Iron in PDB 8bka: Cryo-Em Structure of Mouse Heavy-Chain Apoferritin at 2.7 A Plunged 35MS After Mixing with B-Galactosidase
Enzymatic activity of Cryo-Em Structure of Mouse Heavy-Chain Apoferritin at 2.7 A Plunged 35MS After Mixing with B-Galactosidase
All present enzymatic activity of Cryo-Em Structure of Mouse Heavy-Chain Apoferritin at 2.7 A Plunged 35MS 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 2.7 A Plunged 35MS After Mixing with B-Galactosidase
(pdb code 8bka). 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 2.7 A Plunged 35MS After Mixing with B-Galactosidase, PDB code: 8bka:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 8bka
Go back to
Iron Binding Sites List in 8bka
Iron binding site 1 out
of 6 in the Cryo-Em Structure of Mouse Heavy-Chain Apoferritin at 2.7 A Plunged 35MS 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 2.7 A Plunged 35MS After Mixing with B-Galactosidase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe201
b:66.0
occ:1.00
|
CE1
|
E:HIS173
|
3.1
|
37.6
|
1.0
|
CE1
|
T:HIS173
|
3.1
|
38.6
|
1.0
|
CE1
|
X:HIS173
|
3.1
|
38.8
|
1.0
|
CE1
|
A:HIS173
|
3.1
|
37.6
|
1.0
|
NE2
|
T:HIS173
|
3.6
|
35.5
|
1.0
|
NE2
|
X:HIS173
|
3.6
|
35.2
|
1.0
|
NE2
|
A:HIS173
|
3.6
|
33.6
|
1.0
|
NE2
|
E:HIS173
|
3.6
|
33.9
|
1.0
|
CD2
|
E:LEU169
|
3.9
|
32.0
|
1.0
|
CD2
|
A:LEU169
|
3.9
|
33.9
|
1.0
|
CD2
|
X:LEU169
|
3.9
|
33.3
|
1.0
|
CD2
|
T:LEU169
|
3.9
|
32.6
|
1.0
|
ND1
|
E:HIS173
|
4.3
|
40.1
|
1.0
|
ND1
|
A:HIS173
|
4.3
|
40.0
|
1.0
|
ND1
|
X:HIS173
|
4.3
|
40.9
|
1.0
|
ND1
|
T:HIS173
|
4.3
|
41.2
|
1.0
|
CD1
|
A:LEU169
|
4.6
|
39.1
|
1.0
|
CD1
|
X:LEU169
|
4.6
|
39.2
|
1.0
|
CD1
|
E:LEU169
|
4.6
|
40.2
|
1.0
|
CD1
|
T:LEU169
|
4.6
|
38.7
|
1.0
|
CG
|
E:LEU169
|
4.9
|
36.5
|
1.0
|
CG
|
A:LEU169
|
4.9
|
37.1
|
1.0
|
CG
|
X:LEU169
|
4.9
|
37.1
|
1.0
|
CG
|
T:LEU169
|
4.9
|
37.4
|
1.0
|
CD2
|
T:HIS173
|
5.0
|
33.9
|
1.0
|
CD2
|
X:HIS173
|
5.0
|
33.2
|
1.0
|
CD2
|
E:HIS173
|
5.0
|
32.3
|
1.0
|
CD2
|
A:HIS173
|
5.0
|
31.8
|
1.0
|
|
Iron binding site 2 out
of 6 in 8bka
Go back to
Iron Binding Sites List in 8bka
Iron binding site 2 out
