Iron in PDB 3e1l: Crystal Structure of E. Coli Bacterioferritin (Bfr) Soaked in Phosphate with An Alternative Conformation of the Unoccupied Ferroxidase Centre (Apo-Bfr II).
Protein crystallography data
The structure of Crystal Structure of E. Coli Bacterioferritin (Bfr) Soaked in Phosphate with An Alternative Conformation of the Unoccupied Ferroxidase Centre (Apo-Bfr II)., PDB code: 3e1l
was solved by
A.Crow,
T.Lawson,
A.Lewin,
G.R.Moore,
N.Le Brun,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
34.00 /
2.50
|
Space group
|
P 42 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
208.082,
208.082,
143.107,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
23.6 /
24.8
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of E. Coli Bacterioferritin (Bfr) Soaked in Phosphate with An Alternative Conformation of the Unoccupied Ferroxidase Centre (Apo-Bfr II).
(pdb code 3e1l). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Crystal Structure of E. Coli Bacterioferritin (Bfr) Soaked in Phosphate with An Alternative Conformation of the Unoccupied Ferroxidase Centre (Apo-Bfr II)., PDB code: 3e1l:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 3e1l
Go back to
Iron Binding Sites List in 3e1l
Iron binding site 1 out
of 6 in the Crystal Structure of E. Coli Bacterioferritin (Bfr) Soaked in Phosphate with An Alternative Conformation of the Unoccupied Ferroxidase Centre (Apo-Bfr II).
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure of E. Coli Bacterioferritin (Bfr) Soaked in Phosphate with An Alternative Conformation of the Unoccupied Ferroxidase Centre (Apo-Bfr II). within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe200
b:2.0
occ:0.04
|
FE
|
A:HEM200
|
0.0
|
2.0
|
0.0
|
NC
|
A:HEM200
|
2.1
|
2.0
|
0.0
|
SD
|
A:MET52
|
2.1
|
19.3
|
1.0
|
NB
|
A:HEM200
|
2.1
|
2.0
|
0.0
|
NA
|
A:HEM200
|
2.1
|
2.0
|
0.0
|
ND
|
A:HEM200
|
2.1
|
2.0
|
0.0
|
SD
|
B:MET52
|
2.1
|
19.3
|
1.0
|
CE
|
A:MET52
|
3.1
|
17.9
|
1.0
|
C1C
|
A:HEM200
|
3.1
|
2.0
|
0.0
|
C4C
|
A:HEM200
|
3.1
|
2.0
|
0.0
|
CE
|
B:MET52
|
3.1
|
17.9
|
1.0
|
C4B
|
A:HEM200
|
3.1
|
2.0
|
0.0
|
C1D
|
A:HEM200
|
3.1
|
2.0
|
0.0
|
C1A
|
A:HEM200
|
3.1
|
2.0
|
0.0
|
C4D
|
A:HEM200
|
3.1
|
2.0
|
0.0
|
C1B
|
A:HEM200
|
3.1
|
2.0
|
0.0
|
C4A
|
A:HEM200
|
3.1
|
2.0
|
0.0
|
CHC
|
A:HEM200
|
3.4
|
2.0
|
0.0
|
CHD
|
A:HEM200
|
3.4
|
2.0
|
0.0
|
CG
|
A:MET52
|
3.5
|
16.2
|
1.0
|
CHA
|
A:HEM200
|
3.5
|
2.0
|
0.0
|
CHB
|
A:HEM200
|
3.5
|
2.0
|
0.0
|
CG
|
B:MET52
|
3.5
|
16.2
|
1.0
|
CB
|
A:MET52
|
4.3
|
14.5
|
1.0
|
C2C
|
A:HEM200
|
4.3
|
2.0
|
0.0
|
C3C
|
A:HEM200
|
4.3
|
2.0
|
0.0
|
C3B
|
A:HEM200
|
4.3
|
2.0
|
0.0
|
C2B
|
A:HEM200
|
4.3
|
2.0
|
0.0
|
CB
|
B:MET52
|
4.3
|
14.5
|
1.0
|
C2A
|
A:HEM200
|
4.3
|
2.0
|
0.0
|
C3A
|
A:HEM200
|
4.3
|
2.0
|
0.0
|
C2D
|
A:HEM200
|
4.4
|
2.0
|
0.0
|
C3D
|
A:HEM200
|
4.4
|
2.0
|
0.0
|
|
Iron binding site 2 out
of 6 in 3e1l
Go back to
Iron Binding Sites List in 3e1l
Iron binding site 2 out
of 6 in the Crystal Structure of E. Coli Bacterioferritin (Bfr) Soaked in Phosphate with An Alternative Conformation of the Unoccupied Ferroxidase Centre (Apo-Bfr II).
