Iron in PDB 8bk9: Cryo-Em Structure of Mouse Heavy-Chain Apoferritin at 2.1 A Plunged 5MS After Mixing with B-Galactosidase
Enzymatic activity of Cryo-Em Structure of Mouse Heavy-Chain Apoferritin at 2.1 A Plunged 5MS After Mixing with B-Galactosidase
All present enzymatic activity of Cryo-Em Structure of Mouse Heavy-Chain Apoferritin at 2.1 A Plunged 5MS After Mixing with B-Galactosidase:
1.16.3.1;
Iron Binding Sites:
The binding sites of Iron atom in the Cryo-Em Structure of Mouse Heavy-Chain Apoferritin at 2.1 A Plunged 5MS After Mixing with B-Galactosidase
(pdb code 8bk9). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Cryo-Em Structure of Mouse Heavy-Chain Apoferritin at 2.1 A Plunged 5MS After Mixing with B-Galactosidase, PDB code: 8bk9:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 8bk9
Go back to
Iron Binding Sites List in 8bk9
Iron binding site 1 out
of 6 in the Cryo-Em Structure of Mouse Heavy-Chain Apoferritin at 2.1 A Plunged 5MS After Mixing with B-Galactosidase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Cryo-Em Structure of Mouse Heavy-Chain Apoferritin at 2.1 A Plunged 5MS After Mixing with B-Galactosidase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe201
b:45.9
occ:1.00
|
CE1
|
A:HIS173
|
2.9
|
13.1
|
1.0
|
CE1
|
E:HIS173
|
2.9
|
12.7
|
1.0
|
CE1
|
X:HIS173
|
3.0
|
12.8
|
1.0
|
CE1
|
T:HIS173
|
3.0
|
12.4
|
1.0
|
NE2
|
T:HIS173
|
3.5
|
15.1
|
1.0
|
NE2
|
X:HIS173
|
3.5
|
15.8
|
1.0
|
NE2
|
A:HIS173
|
3.5
|
16.0
|
1.0
|
NE2
|
E:HIS173
|
3.5
|
16.4
|
1.0
|
ND1
|
E:HIS173
|
4.1
|
12.1
|
1.0
|
ND1
|
A:HIS173
|
4.1
|
10.8
|
1.0
|
ND1
|
X:HIS173
|
4.1
|
10.6
|
1.0
|
ND1
|
T:HIS173
|
4.1
|
11.4
|
1.0
|
CD2
|
E:LEU169
|
4.2
|
7.6
|
1.0
|
CD2
|
T:LEU169
|
4.3
|
7.2
|
1.0
|
CD2
|
A:LEU169
|
4.3
|
6.8
|
1.0
|
CD2
|
X:LEU169
|
4.3
|
7.3
|
1.0
|
CD2
|
X:HIS173
|
4.8
|
14.0
|
1.0
|
CD2
|
T:HIS173
|
4.8
|
12.8
|
1.0
|
CD2
|
A:HIS173
|
4.8
|
14.8
|
1.0
|
CD2
|
E:HIS173
|
4.8
|
13.4
|
1.0
|
CD1
|
T:LEU169
|
5.0
|
9.9
|
1.0
|
CD1
|
A:LEU169
|
5.0
|
8.9
|
1.0
|
CD1
|
X:LEU169
|
5.0
|
10.7
|
1.0
|
CD1
|
E:LEU169
|
5.0
|
9.0
|
1.0
|
|
Iron binding site 2 out
of 6 in 8bk9
Go back to
Iron Binding Sites List in 8bk9
Iron binding site 2 out