of 6 in the Cryo-Em Structure of Mouse Heavy-Chain Apoferritin at 2.7 A Plunged 35MS 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 2.7 A Plunged 35MS After Mixing with B-Galactosidase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe201
b:65.9
occ:1.00
|
CE1
|
G:HIS173
|
3.1
|
38.3
|
1.0
|
CE1
|
B:HIS173
|
3.1
|
38.7
|
1.0
|
CE1
|
L:HIS173
|
3.2
|
37.3
|
1.0
|
CE1
|
S:HIS173
|
3.2
|
36.3
|
1.0
|
NE2
|
G:HIS173
|
3.6
|
34.5
|
1.0
|
NE2
|
B:HIS173
|
3.6
|
35.7
|
1.0
|
NE2
|
S:HIS173
|
3.6
|
32.8
|
1.0
|
NE2
|
L:HIS173
|
3.6
|
34.5
|
1.0
|
CD2
|
L:LEU169
|
3.9
|
33.2
|
1.0
|
CD2
|
B:LEU169
|
3.9
|
33.2
|
1.0
|
CD2
|
S:LEU169
|
3.9
|
33.0
|
1.0
|
CD2
|
G:LEU169
|
3.9
|
32.6
|
1.0
|
ND1
|
G:HIS173
|
4.3
|
41.1
|
1.0
|
ND1
|
B:HIS173
|
4.3
|
41.1
|
1.0
|
ND1
|
L:HIS173
|
4.3
|
39.4
|
1.0
|
ND1
|
S:HIS173
|
4.3
|
39.2
|
1.0
|
CD1
|
L:LEU169
|
4.6
|
39.5
|
1.0
|
CD1
|
S:LEU169
|
4.6
|
39.9
|
1.0
|
CD1
|
G:LEU169
|
4.6
|
38.3
|
1.0
|
CD1
|
B:LEU169
|
4.6
|
39.7
|
1.0
|
CG
|
L:LEU169
|
4.9
|
37.4
|
1.0
|
CG
|
S:LEU169
|
4.9
|
37.1
|
1.0
|
CG
|
G:LEU169
|
4.9
|
36.4
|
1.0
|
CG
|
B:LEU169
|
4.9
|
36.4
|
1.0
|
CD2
|
G:HIS173
|
5.0
|
33.1
|
1.0
|
CD2
|
B:HIS173
|
5.0
|
34.1
|
1.0
|
CD2
|
S:HIS173
|
5.0
|
31.2
|
1.0
|
CD2
|
L:HIS173
|
5.0
|
32.5
|
1.0
|
|
Iron binding site 3 out
of 6 in 8bka
Go back to
Iron Binding Sites List in 8bka
Iron binding site 3 out
of 6 in the Cryo-Em Structure of Mouse Heavy-Chain Apoferritin at 2.7 A Plunged 35MS 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 2.7 A Plunged 35MS After Mixing with B-Galactosidase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe201
b:64.9
occ:1.00
|
CE1
|
M:HIS173
|
3.1
|
38.5
|
1.0
|
CE1
|
C:HIS173
|
3.1
|
39.1
|
1.0
|
CE1
|
K:HIS173
|
3.1
|
38.1
|
1.0
|
CE1
|
R:HIS173
|
3.2
|
36.3
|
1.0
|
NE2
|
M:HIS173
|
3.6
|
34.4
|
1.0
|
NE2
|
C:HIS173
|
3.6
|
35.3
|
1.0
|
NE2
|
K:HIS173
|
3.6
|
34.7
|
1.0
|
NE2
|
R:HIS173
|
3.6
|
33.2
|
1.0
|
CD2
|
R:LEU169
|
3.9
|
31.5
|
1.0
|
CD2
|
K:LEU169
|
3.9
|
32.0
|
1.0
|
CD2
|
M:LEU169
|
3.9
|
32.3
|
1.0
|
CD2
|
C:LEU169
|
3.9
|
32.3
|
1.0
|
ND1
|
M:HIS173
|
4.3
|
40.5
|
1.0
|
ND1
|
C:HIS173
|
4.3
|
40.6
|
1.0
|
ND1
|
K:HIS173
|
4.3
|
39.3
|
1.0
|
ND1
|
R:HIS173
|
4.4
|
39.2
|
1.0
|
CD1
|
R:LEU169
|
4.6
|
38.6
|
1.0
|
CD1
|
K:LEU169
|
4.6
|
38.3
|
1.0
|
CD1
|
C:LEU169
|
4.6
|
38.4
|
1.0
|
CD1
|
M:LEU169
|
4.6
|
38.7
|