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure of E. Coli Bacterioferritin (Bfr) Soaked in Phosphate with An Alternative Conformation of the Unoccupied Ferroxidase Centre (Apo-Bfr II). within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe200
b:2.0
occ:0.04
|
FE
|
C:HEM200
|
0.0
|
2.0
|
0.0
|
SD
|
D:MET52
|
2.1
|
19.3
|
1.0
|
NC
|
C:HEM200
|
2.1
|
2.0
|
0.0
|
NB
|
C:HEM200
|
2.1
|
2.0
|
0.0
|
NA
|
C:HEM200
|
2.1
|
2.0
|
0.0
|
SD
|
C:MET52
|
2.1
|
19.3
|
1.0
|
ND
|
C:HEM200
|
2.1
|
2.0
|
0.0
|
CE
|
D:MET52
|
3.1
|
17.9
|
1.0
|
C1C
|
C:HEM200
|
3.1
|
2.0
|
0.0
|
C4B
|
C:HEM200
|
3.1
|
2.0
|
0.0
|
CE
|
C:MET52
|
3.1
|
17.9
|
1.0
|
C4C
|
C:HEM200
|
3.1
|
2.0
|
0.0
|
C1B
|
C:HEM200
|
3.1
|
2.0
|
0.0
|
C1A
|
C:HEM200
|
3.1
|
2.0
|
0.0
|
C4D
|
C:HEM200
|
3.1
|
2.0
|
0.0
|
C1D
|
C:HEM200
|
3.1
|
2.0
|
0.0
|
C4A
|
C:HEM200
|
3.1
|
2.0
|
0.0
|
CHC
|
C:HEM200
|
3.4
|
2.0
|
0.0
|
CG
|
D:MET52
|
3.4
|
16.2
|
1.0
|
CHD
|
C:HEM200
|
3.5
|
2.0
|
0.0
|
CHA
|
C:HEM200
|
3.5
|
2.0
|
0.0
|
CHB
|
C:HEM200
|
3.5
|
2.0
|
0.0
|
CG
|
C:MET52
|
3.5
|
16.2
|
1.0
|
CB
|
D:MET52
|
4.2
|
14.5
|
1.0
|
C2C
|
C:HEM200
|
4.3
|
2.0
|
0.0
|
C3B
|
C:HEM200
|
4.3
|
2.0
|
0.0
|
C3C
|
C:HEM200
|
4.3
|
2.0
|
0.0
|
C2B
|
C:HEM200
|
4.3
|
2.0
|
0.0
|
CB
|
C:MET52
|
4.3
|
14.5
|
1.0
|
C2A
|
C:HEM200
|
4.3
|
2.0
|
0.0
|
C3A
|
C:HEM200
|
4.3
|
2.0
|
0.0
|
C3D
|
C:HEM200
|
4.4
|
2.0
|
0.0
|
C2D
|
C:HEM200
|
4.4
|
2.0
|
0.0
|
|
Iron binding site 3 out
of 6 in 3e1l
Go back to
Iron Binding Sites List in 3e1l
Iron binding site 3 out
of 6 in the Crystal Structure of E. Coli Bacterioferritin (Bfr) Soaked in Phosphate with An Alternative Conformation of the Unoccupied Ferroxidase Centre (Apo-Bfr II).
