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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

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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

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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

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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

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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

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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

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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

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