ:0.40
|
O
|
A:HOH325
|
2.2
|
11.0
|
0.4
|
O
|
A:HOH311
|
2.2
|
53.6
|
1.0
|
OE1
|
A:GLU11
|
2.6
|
19.5
|
1.0
|
O
|
A:HOH446
|
2.7
|
20.4
|
1.0
|
OE2
|
A:GLU11
|
2.8
|
27.9
|
1.0
|
O
|
A:HOH547
|
2.8
|
41.3
|
1.0
|
CD
|
A:GLU11
|
3.0
|
24.7
|
1.0
|
OG1
|
A:THR10
|
3.8
|
22.7
|
1.0
|
CB
|
A:SER9
|
4.4
|
14.1
|
1.0
|
OE1
|
A:GLN120
|
4.5
|
35.6
|
1.0
|
CG
|
A:GLU11
|
4.5
|
21.1
|
1.0
|
O
|
A:HOH439
|
4.7
|
45.8
|
1.0
|
N
|
A:THR10
|
4.7
|
13.8
|
1.0
|
NE2
|
A:GLN120
|
4.8
|
34.1
|
1.0
|
N
|
A:GLU11
|
5.0
|
15.3
|
1.0
|
CD
|
A:GLN120
|
5.0
|
32.3
|
1.0
|
|
Cadmium binding site 2 out
of 9 in 5ix6
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Cadmium Binding Sites List in 5ix6
Cadmium binding site 2 out
of 9 in the X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin
 Mono view
 Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 2 of X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd209
b:58.7
occ:0.45
|
OE1
|
A:GLU53
|
2.4
|
18.3
|
0.3
|
OE1
|
A:GLU56
|
2.5
|
52.8
|
1.0
|
OE2
|
A:GLU53
|
2.7
|
19.5
|
0.3
|
CD
|
A:GLU53
|
2.9
|
17.6
|
0.3
|
CD
|
A:GLU56
|
3.3
|
38.8
|
1.0
|
OE2
|
A:GLU56
|
3.4
|
51.5
|
1.0
|
O
|
A:HOH329
|
3.9
|
40.6
|
1.0
|
CG
|
A:GLU53
|
4.4
|
17.0
|
0.3
|
CG
|
A:GLU56
|
4.7
|
30.0
|
1.0
|
CG
|
A:GLU53
|
4.7
|
27.3
|
0.7
|
|
Cadmium binding site 3 out
of 9 in 5ix6
Go back to
Cadmium Binding Sites List in 5ix6
Cadmium binding site 3 out
of 9 in the X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin
 Mono view
 Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 3 of X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd210
b:15.6
occ:0.50
|
OD2
|
A:ASP80
|
2.2
|
13.8
|
1.0
|
O
|
A:HOH495
|
2.4
|
5.4
|
1.0
|
OD1
|
A:ASP80
|
2.4
|
13.3
|
1.0
|
CG
|
A:ASP80
|
2.7
|
14.1
|
1.0
|
CB
|
A:ASP80
|
4.2
|
13.4
|
1.0
|
O
|
A:HOH402
|
4.3
|
14.4
|
1.0
|
O
|
A:HOH380
|
4.6
|
27.8
|
1.0
|
|
Cadmium binding site 4 out
of 9 in 5ix6
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Cadmium Binding Sites List in 5ix6
Cadmium binding site 4 out
of 9 in the X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin
 Mono view
 Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 4 of X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd211
b:43.6
occ:0.50
|
O
|
A:HOH415
|
2.1
|
13.9
|
0.5
|
NE2
|
A:HIS132
|
2.3
|
54.7
|
1.0
|
CE1
|
A:HIS132
|
2.8
|
52.1
|
1.0
|
CD2
|
A:HIS132
|
3.5
|
49.3
|
1.0
|
O
|
A:HOH417
|
3.8
|
14.0
|
0.5
|
ND1
|
A:HIS132
|
4.0
|
54.4
|
1.0
|
CG
|
A:HIS132
|
4.4
|
44.8
|
1.0
|
O
|
A:HOH478
|
4.9
|
45.0
|
1.0
|
|
Cadmium binding site 5 out
of 9 in 5ix6
Go back to
Cadmium Binding Sites List in 5ix6
Cadmium binding site 5 out
of 9 in the X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin
 Mono view
 Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 5 of X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd212
b:28.2
occ:0.30
|
OE1
|
A:GLU130
|
2.5
|
34.1
|
1.0
|
OE2
|
A:GLU130
|
2.5
|
36.1
|
1.0
|
CD
|
A:GLU130
|
2.8
|
31.6
|
1.0
|
O
|
A:HOH301
|
4.0
|
28.4
|
1.0
|
O
|
A:HOH490
|
4.2
|
33.0
|
1.0
|
CG
|
A:GLU130
|
4.4
|
29.6
|
1.0
|
O
|
A:HOH307
|
4.4
|
40.4
|
1.0
|
CD
|
A:CD214
|
5.0
|
37.4
|
0.2
|
|
Cadmium binding site 6 out
of 9 in 5ix6
Go back to
Cadmium Binding Sites List in 5ix6
Cadmium binding site 6 out
