Iron in PDB 8aav: Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand
Protein crystallography data
The structure of Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand, PDB code: 8aav
was solved by
H.Boehler,
T.Beck,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.54 /
2.00
|
Space group
|
P 2 3
|
Cell size a, b, c (Å), α, β, γ (°)
|
181.44,
181.44,
181.44,
90,
90,
90
|
R / Rfree (%)
|
14.4 /
17.7
|
Other elements in 8aav:
The structure of Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand
(pdb code 8aav). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the
Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand, PDB code: 8aav:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iron binding site 1 out
of 8 in 8aav
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Iron Binding Sites List in 8aav
Iron binding site 1 out
of 8 in the Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe203
b:23.1
occ:1.00
|
OE1
|
A:GLU27
|
2.0
|
15.3
|
1.0
|
OE1
|
A:GLU62
|
2.0
|
19.2
|
1.0
|
O
|
A:HOH318
|
2.2
|
15.4
|
1.0
|
O
|
A:HOH306
|
2.2
|
28.4
|
1.0
|
ND1
|
A:HIS65
|
2.2
|
17.5
|
1.0
|
O
|
A:HOH307
|
2.2
|
43.8
|
1.0
|
CD
|
A:GLU62
|
3.0
|
19.3
|
1.0
|
CD
|
A:GLU27
|
3.0
|
16.4
|
1.0
|
CE1
|
A:HIS65
|
3.1
|
20.8
|
1.0
|
CG
|
A:HIS65
|
3.3
|
17.1
|
1.0
|
OE2
|
A:GLU62
|
3.3
|
25.4
|
1.0
|
OE2
|
A:GLU27
|
3.4
|
16.8
|
1.0
|
CB
|
A:HIS65
|
3.6
|
15.7
|
1.0
|
OE1
|
A:GLN141
|
4.1
|
27.9
|
1.0
|
CG
|
A:GLU27
|
4.3
|
14.5
|
1.0
|
O
|
A:HOH358
|
4.3
|
49.3
|
1.0
|
NE2
|
A:HIS65
|
4.3
|
19.5
|
1.0
|
CG
|
A:GLU62
|
4.3
|
15.6
|
1.0
|
CG1
|
A:VAL110
|
4.4
|
16.7
|
1.0
|
CD2
|
A:HIS65
|
4.4
|
18.9
|
1.0
|
CA
|
A:GLU62
|
4.5
|
14.4
|
1.0
|
CB
|
A:GLU27
|
4.7
|
13.5
|
1.0
|
CB
|
A:GLU62
|
4.7
|
14.4
|
1.0
|
OE1
|
A:GLU107
|
4.9
|
30.8
|
1.0
|
CD
|
A:GLN141
|
4.9
|
20.2
|
1.0
|
CA
|
A:GLU27
|
5.0
|
13.6
|
1.0
|
|
Iron binding site 2 out
of 8 in 8aav
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Iron Binding Sites List in 8aav
Iron binding site 2 out
of 8 in the Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe203
b:23.6
occ:1.00
|
OE1
|
B:GLU27
|
2.0
|
16.8
|
1.0
|
ND1
|
B:HIS65
|
2.1
|
19.7
|
1.0
|
OE1
|
B:GLU62
|
2.1
|
20.3
|
1.0
|
O
|
B:HOH319
|
2.2
|
18.2
|
1.0
|
O
|
B:HOH310
|
2.3
|
30.4
|
1.0
|
CE1
|
B:HIS65
|
2.9
|
23.8
|
1.0
|
CD
|
B:GLU62
|
3.0
|
20.9
|
1.0
|
CD
|
B:GLU27
|
3.0
|
15.2
|
1.0
|
CG
|
B:HIS65
|
3.2
|
19.8
|
1.0
|
OE2
|
B:GLU62
|
3.3
|
27.2
|
1.0
|
OE2
|
B:GLU27
|
3.4
|
16.1
|
1.0
|
CB
|
B:HIS65
|
3.6
