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Iron in PDB 3jbt: Atomic Structure of the Apaf-1 Apoptosome

Other elements in 3jbt:

The structure of Atomic Structure of the Apaf-1 Apoptosome also contains other interesting chemical elements:

Magnesium (Mg) 7 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Atomic Structure of the Apaf-1 Apoptosome (pdb code 3jbt). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 7 binding sites of Iron where determined in the Atomic Structure of the Apaf-1 Apoptosome, PDB code: 3jbt:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7;

Iron binding site 1 out of 7 in 3jbt

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Iron binding site 1 out of 7 in the Atomic Structure of the Apaf-1 Apoptosome


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Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Atomic Structure of the Apaf-1 Apoptosome within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:23.1
occ:1.00
FE B:HEM201 0.0 23.1 1.0
ND B:HEM201 1.9 23.1 1.0
NA B:HEM201 2.0 23.3 1.0
NC B:HEM201 2.1 22.6 1.0
NB B:HEM201 2.1 23.2 1.0
NE2 B:HIS18 2.4 22.8 1.0
SD B:MET80 2.4 24.9 1.0
C4D B:HEM201 2.9 23.2 1.0
C1D B:HEM201 2.9 23.1 1.0
C1A B:HEM201 2.9 23.4 1.0
CD2 B:HIS18 3.0 22.7 1.0
C4C B:HEM201 3.0 22.8 1.0
C4A B:HEM201 3.0 23.4 1.0
C1B B:HEM201 3.1 23.5 1.0
C4B B:HEM201 3.1 23.4 1.0
CE1 B:HIS18 3.1 22.8 1.0
C1C B:HEM201 3.1 22.9 1.0
CHA B:HEM201 3.3 23.3 1.0
CHD B:HEM201 3.3 22.9 1.0
CHB B:HEM201 3.4 23.5 1.0
CE B:MET80 3.5 25.1 1.0
CHC B:HEM201 3.5 23.2 1.0
CG B:MET80 3.5 26.1 1.0
CG B:HIS18 3.9 22.7 1.0
ND1 B:HIS18 3.9 22.9 1.0
C3D B:HEM201 4.1 23.5 1.0
C2D B:HEM201 4.1 23.2 1.0
C2A B:HEM201 4.1 23.5 1.0
C3A B:HEM201 4.2 23.4 1.0
C3C B:HEM201 4.2 22.8 1.0
CB B:MET80 4.3 26.6 1.0
C2C B:HEM201 4.3 22.8 1.0
C2B B:HEM201 4.3 23.9 1.0
C3B B:HEM201 4.3 23.8 1.0
OH B:TYR67 4.7 33.9 1.0

Iron binding site 2 out of 7 in 3jbt

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Iron binding site 2 out of 7 in the Atomic Structure of the Apaf-1 Apoptosome


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Atomic Structure of the Apaf-1 Apoptosome within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:23.1
occ:1.00
FE D:HEM201 0.0 23.1 1.0
ND D:HEM201 1.9 23.1 1.0
NA D:HEM201 2.0 23.3 1.0
NC D:HEM201 2.1 22.6 1.0
NB D:HEM201 2.1 23.2 1.0
NE2 D:HIS18 2.4 22.8 1.0
SD D:MET80 2.4 24.9 1.0
C4D D:HEM201 2.9 23.2 1.0
C1D D:HEM201 2.9 23.1 1.0
C1A D:HEM201 2.9 23.4 1.0
CD2 D:HIS18 3.0 22.7 1.0
C4C D:HEM201 3.0 22.8 1.0
C4A D:HEM201 3.0 23.4 1.0
C1B D:HEM201 3.1 23.5 1.0
C4B D:HEM201 3.1 23.4 1.0
CE1 D:HIS18 3.1 22.8 1.0
C1C D:HEM201 3.1 22.9 1.0
CHA D:HEM201 3.3 23.3 1.0
CHD D:HEM201 3.3 22.9 1.0
CHB D:HEM201 3.4 23.5 1.0
CE D:MET80 3.5 25.1 1.0
CHC D:HEM201 3.5 23.2 1.0
CG D:MET80 3.5 26.1 1.0
CG D:HIS18 3.9 22.7 1.0
ND1 D:HIS18 3.9 22.9 1.0
C3D D:HEM201 4.1 23.5 1.0
C2D D:HEM201 4.1 23.2 1.0
C2A D:HEM201 4.1 23.5 1.0
C3A D:HEM201 4.2 23.4 1.0
C3C D:HEM201 4.2 22.8 1.0
CB D:MET80 4.3 26.6 1.0
C2C D:HEM201 4.3 22.8 1.0
C2B D:HEM201 4.3 23.9 1.0
C3B D:HEM201 4.3 23.8 1.0
OH D:TYR67 4.7 33.9 1.0

