Cadmium in PDB 3f38: Apoferritin: Complex with 2,6-Dimethylphenol
Protein crystallography data
The structure of Apoferritin: Complex with 2,6-Dimethylphenol, PDB code: 3f38
was solved by
L.S.Vedula,
N.J.Economou,
M.J.Rossi,
R.G.Eckenhoff,
P.J.Loll,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.88 /
1.75
|
Space group
|
F 4 3 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
181.988,
181.988,
181.988,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.2 /
22.2
|
Cadmium Binding Sites:
The binding sites of Cadmium atom in the Apoferritin: Complex with 2,6-Dimethylphenol
(pdb code 3f38). This binding sites where shown within
5.0 Angstroms radius around Cadmium atom.
In total 10 binding sites of Cadmium where determined in the
Apoferritin: Complex with 2,6-Dimethylphenol, PDB code: 3f38:
Jump to Cadmium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Cadmium binding site 1 out
of 10 in 3f38
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Cadmium Binding Sites List in 3f38
Cadmium binding site 1 out
of 10 in the Apoferritin: Complex with 2,6-Dimethylphenol
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 1 of Apoferritin: Complex with 2,6-Dimethylphenol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd1001
b:19.0
occ:0.25
|
CD
|
A:CD1001
|
0.0
|
19.0
|
0.2
|
CD
|
A:CD1001
|
1.4
|
21.3
|
0.2
|
OD2
|
A:ASP80
|
1.8
|
36.3
|
1.0
|
CG
|
A:ASP80
|
2.5
|
25.0
|
1.0
|
OD1
|
A:ASP80
|
2.5
|
24.2
|
1.0
|
CB
|
A:ASP80
|
3.9
|
22.5
|
1.0
|
O
|
A:HOH222
|
4.2
|
33.8
|
1.0
|
CA
|
A:ASP80
|
5.0
|
25.2
|
1.0
|
|
Cadmium binding site 2 out
of 10 in 3f38
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Cadmium Binding Sites List in 3f38
Cadmium binding site 2 out
of 10 in the Apoferritin: Complex with 2,6-Dimethylphenol
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 2 of Apoferritin: Complex with 2,6-Dimethylphenol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd1001
b:21.3
occ:0.25
|
CD
|
A:CD1001
|
0.0
|
21.3
|
0.2
|
CD
|
A:CD1001
|
1.4
|
19.0
|
0.2
|
OD1
|
A:ASP80
|
2.9
|
24.2
|
1.0
|
OD2
|
A:ASP80
|
3.0
|
36.3
|
1.0
|
CG
|
A:ASP80
|
3.4
|
25.0
|
1.0
|
O
|
A:HOH222
|
4.9
|
33.8
|
1.0
|
CB
|
A:ASP80
|
4.9
|
22.5
|
1.0
|
|
Cadmium binding site 3 out
of 10 in 3f38
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Cadmium Binding Sites List in 3f38
Cadmium binding site 3 out
of 10 in the Apoferritin: Complex with 2,6-Dimethylphenol
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 3 of Apoferritin: Complex with 2,6-Dimethylphenol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd1002
b:31.7
occ:0.16
|
CD
|
A:CD1002
|
0.0
|
31.7
|
0.2
|
CD
|
A:CD1002
|
1.8
|
47.0
|
0.2
|
OE2
|
A:GLU130
|
3.2
|
36.5
|
1.0
|
OE1
|
A:GLU130
|
3.3
|
33.6
|
1.0
|
CD
|
A:GLU130
|
3.7
|
33.5
|
1.0
|
O
|
A:HOH270
|
3.9
|
52.2
|
1.0
|
O
|
A:HOH287
|
4.2
|
43.6
|
1.0
|
CB
|
A:CYS126
|
4.5
|
26.4
|
1.0
|
N
|
A:ASP127
|
4.7
|
25.4
|
1.0
|
CA
|
A:ASP127