of 9 in the X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin
 Mono view
 Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 6 of X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd213
b:65.1
occ:0.35
|
O
|
A:HOH465
|
2.0
|
11.2
|
0.3
|
O
|
A:HOH388
|
2.9
|
40.2
|
1.0
|
OE1
|
A:GLU45
|
2.9
|
28.7
|
1.0
|
O
|
A:HOH349
|
3.2
|
32.4
|
1.0
|
O
|
A:HOH345
|
3.3
|
29.5
|
1.0
|
CD
|
A:GLU45
|
3.9
|
32.1
|
1.0
|
OE2
|
A:GLU45
|
4.2
|
43.1
|
1.0
|
CD2
|
A:HIS173
|
4.4
|
77.5
|
1.0
|
NH1
|
A:ARG168
|
4.5
|
14.9
|
1.0
|
NH2
|
A:ARG168
|
4.8
|
14.9
|
1.0
|
O
|
A:HOH330
|
4.9
|
51.6
|
1.0
|
|
Cadmium binding site 7 out
of 9 in 5ix6
Go back to
Cadmium Binding Sites List in 5ix6
Cadmium binding site 7 out
of 9 in the X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin
 Mono view
 Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 7 of X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd214
b:37.4
occ:0.20
|
O
|
A:HOH301
|
2.3
|
28.4
|
1.0
|
O
|
A:HOH427
|
2.4
|
37.8
|
1.0
|
OD1
|
A:ASP127
|
3.8
|
28.5
|
1.0
|
OE1
|
A:GLU130
|
4.0
|
34.1
|
1.0
|
OG
|
A:SER131
|
4.5
|
44.4
|
1.0
|
O
|
A:HOH350
|
4.7
|
27.2
|
0.4
|
CB
|
A:GLU130
|
4.9
|
28.0
|
1.0
|
CD
|
A:CD212
|
5.0
|
28.2
|
0.3
|
|
Cadmium binding site 8 out
of 9 in 5ix6
Go back to
Cadmium Binding Sites List in 5ix6
Cadmium binding site 8 out
of 9 in the X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin
 Mono view
 Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 8 of X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd215
b:41.9
occ:0.40
|
OE2
|
A:GLU60
|
2.4
|
37.5
|
1.0
|
O
|
A:HOH472
|
2.5
|
19.7
|
0.4
|
OE2
|
A:GLU56
|
2.7
|
51.5
|
1.0
|
OE2
|
A:GLU57
|
2.7
|
42.2
|
1.0
|
OE1
|
A:GLU60
|
2.8
|
34.0
|
1.0
|
CD
|
A:GLU60
|
2.9
|
28.2
|
1.0
|
O
|
A:HOH329
|
3.4
|
40.6
|
1.0
|
CD
|
A:GLU56
|
3.5
|
38.8
|
1.0
|
CD
|
A:GLU57
|
3.9
|
35.0
|
1.0
|
CG
|
A:GLU56
|
3.9
|
30.0
|
1.0
|
O
|
A:HOH456
|
4.2
|
70.1
|
1.0
|
O
|
A:HOH303
|
4.2
|
39.3
|
1.0
|
OE1
|
A:GLU57
|
4.4
|
46.2
|
1.0
|
CG
|
A:GLU60
|
4.4
|
23.2
|
1.0
|
OE1
|
A:GLU56
|
4.6
|
52.8
|
1.0
|
|
Cadmium binding site 9 out
of 9 in 5ix6
Go back to
Cadmium Binding Sites List in 5ix6
Cadmium binding site 9 out
of 9 in the X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin
 Mono view
 Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 9 of X-Ray Structure of AUOXO3-Encapsulated Horse Spleen Apoferritin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd216
b:42.0
occ:0.15
|
OE2
|
A:GLU53
|
1.9
|
47.3
|
0.7
|
CD
|
A:GLU53
|
3.1
|
35.5
|
0.7
|
O
|
A:HOH316
|
3.3
|
52.6
|
1.0
|
O
|
A:HOH462
|
3.4
|
38.5
|
0.7
|
OE1
|
A:GLU53
|
3.7
|
37.1
|
0.7
|
CB
|
A:LYS172
|
4.1
|
57.7
|
1.0
|
CG
|
A:GLU53
|
4.3
|
27.3
|
0.7
|
CG
|
A:GLU53
|
4.5
|
17.0
|
0.3
|
OE1
|
A:GLU53
|
4.8
|
18.3
|
0.3
|
CD
|
A:GLU53
|
4.9
|
17.6
|
0.3
|
|
Reference:
G.Ferraro,
D.M.Monti,
A.Amoresano,
N.Pontillo,
G.Petruk,
F.Pane,
M.A.Cinellu,
A.Merlino.
Gold-Based Drug Encapsulation Within A Ferritin Nanocage: X-Ray Structure and Biological Evaluation As A Potential Anticancer Agent of the AUOXO3-Loaded Protein. Chem.Commun.(Camb.) V. 52 9518 2016.
ISSN: ESSN 1364-548X
PubMed: 27326513
DOI: 10.1039/C6CC02516A
Page generated: Fri Jul 19 18:29:54 2024
|