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure of E. Coli Bacterioferritin (Bfr) Soaked in Phosphate with An Alternative Conformation of the Unoccupied Ferroxidase Centre (Apo-Bfr II). within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe200
b:2.0
occ:0.04
|
FE
|
E:HEM200
|
0.0
|
2.0
|
0.0
|
SD
|
E:MET52
|
2.0
|
19.3
|
1.0
|
SD
|
F:MET52
|
2.1
|
19.3
|
1.0
|
NC
|
E:HEM200
|
2.1
|
2.0
|
0.0
|
NA
|
E:HEM200
|
2.1
|
2.0
|
0.0
|
ND
|
E:HEM200
|
2.1
|
2.0
|
0.0
|
NB
|
E:HEM200
|
2.1
|
2.0
|
0.0
|
CE
|
E:MET52
|
3.1
|
17.9
|
1.0
|
CE
|
F:MET52
|
3.1
|
17.9
|
1.0
|
C1A
|
E:HEM200
|
3.1
|
2.0
|
0.0
|
C1C
|
E:HEM200
|
3.1
|
2.0
|
0.0
|
C4C
|
E:HEM200
|
3.1
|
2.0
|
0.0
|
C4D
|
E:HEM200
|
3.1
|
2.0
|
0.0
|
C1D
|
E:HEM200
|
3.1
|
2.0
|
0.0
|
C4B
|
E:HEM200
|
3.1
|
2.0
|
0.0
|
C4A
|
E:HEM200
|
3.1
|
2.0
|
0.0
|
C1B
|
E:HEM200
|
3.1
|
2.0
|
0.0
|
CHA
|
E:HEM200
|
3.4
|
2.0
|
0.0
|
CHD
|
E:HEM200
|
3.4
|
2.0
|
0.0
|
CHC
|
E:HEM200
|
3.5
|
2.0
|
0.0
|
CHB
|
E:HEM200
|
3.5
|
2.0
|
0.0
|
CG
|
F:MET52
|
3.5
|
16.2
|
1.0
|
CG
|
E:MET52
|
3.5
|
16.2
|
1.0
|
CB
|
F:MET52
|
4.3
|
14.5
|
1.0
|
CB
|
E:MET52
|
4.3
|
14.5
|
1.0
|
C2C
|
E:HEM200
|
4.3
|
2.0
|
0.0
|
C3C
|
E:HEM200
|
4.3
|
2.0
|
0.0
|
C2A
|
E:HEM200
|
4.3
|
2.0
|
0.0
|
C3A
|
E:HEM200
|
4.3
|
2.0
|
0.0
|
C3D
|
E:HEM200
|
4.3
|
2.0
|
0.0
|
C2D
|
E:HEM200
|
4.3
|
2.0
|
0.0
|
C3B
|
E:HEM200
|
4.3
|
2.0
|
0.0
|
C2B
|
E:HEM200
|
4.4
|
2.0
|
0.0
|
CD1
|
E:ILE49
|
4.9
|
16.3
|
1.0
|
CD1
|
F:ILE49
|
4.9
|
16.3
|
1.0
|
|
Iron binding site 4 out
of 6 in 3e1l
Go back to
Iron Binding Sites List in 3e1l
Iron binding site 4 out
of 6 in the Crystal Structure of E. Coli Bacterioferritin (Bfr) Soaked in Phosphate with An Alternative Conformation of the Unoccupied Ferroxidase Centre (Apo-Bfr II).