of 6 in the Cryo-Em Structure of Mouse Heavy-Chain Apoferritin at 2.1 A Plunged 5MS After Mixing with B-Galactosidase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Cryo-Em Structure of Mouse Heavy-Chain Apoferritin at 2.1 A Plunged 5MS After Mixing with B-Galactosidase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe201
b:45.5
occ:1.00
|
CE1
|
L:HIS173
|
3.0
|
12.4
|
1.0
|
CE1
|
S:HIS173
|
3.0
|
12.8
|
1.0
|
CE1
|
B:HIS173
|
3.0
|
13.9
|
1.0
|
CE1
|
G:HIS173
|
3.0
|
11.7
|
1.0
|
NE2
|
G:HIS173
|
3.5
|
14.8
|
1.0
|
NE2
|
B:HIS173
|
3.5
|
15.7
|
1.0
|
NE2
|
S:HIS173
|
3.5
|
14.7
|
1.0
|
NE2
|
L:HIS173
|
3.5
|
16.0
|
1.0
|
ND1
|
S:HIS173
|
4.1
|
11.7
|
1.0
|
ND1
|
L:HIS173
|
4.1
|
12.4
|
1.0
|
ND1
|
B:HIS173
|
4.1
|
9.7
|
1.0
|
ND1
|
G:HIS173
|
4.1
|
11.3
|
1.0
|
CD2
|
G:LEU169
|
4.3
|
7.4
|
1.0
|
CD2
|
B:LEU169
|
4.3
|
6.6
|
1.0
|
CD2
|
S:LEU169
|
4.3
|
7.3
|
1.0
|
CD2
|
L:LEU169
|
4.3
|
7.3
|
1.0
|
CD2
|
G:HIS173
|
4.8
|
14.0
|
1.0
|
CD2
|
B:HIS173
|
4.8
|
14.2
|
1.0
|
CD2
|
L:HIS173
|
4.8
|
13.6
|
1.0
|
CD2
|
S:HIS173
|
4.8
|
13.1
|
1.0
|
CD1
|
B:LEU169
|
5.0
|
10.3
|
1.0
|
CD1
|
G:LEU169
|
5.0
|
9.6
|
1.0
|
CD1
|
S:LEU169
|
5.0
|
8.1
|
1.0
|
CD1
|
L:LEU169
|
5.0
|
8.8
|
1.0
|
|
Iron binding site 3 out
of 6 in 8bk9
Go back to
Iron Binding Sites List in 8bk9
Iron binding site 3 out
of 6 in the Cryo-Em Structure of Mouse Heavy-Chain Apoferritin at 2.1 A Plunged 5MS After Mixing with B-Galactosidase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Cryo-Em Structure of Mouse Heavy-Chain Apoferritin at 2.1 A Plunged 5MS After Mixing with B-Galactosidase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe201
b:47.3
occ:1.00
|
CE1
|
K:HIS173
|
3.0
|
12.3
|
1.0
|
CE1
|
M:HIS173
|
3.0
|
12.9
|
1.0
|
CE1
|
R:HIS173
|
3.0
|
12.9
|
1.0
|
CE1
|
C:HIS173
|
3.0
|
13.4
|
1.0
|
NE2
|
K:HIS173
|
3.5
|
16.5
|
1.0
|
NE2
|
C:HIS173
|
3.5
|
15.6
|
1.0
|
NE2
|
R:HIS173
|
3.5
|
16.1
|
1.0
|
NE2
|
M:HIS173
|
3.5
|
15.5
|
1.0
|
ND1
|
K:HIS173
|
4.1
|
11.4
|
1.0
|
ND1
|
R:HIS173
|
4.1
|
11.4
|
1.0
|
ND1
|
M:HIS173
|
4.1
|
11.8
|
1.0
|
ND1
|
C:HIS173
|
4.1
|
11.1
|
1.0
|
CD2
|
M:LEU169
|
4.3
|
8.3
|
1.0
|
CD2
|
K:LEU169
|
4.3
|
6.5
|
1.0
|
CD2
|
R:LEU169
|
4.3
|
8.0
|
1.0
|
CD2
|
C:LEU169
|
4.3
|
8.2
|
1.0
|
CD2
|
C:HIS173
|
4.8
|
14.2
|
1.0
|
CD2
