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:
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
Go back to
Iron Binding Sites List in 3jbt
Iron binding site 1 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 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
Go back to
Iron Binding Sites List in 3jbt
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
Go back to
Iron Binding Sites List in 3jbt
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
Go back to
Iron Binding Sites List in 3jbt
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
Go back to
Iron Binding Sites List in 3jbt
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
Go back to
Iron Binding Sites List in 3jbt
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
Go back to
Iron Binding Sites List in 3jbt
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
|