Iron binding site 3 out of 7 in 3jbt

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Iron binding site 3 out of 7 in the Atomic Structure of the Apaf-1 Apoptosome


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Atomic Structure of the Apaf-1 Apoptosome within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe201

b:23.1
occ:1.00
FE F:HEM201 0.0 23.1 1.0
ND F:HEM201 1.9 23.1 1.0
NA F:HEM201 2.0 23.3 1.0
NC F:HEM201 2.1 22.6 1.0
NB F:HEM201 2.1 23.2 1.0
NE2 F:HIS18 2.4 22.8 1.0
SD F:MET80 2.4 24.9 1.0
C4D F:HEM201 2.9 23.2 1.0
C1D F:HEM201 2.9 23.1 1.0
C1A F:HEM201 2.9 23.4 1.0
CD2 F:HIS18 3.0 22.7 1.0
C4C F:HEM201 3.0 22.8 1.0
C4A F:HEM201 3.0 23.4 1.0
C1B F:HEM201 3.1 23.5 1.0
C4B F:HEM201 3.1 23.4 1.0
CE1 F:HIS18 3.1 22.8 1.0
C1C F:HEM201 3.1 22.9 1.0
CHA F:HEM201 3.3 23.3 1.0
CHD F:HEM201 3.3 22.9 1.0
CHB F:HEM201 3.4 23.5 1.0
CE F:MET80 3.5 25.1 1.0
CHC F:HEM201 3.5 23.2 1.0
CG F:MET80 3.5 26.1 1.0
CG F:HIS18 3.9 22.7 1.0
ND1 F:HIS18 3.9 22.9 1.0
C3D F:HEM201 4.1 23.5 1.0
C2D F:HEM201 4.1 23.2 1.0
C2A F:HEM201 4.1 23.5 1.0
C3A F:HEM201 4.2 23.4 1.0
C3C F:HEM201 4.2 22.8 1.0
CB F:MET80 4.3 26.6 1.0
C2C F:HEM201 4.3 22.8 1.0
C2B F:HEM201 4.3 23.9 1.0
C3B F:HEM201 4.3 23.8 1.0
OH F:TYR67 4.7 33.9 1.0

Iron binding site 4 out of 7 in 3jbt

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Iron binding site 4 out of 7 in the Atomic Structure of the Apaf-1 Apoptosome


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Atomic Structure of the Apaf-1 Apoptosome within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe201