1.0
|
CG
|
R:LEU169
|
4.9
|
36.3
|
1.0
|
CG
|
K:LEU169
|
4.9
|
36.1
|
1.0
|
CG
|
C:LEU169
|
4.9
|
35.7
|
1.0
|
CG
|
M:LEU169
|
4.9
|
35.7
|
1.0
|
CD2
|
M:HIS173
|
5.0
|
30.4
|
1.0
|
CD2
|
C:HIS173
|
5.0
|
32.9
|
1.0
|
CD2
|
K:HIS173
|
5.0
|
33.1
|
1.0
|
CD2
|
R:HIS173
|
5.0
|
30.8
|
1.0
|
|
Iron binding site 4 out
of 6 in 8bka
Go back to
Iron Binding Sites List in 8bka
Iron binding site 4 out
of 6 in the Cryo-Em Structure of Mouse Heavy-Chain Apoferritin at 2.7 A Plunged 35MS 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 2.7 A Plunged 35MS After Mixing with B-Galactosidase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe201
b:64.2
occ:1.00
|
CE1
|
I:HIS173
|
3.1
|
37.3
|
1.0
|
CE1
|
D:HIS173
|
3.1
|
36.6
|
1.0
|
CE1
|
J:HIS173
|
3.1
|
36.9
|
1.0
|
CE1
|
F:HIS173
|
3.2
|
36.8
|
1.0
|
NE2
|
I:HIS173
|
3.6
|
32.7
|
1.0
|
NE2
|
J:HIS173
|
3.6
|
33.7
|
1.0
|
NE2
|
D:HIS173
|
3.6
|
33.9
|
1.0
|
NE2
|
F:HIS173
|
3.6
|
32.9
|
1.0
|
CD2
|
F:LEU169
|
3.9
|
32.5
|
1.0
|
CD2
|
J:LEU169
|
3.9
|
31.4
|
1.0
|
CD2
|
D:LEU169
|
3.9
|
32.6
|
1.0
|
CD2
|
I:LEU169
|
3.9
|
31.7
|
1.0
|
ND1
|
I:HIS173
|
4.3
|
39.0
|
1.0
|
ND1
|
D:HIS173
|
4.3
|
38.8
|
1.0
|
ND1
|
J:HIS173
|
4.3
|
39.4
|
1.0
|
ND1
|
F:HIS173
|
4.3
|
39.8
|
1.0
|
CD1
|
J:LEU169
|
4.6
|
38.3
|
1.0
|
CD1
|
D:LEU169
|
4.6
|
37.5
|
1.0
|
CD1
|
I:LEU169
|
4.6
|
38.6
|
1.0
|
CD1
|
F:LEU169
|
4.6
|
38.6
|
1.0
|
CG
|
J:LEU169
|
4.9
|
34.9
|
1.0
|
CG
|
D:LEU169
|
4.9
|
36.3
|
1.0
|
CG
|
I:LEU169
|
4.9
|
36.0
|
1.0
|
CG
|
F:LEU169
|
4.9
|
35.3
|
1.0
|
CD2
|
I:HIS173
|
5.0
|
30.3
|
1.0
|
CD2
|
J:HIS173
|
5.0
|
31.9
|
1.0
|
CD2
|
D:HIS173
|
5.0
|
31.0
|
1.0
|
CD2
|
F:HIS173
|
5.0
|
29.5
|
1.0
|
|
Iron binding site 5 out
of 6 in 8bka
Go back to
Iron Binding Sites List in 8bka
Iron binding site 5 out
of 6 in the Cryo-Em Structure of Mouse Heavy-Chain Apoferritin at 2.7 A Plunged 35MS 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 2.7 A Plunged 35MS After Mixing with B-Galactosidase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Fe201
b:63.7
occ:1.00
|
CE1
|
V:HIS173
|
3.1
|
39.1
|
1.0
|
CE1
|
H:HIS173
|
3.1
|
38.0
|
1.0
|
CE1
|
P:HIS173
|
3.1
|
38.0
|
1.0
|
CE1
|
Y:HIS173
|
3.1
|
37.5
|
1.0
|
NE2
|
H:HIS173
|
3.6
|
34.3
|
1.0
|
NE2
|
V:HIS173