|
4.8
|
23.8
|
1.0
|
C
|
A:CYS126
|
5.0
|
26.2
|
1.0
|
CB
|
A:ASP127
|
5.0
|
26.2
|
1.0
|
|
Cadmium binding site 4 out
of 10 in 3f38
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Cadmium Binding Sites List in 3f38
Cadmium binding site 4 out
of 10 in the Apoferritin: Complex with 2,6-Dimethylphenol
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 4 of Apoferritin: Complex with 2,6-Dimethylphenol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd1002
b:47.0
occ:0.16
|
CD
|
A:CD1002
|
0.0
|
47.0
|
0.2
|
CD
|
A:CD1002
|
1.8
|
31.7
|
0.2
|
OE2
|
A:GLU130
|
2.5
|
36.5
|
1.0
|
CD
|
A:GLU130
|
3.4
|
33.5
|
1.0
|
OE1
|
A:GLU130
|
3.6
|
33.6
|
1.0
|
CD
|
A:CD1003
|
4.2
|
39.5
|
0.2
|
CG
|
A:GLU130
|
4.8
|
25.6
|
1.0
|
OD2
|
A:ASP127
|
4.9
|
49.1
|
1.0
|
|
Cadmium binding site 5 out
of 10 in 3f38
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Cadmium Binding Sites List in 3f38
Cadmium binding site 5 out
of 10 in the Apoferritin: Complex with 2,6-Dimethylphenol
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 5 of Apoferritin: Complex with 2,6-Dimethylphenol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd1003
b:39.5
occ:0.16
|
OD2
|
A:ASP127
|
3.2
|
49.1
|
1.0
|
OG
|
A:SER131
|
4.1
|
46.8
|
0.5
|
CD
|
A:CD1002
|
4.2
|
47.0
|
0.2
|
OE2
|
A:GLU130
|
4.4
|
36.5
|
1.0
|
CG
|
A:ASP127
|
4.4
|
45.9
|
1.0
|
|
Cadmium binding site 6 out
of 10 in 3f38
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Cadmium Binding Sites List in 3f38
Cadmium binding site 6 out
of 10 in the Apoferritin: Complex with 2,6-Dimethylphenol
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 6 of Apoferritin: Complex with 2,6-Dimethylphenol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd1004
b:43.8
occ:0.30
|
CD
|
A:CD1004
|
0.0
|
43.8
|
0.3
|
CD
|
A:CD1004
|
1.6
|
22.3
|
0.1
|
CD
|
A:CD1004
|
1.6
|
23.2
|
0.1
|
OE2
|
A:GLU60
|
2.6
|
37.7
|
1.0
|
OE1
|
A:GLU57
|
2.6
|
67.5
|
1.0
|
OE1
|
A:GLU60
|
2.7
|
45.2
|
1.0
|
CD
|
A:GLU60
|
3.0
|
40.6
|
1.0
|
OE2
|
A:GLU56
|
3.2
|
64.5
|
1.0
|
CD
|
A:GLU57
|
3.7
|
88.8
|
1.0
|
CD
|
A:GLU56
|
3.7
|
65.1
|
1.0
|
CG
|
A:GLU56
|
3.9
|
30.9
|
1.0
|
OE2
|
A:GLU57
|
4.1
|
64.9
|
1.0
|
CG
|
A:GLU60
|
4.5
|
27.6
|
1.0
|
OE1
|
A:GLU56
|
4.6
|
49.6
|
1.0
|
O
|
A:HOH202
|
4.6
|
45.4
|
1.0
|
CG
|
A:GLU57
|
4.9
|
32.3
|
1.0
|
|
Cadmium binding site 7 out
of 10 in 3f38
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Cadmium Binding Sites List in 3f38
Cadmium binding site 7 out
of 10 in the Apoferritin: Complex with 2,6-Dimethylphenol
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 7 of Apoferritin: Complex with 2,6-Dimethylphenol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd1004
b:23.2
occ:0.10
|
CD
|
A:CD1004
|
0.0
|
23.2
|
0.1
|
CD
|
A:CD1004
|
1.6
|
43.8
|
0.3
|
OE2
|
A:GLU60
|
2.4
|
37.7
|
1.0
|
OE1
|
A:GLU57
|
2.5
|
67.5
|
1.0
|
OE2
|
A:GLU57
|
3.0
|
64.9
|
1.0
|
CD
|
A:CD1004
|
3.0
|
22.3
|
0.1
|
CD
|