b:23.1
occ:1.00
FE H:HEM201 0.0 23.1 1.0
ND H:HEM201 1.9 23.1 1.0
NA H:HEM201 2.0 23.3 1.0
NC H:HEM201 2.1 22.6 1.0
NB H:HEM201 2.1 23.2 1.0
NE2 H:HIS18 2.4 22.8 1.0
SD H:MET80 2.4 24.9 1.0
C4D H:HEM201 2.9 23.2 1.0
C1D H:HEM201 2.9 23.1 1.0
C1A H:HEM201 2.9 23.4 1.0
CD2 H:HIS18 3.0 22.7 1.0
C4C H:HEM201 3.0 22.8 1.0
C4A H:HEM201 3.0 23.4 1.0
C1B H:HEM201 3.1 23.5 1.0
C4B H:HEM201 3.1 23.4 1.0
CE1 H:HIS18 3.1 22.8 1.0
C1C H:HEM201 3.1 22.9 1.0
CHA H:HEM201 3.3 23.3 1.0
CHD H:HEM201 3.3 22.9 1.0
CHB H:HEM201 3.4 23.5 1.0
CE H:MET80 3.5 25.1 1.0
CHC H:HEM201 3.5 23.2 1.0
CG H:MET80 3.5 26.1 1.0
CG H:HIS18 3.9 22.7 1.0
ND1 H:HIS18 3.9 22.9 1.0
C3D H:HEM201 4.1 23.5 1.0
C2D H:HEM201 4.1 23.2 1.0
C2A H:HEM201 4.1 23.5 1.0
C3A H:HEM201 4.2 23.4 1.0
C3C H:HEM201 4.2 22.8 1.0
CB H:MET80 4.3 26.6 1.0
C2C H:HEM201 4.3 22.8 1.0
C2B H:HEM201 4.3 23.9 1.0
C3B H:HEM201 4.3 23.8 1.0
OH H:TYR67 4.7 33.9 1.0

Iron binding site 5 out of 7 in 3jbt

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Iron binding site 5 out of 7 in the Atomic Structure of the Apaf-1 Apoptosome


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Atomic Structure of the Apaf-1 Apoptosome within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe201

b:23.1
occ:1.00
FE J:HEM201 0.0 23.1 1.0
ND J:HEM201 1.9 23.1 1.0
NA J:HEM201 2.0 23.3 1.0
NC J:HEM201 2.1 22.6 1.0
NB J:HEM201 2.1 23.2 1.0
NE2 J:HIS18 2.4 22.8 1.0
SD J:MET80 2.4 24.9 1.0
C4D J:HEM201 2.9 23.2 1.0
C1D J:HEM201 2.9 23.1 1.0
C1A J:HEM201 2.9 23.4 1.0
CD2 J:HIS18 3.0 22.7 1.0
C4C J:HEM201 3.0 22.8 1.0
C4A J:HEM201 3.0 23.4 1.0
C1B J:HEM201 3.1 23.5 1.0
C4B J:HEM201 3.1 23.4 1.0
CE1 J:HIS18 3.1 22.8 1.0
C1C J:HEM201 3.1 22.9 1.0
CHA J:HEM201 3.3 23.3 1.0
CHD J:HEM201 3.3 22.9 1.0
CHB J:HEM201 3.5 23.5 1.0
CE J:MET80 3.5 25.1 1.0
CHC J:HEM201 3.5 23.2 1.0
CG J:MET80 3.5 26.1 1.0
CG J:HIS18 3.9 22.7 1.0
ND1 J:HIS18 3.9 22.9 1.0
C3D J:HEM201 4.1 23.5 1.0
C2D J:HEM201 4.1 23.2 1.0
C2A J:HEM201 4.1 23.5 1.0
C3A J:HEM201 4.2 23.4 1.0
C3C J:HEM201 4.2 22.8 1.0
CB J:MET80 4.3 26.6 1.0
C2C J:HEM201 4.3 22.8 1.0
C2B J:HEM201 4.3 23.9 1.0
C3B J:HEM201 4.3 23.8 1.0
OH J:TYR67 4.7 33.9 1.0

Iron binding site 6 out of 7 in 3jbt

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Iron binding site 6 out of 7 in the Atomic Structure of the Apaf-1 Apoptosome


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Atomic Structure of the Apaf-1 Apoptosome within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Fe201