|
17.6
|
1.0
|
O
|
B:HOH311
|
3.8
|
56.3
|
1.0
|
OE1
|
B:GLN141
|
3.9
|
29.0
|
1.0
|
NE2
|
B:HIS65
|
4.1
|
22.4
|
1.0
|
CD2
|
B:HIS65
|
4.2
|
22.4
|
1.0
|
CG1
|
B:VAL110
|
4.3
|
18.0
|
1.0
|
CG
|
B:GLU27
|
4.3
|
14.2
|
1.0
|
CG
|
B:GLU62
|
4.3
|
17.2
|
1.0
|
O
|
B:HOH356
|
4.4
|
49.6
|
1.0
|
CA
|
B:GLU62
|
4.5
|
15.5
|
1.0
|
CB
|
B:GLU62
|
4.7
|
15.5
|
1.0
|
CB
|
B:GLU27
|
4.7
|
13.3
|
1.0
|
CA
|
B:GLU27
|
4.9
|
13.1
|
1.0
|
CD
|
B:GLN141
|
5.0
|
22.2
|
1.0
|
OE1
|
B:GLU107
|
5.0
|
34.2
|
1.0
|
|
Iron binding site 3 out
of 8 in 8aav
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Iron Binding Sites List in 8aav
Iron binding site 3 out
of 8 in the Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe203
b:23.6
occ:1.00
|
OE1
|
C:GLU27
|
2.0
|
15.7
|
1.0
|
OE1
|
C:GLU62
|
2.0
|
17.3
|
1.0
|
O
|
C:HOH325
|
2.1
|
31.0
|
1.0
|
ND1
|
C:HIS65
|
2.2
|
18.7
|
1.0
|
O
|
C:HOH352
|
2.2
|
19.5
|
1.0
|
CD
|
C:GLU62
|
3.0
|
20.3
|
1.0
|
CD
|
C:GLU27
|
3.0
|
16.2
|
1.0
|
CE1
|
C:HIS65
|
3.1
|
23.2
|
1.0
|
CG
|
C:HIS65
|
3.2
|
19.7
|
1.0
|
OE2
|
C:GLU62
|
3.3
|
26.8
|
1.0
|
OE2
|
C:GLU27
|
3.4
|
17.3
|
1.0
|
CB
|
C:HIS65
|
3.5
|
16.5
|
1.0
|
OE1
|
C:GLN141
|
3.9
|
29.1
|
1.0
|
O
|
C:HOH357
|
4.1
|
29.5
|
1.0
|
NE2
|
C:HIS65
|
4.3
|
19.1
|
1.0
|
CG
|
C:GLU27
|
4.3
|
13.3
|
1.0
|
CG
|
C:GLU62
|
4.3
|
18.1
|
1.0
|
CD2
|
C:HIS65
|
4.3
|
19.5
|
1.0
|
CG1
|
C:VAL110
|
4.3
|
16.2
|
1.0
|
CA
|
C:GLU62
|
4.5
|
14.4
|
1.0
|
CB
|
C:GLU62
|
4.7
|
15.3
|
1.0
|
CB
|
C:GLU27
|
4.7
|
12.5
|
1.0
|
CD
|
C:GLN141
|
4.9
|
21.9
|
1.0
|
CA
|
C:GLU27
|
4.9
|
12.5
|
1.0
|
|
Iron binding site 4 out
of 8 in 8aav
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Iron Binding Sites List in 8aav
Iron binding site 4 out
of 8 in the Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe203
b:24.0
occ:1.00
|
OE1
|
D:GLU27
|
2.0
|
16.7
|
1.0
|
OE1
|
D:GLU62
|
2.1
|
19.2
|
1.0
|
O
|
D:HOH324
|
2.1
|
29.7
|
1.0
|
ND1
|
D:HIS65
|
2.2
|
19.4
|
1.0
|
O
|
D:HOH315
|
2.2
|
18.6
|
1.0
|
CD
|
D:GLU62
|
3.0
|
20.6
|
1.0
|
CD
|
D:GLU27
|
3.0
|
15.7
|
1.0
|
CE1
|
D:HIS65
|
3.1
|
21.7
|
1.0
|
CG
|
D:HIS65
|
3.2
|
18.4
|
1.0
|
OE2
|
D:GLU62
|
3.3
|
22.4
|
1.0
|
OE2
|
D:GLU27
|
3.4
|
16.6
|
1.0
|
CB
|
D:HIS65
|
3.5
|
14.9
|
1.0
|
OE1
|
D:GLN141
|
4.1
|
28.6
|
1.0
|
NE2
|
D:HIS65
|
4.3
|
21.4
|
1.0
|
CG
|
D:GLU27
|
4.3
|
14.3
|
1.0
|
CG
|
D:GLU62
|
4.3
|
17.1
|
1.0
|
CD2
|
D:HIS65
|
4.4
|
21.9
|
1.0
|
CG1
|
D:VAL110
|
4.4
|
16.6
|
1.0
|
CA
|
D:GLU62
|
4.5
|
16.0
|
1.0
|
CB
|
D:GLU27
|
4.7
|
