Cadmium in PDB 9kn7: Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F)
Protein crystallography data
The structure of Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F), PDB code: 9kn7
was solved by
T.Suzuki,
Y.Hishikawa,
B.Maity,
S.Abe,
T.Ueno,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
18.94 /
1.50
|
Space group
|
F 4 3 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
180.715,
180.715,
180.715,
90,
90,
90
|
R / Rfree (%)
|
16.5 /
17.8
|
Other elements in 9kn7:
The structure of Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F) also contains other interesting chemical elements:
Cadmium Binding Sites:
The binding sites of Cadmium atom in the Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F)
(pdb code 9kn7). This binding sites where shown within
5.0 Angstroms radius around Cadmium atom.
In total 8 binding sites of Cadmium where determined in the
Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F), PDB code: 9kn7:
Jump to Cadmium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Cadmium binding site 1 out
of 8 in 9kn7
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Cadmium Binding Sites List in 9kn7
Cadmium binding site 1 out
of 8 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F)
 Mono view
 Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 1 of Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd201
b:14.7
occ:0.41
|
O
|
A:HOH453
|
2.3
|
35.6
|
1.0
|
OD1
|
A:ASP38
|
2.5
|
13.2
|
1.0
|
SG
|
A:CYS48
|
2.6
|
14.2
|
1.0
|
CG
|
A:ASP38
|
3.3
|
9.9
|
1.0
|
CB
|
A:ASP38
|
3.5
|
8.8
|
1.0
|
CB
|
A:CYS48
|
3.5
|
10.9
|
1.0
|
CA
|
A:ASP38
|
4.0
|
8.1
|
1.0
|
CD
|
A:CD208
|
4.3
|
53.5
|
0.2
|
OD2
|
A:ASP38
|
4.4
|
10.8
|
1.0
|
CD2
|
A:HIS49
|
4.4
|
26.7
|
1.0
|
NE2
|
A:HIS49
|
4.5
|
30.0
|
1.0
|
N
|
A:ASP38
|
4.8
|
7.5
|
1.0
|
NH1
|
A:ARG52
|
4.8
|
32.0
|
0.5
|
CG
|
A:GLU45
|
4.8
|
18.7
|
1.0
|
CA
|
A:GLU45
|
4.9
|
9.7
|
1.0
|
CA
|
A:CYS48
|
4.9
|
9.2
|
1.0
|
NE
|
A:ARG52
|
5.0
|
24.8
|
0.5
|
|
Cadmium binding site 2 out
of 8 in 9kn7
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Cadmium Binding Sites List in 9kn7
Cadmium binding site 2 out
of 8 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F)
 Mono view
 Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 2 of Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd202
b:9.8
occ:0.45
|
OD2
|
A:ASP80
|
2.3
|
14.8
|
1.0
|
OD1
|
A:ASP80
|
2.3
|
9.0
|
1.0
|
CL
|
A:CL211
|
2.5
|
23.2
|
1.0
|
CG
|
A:ASP80
|
2.7
|
11.5
|
1.0
|
CB
|
A:ASP80
|
4.2
|
10.1
|
1.0
|
O
|
A:HOH348
|
4.3
|
14.6
|
1.0
|
O
|
A:HOH334
|
4.6
|
17.6
|
1.0
|
|
Cadmium binding site 3 out
of 8 in 9kn7
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Cadmium Binding Sites List in 9kn7
Cadmium binding site 3 out
of 8 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F)
 Mono view
 Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 3 of Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd203
b:25.0
occ:0.13
|
O
|
A:HOH314
|
2.3
|
29.1
|
1.0
|
O
|
A:HOH482
|
3.0
|
39.2
|
0.1
|
OD1
|
A:ASP127
|
3.6
|
20.2
|
1.0
|
OG
|
A:SER131
|
3.7
|
23.4
|
1.0
|
CD
|
A:CD204
|
4.2
|
17.1
|
0.1
|
OE1
|
A:GLU130
|
4.3
|
21.5
|
1.0
|
CG
|
A:ASP127
|
4.7
|
16.7
|
1.0
|
|
Cadmium binding site 4 out
of 8 in 9kn7
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Cadmium Binding Sites List in 9kn7
Cadmium binding site 4 out
of 8 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F)
 Mono view
 Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 4 of Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd204
b:17.1
occ:0.08
|
CD
|
A:CD205
|
1.6
|
18.2
|
0.3
|
OE1
|
A:GLU130
|
2.2
|
21.5
|
1.0
|
CD
|
A:GLU130
|
3.2
|
20.3
|
1.0
|