A:GLU57
|
3.1
|
88.8
|
1.0
|
CD
|
A:GLU60
|
3.4
|
40.6
|
1.0
|
OE1
|
A:GLU60
|
3.6
|
45.2
|
1.0
|
CG
|
A:GLU57
|
4.6
|
32.3
|
1.0
|
NH2
|
A:ARG64
|
4.6
|
50.8
|
0.5
|
CG
|
A:GLU60
|
4.8
|
27.6
|
1.0
|
OE2
|
A:GLU56
|
4.8
|
64.5
|
1.0
|
|
Cadmium binding site 8 out
of 10 in 3f38
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Cadmium Binding Sites List in 3f38
Cadmium binding site 8 out
of 10 in the Apoferritin: Complex with 2,6-Dimethylphenol
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 8 of Apoferritin: Complex with 2,6-Dimethylphenol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd1004
b:22.3
occ:0.10
|
CD
|
A:CD1004
|
0.0
|
22.3
|
0.1
|
CD
|
A:CD1004
|
1.6
|
43.8
|
0.3
|
OE1
|
A:GLU60
|
2.1
|
45.2
|
1.0
|
OE2
|
A:GLU56
|
2.2
|
64.5
|
1.0
|
CD
|
A:GLU60
|
3.0
|
40.6
|
1.0
|
CD
|
A:CD1004
|
3.0
|
23.2
|
0.1
|
CD
|
A:GLU56
|
3.1
|
65.1
|
1.0
|
OE2
|
A:GLU60
|
3.3
|
37.7
|
1.0
|
CG
|
A:GLU56
|
3.6
|
30.9
|
1.0
|
OE1
|
A:GLU57
|
4.0
|
67.5
|
1.0
|
OE1
|
A:GLU56
|
4.1
|
49.6
|
1.0
|
CG
|
A:GLU60
|
4.4
|
27.6
|
1.0
|
O
|
A:HOH202
|
4.4
|
45.4
|
1.0
|
|
Cadmium binding site 9 out
of 10 in 3f38
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Cadmium Binding Sites List in 3f38
Cadmium binding site 9 out
of 10 in the Apoferritin: Complex with 2,6-Dimethylphenol
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 9 of Apoferritin: Complex with 2,6-Dimethylphenol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd1005
b:32.2
occ:0.15
|
O
|
A:HOH202
|
1.6
|
45.4
|
1.0
|
OE1
|
A:GLU56
|
2.3
|
49.6
|
1.0
|
OE2
|
A:GLU53
|
2.5
|
53.8
|
1.0
|
OE1
|
A:GLU53
|
2.9
|
62.6
|
1.0
|
CD
|
A:GLU53
|
3.1
|
0.9
|
1.0
|
CD
|
A:GLU56
|
3.3
|
65.1
|
1.0
|
OE2
|
A:GLU56
|
3.5
|
64.5
|
1.0
|
CG
|
A:GLU53
|
4.6
|
47.8
|
1.0
|
CG
|
A:GLU56
|
4.7
|
30.9
|
1.0
|
CB
|
A:GLU56
|
4.9
|
20.5
|
1.0
|
|
Cadmium binding site 10 out
of 10 in 3f38
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Cadmium Binding Sites List in 3f38
Cadmium binding site 10 out
of 10 in the Apoferritin: Complex with 2,6-Dimethylphenol
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 10 of Apoferritin: Complex with 2,6-Dimethylphenol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd1006
b:51.8
occ:0.30
|
OE2
|
A:GLU11
|
2.6
|
28.7
|
1.0
|
OE1
|
A:GLU11
|
2.6
|
32.9
|
1.0
|
CD
|
A:GLU11
|
2.9
|
30.2
|
1.0
|
O
|
A:HOH252
|
3.2
|
33.3
|
1.0
|
OG1
|
A:THR10
|
4.1
|
27.0
|
1.0
|
CG
|
A:GLU11
|
4.5
|
24.2
|
1.0
|
NE2
|
A:GLN120
|
4.6
|
38.0
|
1.0
|
OE1
|
A:GLN120
|
4.6
|
34.5
|
1.0
|
CB
|
A:SER9
|
4.7
|
22.3
|
1.0
|
N
|
A:THR10
|
5.0
|
22.2
|
1.0
|
|
Reference:
L.S.Vedula,
G.Brannigan,
N.J.Economou,
J.Xi,
M.A.Hall,
R.Liu,
M.J.Rossi,
W.P.Dailey,
K.C.Grasty,
M.L.Klein,
R.G.Eckenhoff,
P.J.Loll.
A Unitary Anesthetic Binding Site at High Resolution. J.Biol.Chem. V. 284 24176 2009.
ISSN: ISSN 0021-9258
PubMed: 19605349
DOI: 10.1074/JBC.M109.017814
Page generated: Fri Jul 19 15:54:21 2024
|