13.7
|
1.0
|
CB
|
D:GLU62
|
4.7
|
15.1
|
1.0
|
CA
|
D:GLU27
|
4.9
|
12.5
|
1.0
|
OE1
|
D:GLU107
|
4.9
|
32.5
|
1.0
|
CD
|
D:GLN141
|
5.0
|
22.0
|
1.0
|
|
Iron binding site 5 out
of 8 in 8aav
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Iron Binding Sites List in 8aav
Iron binding site 5 out
of 8 in the Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe203
b:23.2
occ:1.00
|
O
|
E:HOH341
|
2.0
|
28.6
|
1.0
|
OE1
|
E:GLU62
|
2.0
|
19.1
|
1.0
|
OE1
|
E:GLU27
|
2.0
|
15.9
|
1.0
|
ND1
|
E:HIS65
|
2.2
|
20.2
|
1.0
|
O
|
E:HOH314
|
2.2
|
15.7
|
1.0
|
CD
|
E:GLU62
|
2.9
|
20.6
|
1.0
|
CD
|
E:GLU27
|
3.0
|
15.7
|
1.0
|
CE1
|
E:HIS65
|
3.1
|
24.0
|
1.0
|
CG
|
E:HIS65
|
3.2
|
19.2
|
1.0
|
OE2
|
E:GLU62
|
3.2
|
27.2
|
1.0
|
OE2
|
E:GLU27
|
3.4
|
17.5
|
1.0
|
CB
|
E:HIS65
|
3.5
|
16.4
|
1.0
|
O
|
E:HOH306
|
3.9
|
67.0
|
1.0
|
OE1
|
E:GLN141
|
3.9
|
28.9
|
1.0
|
NE2
|
E:HIS65
|
4.3
|
21.1
|
1.0
|
CG
|
E:GLU27
|
4.3
|
13.2
|
1.0
|
CG
|
E:GLU62
|
4.3
|
17.6
|
1.0
|
CG1
|
E:VAL110
|
4.3
|
17.0
|
1.0
|
CD2
|
E:HIS65
|
4.3
|
21.4
|
1.0
|
CA
|
E:GLU62
|
4.5
|
15.2
|
1.0
|
CB
|
E:GLU62
|
4.6
|
15.4
|
1.0
|
CB
|
E:GLU27
|
4.7
|
13.5
|
1.0
|
CA
|
E:GLU27
|
5.0
|
13.0
|
1.0
|
OE1
|
E:GLU107
|
5.0
|
29.3
|
1.0
|
CD
|
E:GLN141
|
5.0
|
21.0
|
1.0
|
|
Iron binding site 6 out
of 8 in 8aav
Go back to
Iron Binding Sites List in 8aav
Iron binding site 6 out
of 8 in the Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe203
b:22.9
occ:1.00
|
OE1
|
F:GLU62
|
2.0
|
18.4
|
1.0
|
OE1
|
F:GLU27
|
2.0
|
15.8
|
1.0
|
ND1
|
F:HIS65
|
2.1
|
18.3
|
1.0
|
O
|
F:HOH303
|
2.3
|
29.4
|
1.0
|
O
|
F:HOH336
|
2.3
|
18.1
|
1.0
|
CD
|
F:GLU62
|
2.9
|
20.8
|
1.0
|
CD
|
F:GLU27
|
3.0
|
16.8
|
1.0
|
CE1
|
F:HIS65
|
3.0
|
21.3
|
1.0
|
CG
|
F:HIS65
|
3.2
|
17.6
|
1.0
|
OE2
|
F:GLU62
|
3.2
|
27.1
|
1.0
|
OE2
|
F:GLU27
|
3.4
|
17.6
|
1.0
|
CB
|
F:HIS65
|
3.5
|
15.2
|
1.0
|
OE1
|
F:GLN141
|
3.9
|
29.6
|
1.0
|
O
|
F:HOH388
|
4.1
|
26.7
|
1.0
|
NE2
|
F:HIS65
|
4.2
|
20.2
|
1.0
|
CD2
|
F:HIS65
|
4.3
|
19.2
|
1.0
|
CG1
|
F:VAL110
|
4.3
|
15.5
|
1.0
|
CG
|
F:GLU27
|
4.3
|
14.1
|
1.0
|
CG
|
F:GLU62
|
4.3
|
16.8
|
1.0
|
O
|
F:HOH426
|
4.4
|
48.0
|
1.0
|
CA
|
F:GLU62
|
4.5
|
14.5
|
1.0
|
CB
|
F:GLU27
|
4.7
|
12.4
|
1.0
|
CB
|
F:GLU62
|
4.7
|
14.7
|
1.0
|
CA
|
F:GLU27
|
4.9
|
11.9
|
1.0
|
OE1
|
F:GLU107
|
4.9
|
30.8
|
1.0
|
CD
|
F:GLN141
|
4.9
|
22.4
|
1.0
|
|
Iron binding site 7 out
of 8 in 8aav
Go back to
Iron Binding Sites List in 8aav
Iron binding site 7 out