OE2
|
A:GLU130
|
3.6
|
15.6
|
1.0
|
CD
|
A:CD203
|
4.2
|
25.0
|
0.1
|
CG
|
A:GLU130
|
4.6
|
15.7
|
1.0
|
CB
|
A:GLU130
|
4.9
|
13.5
|
1.0
|
|
Cadmium binding site 5 out
of 8 in 9kn7
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Cadmium Binding Sites List in 9kn7
Cadmium binding site 5 out
of 8 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F)
 Mono view
 Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 5 of Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd205
b:18.2
occ:0.26
|
CD
|
A:CD204
|
1.6
|
17.1
|
0.1
|
OE1
|
A:GLU130
|
2.4
|
21.5
|
1.0
|
OE2
|
A:GLU130
|
2.9
|
15.6
|
1.0
|
CD
|
A:GLU130
|
3.0
|
20.3
|
1.0
|
N
|
A:ASP127
|
4.4
|
11.1
|
1.0
|
CG
|
A:GLU130
|
4.5
|
15.7
|
1.0
|
CA
|
A:ASP127
|
4.5
|
12.2
|
1.0
|
O
|
A:HOH506
|
4.7
|
33.4
|
1.0
|
CB
|
A:CYS126
|
4.7
|
10.6
|
1.0
|
C
|
A:CYS126
|
4.7
|
10.5
|
1.0
|
CB
|
A:ASP127
|
4.8
|
15.0
|
1.0
|
O
|
A:CYS126
|
5.0
|
11.5
|
1.0
|
|
Cadmium binding site 6 out
of 8 in 9kn7
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Cadmium Binding Sites List in 9kn7
Cadmium binding site 6 out
of 8 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F)
 Mono view
 Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 6 of Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd206
b:26.6
occ:0.23
|
NE2
|
A:HIS132
|
2.6
|
27.9
|
1.0
|
CD2
|
A:HIS132
|
3.5
|
22.4
|
1.0
|
CE1
|
A:HIS132
|
3.6
|
27.5
|
1.0
|
O
|
A:HOH310
|
4.5
|
15.9
|
1.0
|
O
|
A:HOH304
|
4.6
|
31.0
|
1.0
|
CG
|
A:HIS132
|
4.7
|
21.1
|
1.0
|
OD2
|
A:ASP127
|
4.7
|
24.1
|
1.0
|
ND1
|
A:HIS132
|
4.8
|
24.1
|
1.0
|
CD1
|
A:PHE128
|
4.9
|
11.9
|
1.0
|
|
Cadmium binding site 7 out
of 8 in 9kn7
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Cadmium Binding Sites List in 9kn7
Cadmium binding site 7 out
of 8 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F)
 Mono view
 Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 7 of Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd207
b:30.3
occ:0.17
|
OE1
|
A:GLU11
|
2.4
|
14.1
|
1.0
|
O
|
A:HOH429
|
2.7
|
20.5
|
1.0
|
OE2
|
A:GLU11
|
2.9
|
19.8
|
1.0
|
CD
|
A:GLU11
|
3.0
|
16.2
|
1.0
|
OG1
|
A:THR10
|
4.0
|
16.4
|
1.0
|
CB
|
A:SER9
|
4.3
|
8.8
|
1.0
|
NE2
|
A:GLN120
|
4.3
|
11.8
|
0.4
|
OE1
|
A:GLN120
|
4.5
|
16.9
|
0.6
|
CG
|
A:GLU11
|
4.5
|
13.3
|
1.0
|
N
|
A:THR10
|
4.6
|
10.3
|
1.0
|
O
|
A:HOH432
|
4.6
|
44.5
|
1.0
|
NE2
|
A:GLN120
|
4.7
|
18.2
|
0.6
|
N
|
A:GLU11
|
4.9
|
9.8
|
1.0
|
CD
|
A:GLN120
|
4.9
|
15.2
|
0.6
|
CA
|
A:SER9
|
5.0
|
8.5
|
1.0
|
|
Cadmium binding site 8 out
of 8 in 9kn7
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Cadmium Binding Sites List in 9kn7
Cadmium binding site 8 out
of 8 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F)
 Mono view
 Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 8 of Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd208
b:53.5
occ:0.22
|
NE2
|
A:HIS49
|
2.5
|
30.0
|
1.0
|
CE1
|
A:HIS49
|
3.0
|
28.0
|
1.0
|
CD
|
A:GLU45
|
3.6
|
28.3
|
1.0
|
CG
|
A:GLU45
|
3.6
|
18.7
|
1.0
|
CD2
|
A:HIS49
|
3.7
|
26.7
|
1.0
|
OE2
|
A:GLU45
|
3.8
|
38.8
|
1.0
|
OE1
|
A:GLU45
|
4.0
|
30.8
|
1.0
|
ND1
|
A:HIS49
|
4.2
|
31.9
|
1.0
|
CD
|
A:CD201
|
4.3
|
14.7
|
0.4
|
NH1
|
A:ARG52
|
4.5
|
32.0
|
0.5
|
CG
|
A:HIS49
|
4.6
|
21.2
|
1.0
|
O
|
A:HOH453
|
5.0
|
35.6
|
1.0
|
CB
|
A:GLU45
|
5.0
|
12.8
|
1.0
|
|
Reference:
Y.Hishikawa,
T.Suzuki,
B.Maity,
H.Noya,
M.Yoshizawa,
A.Asanuma,
Y.Katagiri,
S.Abe,
S.Nagatoishi,
K.Tsumoto,
T.Ueno.
Design of Aromatic Interaction Networks in A Protein Cage Modulated By Fluorescent Ligand Binding. Adv Sci 17030 2025.
ISSN: ESSN 2198-3844
PubMed: 39973762
DOI: 10.1002/ADVS.202417030
Page generated: Thu Jul 10 16:04:07 2025
|