|
K:HIS173
|
4.8
|
13.5
|
1.0
|
CD2
|
M:HIS173
|
4.8
|
13.1
|
1.0
|
CD2
|
R:HIS173
|
4.8
|
14.5
|
1.0
|
CD1
|
K:LEU169
|
5.0
|
10.0
|
1.0
|
CD1
|
C:LEU169
|
5.0
|
11.8
|
1.0
|
CD1
|
M:LEU169
|
5.0
|
10.4
|
1.0
|
CD1
|
R:LEU169
|
5.0
|
10.0
|
1.0
|
|
Iron binding site 4 out
of 6 in 8bk9
Go back to
Iron Binding Sites List in 8bk9
Iron binding site 4 out
of 6 in the Cryo-Em Structure of Mouse Heavy-Chain Apoferritin at 2.1 A Plunged 5MS After Mixing with B-Galactosidase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Cryo-Em Structure of Mouse Heavy-Chain Apoferritin at 2.1 A Plunged 5MS After Mixing with B-Galactosidase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe201
b:46.7
occ:1.00
|
CE1
|
F:HIS173
|
3.0
|
12.1
|
1.0
|
CE1
|
D:HIS173
|
3.0
|
14.0
|
1.0
|
CE1
|
J:HIS173
|
3.0
|
13.3
|
1.0
|
CE1
|
I:HIS173
|
3.0
|
13.5
|
1.0
|
NE2
|
F:HIS173
|
3.5
|
15.2
|
1.0
|
NE2
|
D:HIS173
|
3.5
|
15.3
|
1.0
|
NE2
|
I:HIS173
|
3.5
|
15.0
|
1.0
|
NE2
|
J:HIS173
|
3.5
|
15.1
|
1.0
|
ND1
|
F:HIS173
|
4.1
|
12.3
|
1.0
|
ND1
|
D:HIS173
|
4.1
|
12.5
|
1.0
|
ND1
|
J:HIS173
|
4.1
|
11.4
|
1.0
|
ND1
|
I:HIS173
|
4.1
|
9.7
|
1.0
|
CD2
|
F:LEU169
|
4.3
|
7.5
|
1.0
|
CD2
|
D:LEU169
|
4.3
|
8.7
|
1.0
|
CD2
|
I:LEU169
|
4.3
|
7.7
|
1.0
|
CD2
|
J:LEU169
|
4.3
|
7.1
|
1.0
|
CD2
|
F:HIS173
|
4.8
|
13.0
|
1.0
|
CD2
|
D:HIS173
|
4.8
|
13.7
|
1.0
|
CD2
|
I:HIS173
|
4.8
|
13.5
|
1.0
|
CD2
|
J:HIS173
|
4.8
|
13.4
|
1.0
|
CD1
|
I:LEU169
|
5.0
|
10.1
|
1.0
|
CD1
|
F:LEU169
|
5.0
|
9.9
|
1.0
|
CD1
|
J:LEU169
|
5.0
|
9.2
|
1.0
|
CD1
|
D:LEU169
|
5.0
|
9.5
|
1.0
|
|
Iron binding site 5 out
of 6 in 8bk9
Go back to
Iron Binding Sites List in 8bk9
Iron binding site 5 out
of 6 in the Cryo-Em Structure of Mouse Heavy-Chain Apoferritin at 2.1 A Plunged 5MS After Mixing with B-Galactosidase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Cryo-Em Structure of Mouse Heavy-Chain Apoferritin at 2.1 A Plunged 5MS After Mixing with B-Galactosidase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Fe201
b:45.6
occ:1.00
|
CE1
|
W:HIS173
|
3.0
|
12.0
|
1.0
|
CE1
|
Q:HIS173
|
3.0
|
12.5
|
1.0
|
CE1
|
N:HIS173
|
3.0
|
13.5
|
1.0
|
CE1
|
O:HIS173
|
3.0
|
13.1
|
1.0
|
NE2
|
O:HIS173
|
3.5
|
14.8
|
1.0
|
NE2
|
W:HIS173
|
3.5
|
16.0
|
1.0
|
