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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

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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

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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

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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

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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

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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

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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: Thu Aug 7 13:56:01 2025

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