b:23.1
occ:1.00
FE L:HEM201 0.0 23.1 1.0
ND L:HEM201 1.9 23.1 1.0
NA L:HEM201 2.0 23.3 1.0
NC L:HEM201 2.1 22.6 1.0
NB L:HEM201 2.1 23.2 1.0
NE2 L:HIS18 2.4 22.8 1.0
SD L:MET80 2.4 24.9 1.0
C4D L:HEM201 2.9 23.2 1.0
C1D L:HEM201 2.9 23.1 1.0
C1A L:HEM201 2.9 23.4 1.0
CD2 L:HIS18 3.0 22.7 1.0
C4C L:HEM201 3.0 22.8 1.0
C4A L:HEM201 3.0 23.4 1.0
C1B L:HEM201 3.1 23.5 1.0
C4B L:HEM201 3.1 23.4 1.0
CE1 L:HIS18 3.1 22.8 1.0
C1C L:HEM201 3.1 22.9 1.0
CHA L:HEM201 3.3 23.3 1.0
CHD L:HEM201 3.3 22.9 1.0
CHB L:HEM201 3.5 23.5 1.0
CE L:MET80 3.5 25.1 1.0
CHC L:HEM201 3.5 23.2 1.0
CG L:MET80 3.5 26.1 1.0
CG L:HIS18 3.9 22.7 1.0
ND1 L:HIS18 3.9 22.9 1.0
C3D L:HEM201 4.1 23.5 1.0
C2D L:HEM201 4.1 23.2 1.0
C2A L:HEM201 4.1 23.5 1.0
C3A L:HEM201 4.2 23.4 1.0
C3C L:HEM201 4.2 22.8 1.0
CB L:MET80 4.3 26.6 1.0
C2C L:HEM201 4.3 22.8 1.0
C2B L:HEM201 4.3 23.9 1.0
C3B L:HEM201 4.3 23.8 1.0
OH L:TYR67 4.7 33.9 1.0

Iron binding site 7 out of 7 in 3jbt

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Iron binding site 7 out of 7 in the Atomic Structure of the Apaf-1 Apoptosome


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Atomic Structure of the Apaf-1 Apoptosome within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe201

b:23.1
occ:1.00
FE N:HEM201 0.0 23.1 1.0
ND N:HEM201 1.9 23.1 1.0
NA N:HEM201 2.0 23.3 1.0
NC N:HEM201 2.1 22.6 1.0
NB N:HEM201 2.1 23.2 1.0
NE2 N:HIS18 2.4 22.8 1.0
SD N:MET80 2.4 24.9 1.0
C4D N:HEM201 2.9 23.2 1.0
C1D N:HEM201 2.9 23.1 1.0
C1A N:HEM201 2.9 23.4 1.0
CD2 N:HIS18 3.0 22.7 1.0
C4C N:HEM201 3.0 22.8 1.0
C4A N:HEM201 3.0 23.4 1.0
C1B N:HEM201 3.1 23.5 1.0
C4B N:HEM201 3.1 23.4 1.0
CE1 N:HIS18 3.1 22.8 1.0
C1C N:HEM201 3.1 22.9 1.0
CHA N:HEM201 3.3 23.3 1.0
CHD N:HEM201 3.3 22.9 1.0
CHB N:HEM201 3.5 23.5 1.0
CE N:MET80 3.5 25.1 1.0
CHC N:HEM201 3.5 23.2 1.0
CG N:MET80 3.5 26.1 1.0
CG N:HIS18 3.9 22.7 1.0
ND1 N:HIS18 3.9 22.9 1.0
C3D N:HEM201 4.1 23.5 1.0
C2D N:HEM201 4.1 23.2 1.0
C2A N:HEM201 4.1 23.5 1.0
C3A N:HEM201 4.2 23.4 1.0
C3C N:HEM201 4.2 22.8 1.0
CB N:MET80 4.3 26.6 1.0
C2C N:HEM201 4.3 22.8 1.0
C2B N:HEM201 4.3 23.9 1.0
C3B N:HEM201 4.3 23.8 1.0
OH N:TYR67 4.7 33.9 1.0

Reference:

M.Zhou, Y.Li, Q.Hu, X.C.Bai, W.Huang, C.Yan, S.H.W.Scheres, Y.Shi. Atomic Structure of the Apoptosome: Mechanism of Cytochrome C- and Datp-Mediated Activation of Apaf-1 Genes Dev. V. 29 2349 2015.
ISSN: ISSN 1549-5477
PubMed: 26543158
DOI: 10.1101/GAD.272278.115
Page generated: Sun Aug 4 13:35:12 2024

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