NE2
|
Q:HIS173
|
3.5
|
16.2
|
1.0
|
NE2
|
N:HIS173
|
3.5
|
15.7
|
1.0
|
ND1
|
N:HIS173
|
4.1
|
11.4
|
1.0
|
ND1
|
W:HIS173
|
4.1
|
11.9
|
1.0
|
ND1
|
Q:HIS173
|
4.1
|
11.2
|
1.0
|
ND1
|
O:HIS173
|
4.1
|
11.5
|
1.0
|
CD2
|
W:LEU169
|
4.3
|
7.5
|
1.0
|
CD2
|
O:LEU169
|
4.3
|
7.5
|
1.0
|
CD2
|
Q:LEU169
|
4.3
|
7.6
|
1.0
|
CD2
|
N:LEU169
|
4.3
|
7.6
|
1.0
|
CD2
|
O:HIS173
|
4.8
|
14.0
|
1.0
|
CD2
|
N:HIS173
|
4.8
|
13.4
|
1.0
|
CD2
|
Q:HIS173
|
4.8
|
12.9
|
1.0
|
CD2
|
W:HIS173
|
4.8
|
13.2
|
1.0
|
CD1
|
N:LEU169
|
5.0
|
10.2
|
1.0
|
CD1
|
W:LEU169
|
5.0
|
9.5
|
1.0
|
CD1
|
Q:LEU169
|
5.0
|
9.5
|
1.0
|
CD1
|
O:LEU169
|
5.0
|
9.5
|
1.0
|
|
Iron binding site 6 out
of 6 in 8bk9
Go back to
Iron Binding Sites List in 8bk9
Iron binding site 6 out
of 6 in the Cryo-Em Structure of Mouse Heavy-Chain Apoferritin at 2.1 A Plunged 5MS After Mixing with B-Galactosidase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Cryo-Em Structure of Mouse Heavy-Chain Apoferritin at 2.1 A Plunged 5MS After Mixing with B-Galactosidase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
V:Fe201
b:47.7
occ:1.00
|
CE1
|
V:HIS173
|
3.0
|
14.5
|
1.0
|
CE1
|
P:HIS173
|
3.0
|
13.4
|
1.0
|
CE1
|
H:HIS173
|
3.0
|
13.6
|
1.0
|
CE1
|
Y:HIS173
|
3.0
|
12.6
|
1.0
|
NE2
|
V:HIS173
|
3.5
|
15.5
|
1.0
|
NE2
|
Y:HIS173
|
3.5
|
16.7
|
1.0
|
NE2
|
H:HIS173
|
3.5
|
16.0
|
1.0
|
NE2
|
P:HIS173
|
3.5
|
16.5
|
1.0
|
ND1
|
H:HIS173
|
4.1
|
12.6
|
1.0
|
ND1
|
P:HIS173
|
4.1
|
11.6
|
1.0
|
ND1
|
V:HIS173
|
4.1
|
11.3
|
1.0
|
ND1
|
Y:HIS173
|
4.1
|
13.3
|
1.0
|
CD2
|
H:LEU169
|
4.3
|
7.6
|
1.0
|
CD2
|
P:LEU169
|
4.3
|
8.4
|
1.0
|
CD2
|
Y:LEU169
|
4.3
|
7.5
|
1.0
|
CD2
|
V:LEU169
|
4.3
|
7.3
|
1.0
|
CD2
|
V:HIS173
|
4.8
|
12.7
|
1.0
|
CD2
|
Y:HIS173
|
4.8
|
13.3
|
1.0
|
CD2
|
H:HIS173
|
4.8
|
14.8
|
1.0
|
CD2
|
P:HIS173
|
4.8
|
13.4
|
1.0
|
CD1
|
V:LEU169
|
5.0
|
10.4
|
1.0
|
CD1
|
Y:LEU169
|
5.0
|
10.6
|
1.0
|
CD1
|
H:LEU169
|
5.0
|
9.4
|
1.0
|
CD1
|
P:LEU169
|
5.0
|
11.8
|
1.0
|
|
Reference:
S.Torino,
M.Dhurandhar,
A.Stroobants,
R.Claessens,
R.Efremov.
Time-Resolved Cryo-Em Using A Combination of Droplet Microfluidics with on-Demand Jetting Nat.Methods 2023.
ISSN: ESSN 1548-7105
DOI: 10.1038/S41592-023-01967-Z
Page generated: Fri Aug 9 19:54:29 2024
|