of 8 in the Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Fe203
b:23.5
occ:1.00
|
OE1
|
G:GLU62
|
2.1
|
16.4
|
1.0
|
OE1
|
G:GLU27
|
2.1
|
16.8
|
1.0
|
ND1
|
G:HIS65
|
2.1
|
18.8
|
1.0
|
O
|
G:HOH318
|
2.1
|
28.9
|
1.0
|
O
|
G:HOH313
|
2.3
|
17.2
|
1.0
|
CD
|
G:GLU62
|
3.0
|
18.6
|
1.0
|
CE1
|
G:HIS65
|
3.0
|
21.0
|
1.0
|
CD
|
G:GLU27
|
3.0
|
14.5
|
1.0
|
CG
|
G:HIS65
|
3.2
|
16.7
|
1.0
|
OE2
|
G:GLU62
|
3.3
|
24.9
|
1.0
|
OE2
|
G:GLU27
|
3.4
|
17.2
|
1.0
|
CB
|
G:HIS65
|
3.5
|
16.0
|
1.0
|
OE1
|
G:GLN141
|
3.9
|
28.4
|
1.0
|
NE2
|
G:HIS65
|
4.2
|
19.1
|
1.0
|
CD2
|
G:HIS65
|
4.3
|
18.4
|
1.0
|
CG
|
G:GLU27
|
4.3
|
12.9
|
1.0
|
O
|
G:HOH306
|
4.3
|
49.2
|
1.0
|
CG
|
G:GLU62
|
4.3
|
16.8
|
1.0
|
CG1
|
G:VAL110
|
4.4
|
16.3
|
1.0
|
CA
|
G:GLU62
|
4.5
|
15.8
|
1.0
|
CB
|
G:GLU62
|
4.7
|
15.8
|
1.0
|
CB
|
G:GLU27
|
4.7
|
12.3
|
1.0
|
CA
|
G:GLU27
|
4.9
|
12.4
|
1.0
|
OE1
|
G:GLU107
|
4.9
|
29.3
|
1.0
|
CD
|
G:GLN141
|
4.9
|
21.1
|
1.0
|
|
Iron binding site 8 out
of 8 in 8aav
Go back to
Iron Binding Sites List in 8aav
Iron binding site 8 out
of 8 in the Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Human Heavy Chain Ferritin with Introduced Cys Residues Modified with C10 Ligand within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Fe203
b:23.6
occ:1.00
|
OE1
|
H:GLU27
|
2.0
|
18.1
|
1.0
|
OE1
|
H:GLU62
|
2.1
|
19.7
|
1.0
|
ND1
|
H:HIS65
|
2.2
|
20.3
|
1.0
|
O
|
H:HOH305
|
2.2
|
13.9
|
1.0
|
O
|
H:HOH319
|
2.2
|
33.2
|
1.0
|
CD
|
H:GLU62
|
3.0
|
20.2
|
1.0
|
CD
|
H:GLU27
|
3.0
|
17.4
|
1.0
|
CE1
|
H:HIS65
|
3.1
|
26.2
|
1.0
|
CG
|
H:HIS65
|
3.2
|
20.2
|
1.0
|
OE2
|
H:GLU62
|
3.2
|
25.3
|
1.0
|
OE2
|
H:GLU27
|
3.3
|
17.3
|
1.0
|
CB
|
H:HIS65
|
3.6
|
16.2
|
1.0
|
OE1
|
H:GLN141
|
4.0
|
28.4
|
1.0
|
O
|
H:HOH378
|
4.0
|
33.4
|
1.0
|
NE2
|
H:HIS65
|
4.2
|
22.6
|
1.0
|
CG1
|
H:VAL110
|
4.3
|
17.0
|
1.0
|
CD2
|
H:HIS65
|
4.3
|
23.5
|
1.0
|
CG
|
H:GLU27
|
4.3
|
15.7
|
1.0
|
CG
|
H:GLU62
|
4.3
|
18.2
|
1.0
|
O
|
H:HOH407
|
4.4
|
54.7
|
1.0
|
CA
|
H:GLU62
|
4.6
|
15.2
|
1.0
|
CB
|
H:GLU27
|
4.7
|
13.8
|
1.0
|
CB
|
H:GLU62
|
4.7
|
16.2
|
1.0
|
CA
|
H:GLU27
|
4.9
|
13.0
|
1.0
|
OE1
|
H:GLU107
|
5.0
|
32.1
|
1.0
|
CD
|
H:GLN141
|
5.0
|
22.5
|
1.0
|
|
Reference:
H.Bohler,
S.Orth-Alampour,
C.Baaten,
M.Riedner,
J.Jankowski,
T.Beck.
Assembly of Chemically Modified Protein Nanocages Into 3D Materials For the Adsorption of Uremic Toxins. J Mater Chem B V. 11 55 2022.
ISSN: ESSN 2050-7518
PubMed: 36504125
DOI: 10.1039/D2TB02386E
Page generated: Fri Aug 9 16:14:47 2024
|