|
3.6
|
34.1
|
1.0
|
NE2
|
P:HIS173
|
3.6
|
32.4
|
1.0
|
NE2
|
Y:HIS173
|
3.6
|
33.7
|
1.0
|
CD2
|
P:LEU169
|
3.9
|
32.2
|
1.0
|
CD2
|
V:LEU169
|
3.9
|
31.4
|
1.0
|
CD2
|
H:LEU169
|
3.9
|
32.5
|
1.0
|
CD2
|
Y:LEU169
|
3.9
|
31.1
|
1.0
|
ND1
|
V:HIS173
|
4.3
|
41.0
|
1.0
|
ND1
|
P:HIS173
|
4.3
|
39.7
|
1.0
|
ND1
|
H:HIS173
|
4.3
|
39.6
|
1.0
|
ND1
|
Y:HIS173
|
4.3
|
39.1
|
1.0
|
CD1
|
H:LEU169
|
4.6
|
37.3
|
1.0
|
CD1
|
Y:LEU169
|
4.6
|
38.4
|
1.0
|
CD1
|
P:LEU169
|
4.6
|
38.6
|
1.0
|
CD1
|
V:LEU169
|
4.6
|
38.1
|
1.0
|
CG
|
P:LEU169
|
4.9
|
35.8
|
1.0
|
CG
|
Y:LEU169
|
4.9
|
36.6
|
1.0
|
CG
|
H:LEU169
|
4.9
|
35.1
|
1.0
|
CG
|
V:LEU169
|
4.9
|
36.2
|
1.0
|
CD2
|
H:HIS173
|
5.0
|
32.8
|
1.0
|
CD2
|
V:HIS173
|
5.0
|
30.2
|
1.0
|
CD2
|
P:HIS173
|
5.0
|
30.9
|
1.0
|
CD2
|
Y:HIS173
|
5.0
|
30.5
|
1.0
|
|
Iron binding site 6 out
of 6 in 8bka
Go back to
Iron Binding Sites List in 8bka
Iron binding site 6 out
of 6 in the Cryo-Em Structure of Mouse Heavy-Chain Apoferritin at 2.7 A Plunged 35MS 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 2.7 A Plunged 35MS After Mixing with B-Galactosidase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Fe201
b:64.8
occ:1.00
|
CE1
|
W:HIS173
|
3.1
|
37.3
|
1.0
|
CE1
|
N:HIS173
|
3.1
|
38.5
|
1.0
|
CE1
|
Q:HIS173
|
3.2
|
38.4
|
1.0
|
CE1
|
O:HIS173
|
3.2
|
37.4
|
1.0
|
NE2
|
W:HIS173
|
3.6
|
34.2
|
1.0
|
NE2
|
Q:HIS173
|
3.6
|
35.0
|
1.0
|
NE2
|
O:HIS173
|
3.6
|
34.2
|
1.0
|
NE2
|
N:HIS173
|
3.6
|
35.4
|
1.0
|
CD2
|
O:LEU169
|
3.9
|
32.0
|
1.0
|
CD2
|
W:LEU169
|
3.9
|
32.4
|
1.0
|
CD2
|
Q:LEU169
|
3.9
|
33.0
|
1.0
|
CD2
|
N:LEU169
|
3.9
|
31.9
|
1.0
|
ND1
|
W:HIS173
|
4.3
|
40.3
|
1.0
|
ND1
|
N:HIS173
|
4.3
|
41.0
|
1.0
|
ND1
|
O:HIS173
|
4.3
|
39.6
|
1.0
|
ND1
|
Q:HIS173
|
4.3
|
40.7
|
1.0
|
CD1
|
W:LEU169
|
4.6
|
38.8
|
1.0
|
CD1
|
N:LEU169
|
4.6
|
38.1
|
1.0
|
CD1
|
O:LEU169
|
4.6
|
39.5
|
1.0
|
CD1
|
Q:LEU169
|
4.6
|
38.8
|
1.0
|
CG
|
W:LEU169
|
4.9
|
36.4
|
1.0
|
CG
|
N:LEU169
|
4.9
|
37.3
|
1.0
|
CG
|
O:LEU169
|
4.9
|
37.0
|
1.0
|
CG
|
Q:LEU169
|
4.9
|
37.1
|
1.0
|
CD2
|
W:HIS173
|
5.0
|
32.2
|
1.0
|
CD2
|
Q:HIS173
|
5.0
|
33.4
|
1.0
|
CD2
|
O:HIS173
|
5.0
|
32.9
|
1.0
|
CD2
|
N:HIS173
|
5.0
|
33.5
|
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
|