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure of E. Coli Bacterioferritin (Bfr) Soaked in Phosphate with An Alternative Conformation of the Unoccupied Ferroxidase Centre (Apo-Bfr II). within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Fe200
b:2.0
occ:0.04
|
FE
|
G:HEM200
|
0.0
|
2.0
|
0.0
|
NC
|
G:HEM200
|
2.1
|
2.0
|
0.0
|
SD
|
H:MET52
|
2.1
|
19.3
|
1.0
|
SD
|
G:MET52
|
2.1
|
19.3
|
1.0
|
NB
|
G:HEM200
|
2.1
|
2.0
|
0.0
|
NA
|
G:HEM200
|
2.1
|
2.0
|
0.0
|
ND
|
G:HEM200
|
2.1
|
2.0
|
0.0
|
CE
|
G:MET52
|
3.1
|
17.9
|
1.0
|
C1C
|
G:HEM200
|
3.1
|
2.0
|
0.0
|
C4B
|
G:HEM200
|
3.1
|
2.0
|
0.0
|
C4C
|
G:HEM200
|
3.1
|
2.0
|
0.0
|
CE
|
H:MET52
|
3.1
|
17.9
|
1.0
|
C1A
|
G:HEM200
|
3.1
|
2.0
|
0.0
|
C1B
|
G:HEM200
|
3.1
|
2.0
|
0.0
|
C4D
|
G:HEM200
|
3.1
|
2.0
|
0.0
|
C4A
|
G:HEM200
|
3.1
|
2.0
|
0.0
|
C1D
|
G:HEM200
|
3.1
|
2.0
|
0.0
|
CHC
|
G:HEM200
|
3.4
|
2.0
|
0.0
|
CHA
|
G:HEM200
|
3.5
|
2.0
|
0.0
|
CHD
|
G:HEM200
|
3.5
|
2.0
|
0.0
|
CG
|
H:MET52
|
3.5
|
16.2
|
1.0
|
CHB
|
G:HEM200
|
3.5
|
2.0
|
0.0
|
CG
|
G:MET52
|
3.5
|
16.2
|
1.0
|
CB
|
H:MET52
|
4.2
|
14.4
|
1.0
|
C2C
|
G:HEM200
|
4.3
|
2.0
|
0.0
|
C3C
|
G:HEM200
|
4.3
|
2.0
|
0.0
|
CB
|
G:MET52
|
4.3
|
14.5
|
1.0
|
C3B
|
G:HEM200
|
4.3
|
2.0
|
0.0
|
C2B
|
G:HEM200
|
4.3
|
2.0
|
0.0
|
C2A
|
G:HEM200
|
4.3
|
2.0
|
0.0
|
C3A
|
G:HEM200
|
4.3
|
2.0
|
0.0
|
C3D
|
G:HEM200
|
4.4
|
2.0
|
0.0
|
C2D
|
G:HEM200
|
4.4
|
2.0
|
0.0
|
CD1
|
G:ILE49
|
5.0
|
16.3
|
1.0
|
CD1
|
H:ILE49
|
5.0
|
16.3
|
1.0
|
|
Iron binding site 5 out
of 6 in 3e1l
Go back to
Iron Binding Sites List in 3e1l
Iron binding site 5 out
of 6 in the Crystal Structure of E. Coli Bacterioferritin (Bfr) Soaked in Phosphate with An Alternative Conformation of the Unoccupied Ferroxidase Centre (Apo-Bfr II).
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Crystal Structure of E. Coli Bacterioferritin (Bfr) Soaked in Phosphate with An Alternative Conformation of the Unoccupied Ferroxidase Centre (Apo-Bfr II). within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Fe200
b:2.0
occ:0.04
|
FE
|
I:HEM200
|
0.0
|
2.0
|
0.0
|
SD
|
I:MET52
|
2.1
|
19.3
|
1.0
|
NC
|
I:HEM200
|
2.1
|
2.0
|
0.0
|
SD
|
J:MET52
|
2.1
|
19.3
|
1.0
|
NB
|
I:HEM200
|
2.1
|
2.0
|
0.0
|
NA
|
I:HEM200
|
2.1
|
2.0
|
0.0
|
ND
|
I:HEM200
|
2.1
|
2.0
|
0.0
|
CE
|
I:MET52
|
3.0
|
17.9
|
1.0
|
C1C
|
I:HEM200
|
3.1
|
2.0
|
0.0
|
CE
|
J:MET52
|
3.1
|
17.9
|
1.0
|
C4B
|
I:HEM200
|
3.1
|
2.0
|
0.0
|
C4C
|
I:HEM200
|
3.1
|
2.0
|
0.0
|
C1A
|
I:HEM200
|
3.1
|
2.0
|
0.0
|
C4D
|
I:HEM200
|
3.1
|
2.0
|
0.0
|
C1B
|
I:HEM200
|
3.1
|
2.0
|
0.0
|
C4A
|
I:HEM200
|
3.1
|
2.0
|
0.0
|
C1D
|
I:HEM200
|
3.1
|
2.0
|
0.0
|
CHC
|
I:HEM200
|
3.4
|
2.0
|
0.0
|
CHA
|
I:HEM200
|
3.4
|
2.0
|
0.0
|
CHD
|
I:HEM200
|
3.5
|
2.0
|
0.0
|
CG
|
I:MET52
|
3.5
|
16.2
|
1.0
|
CHB
|
I:HEM200
|
3.5
|
2.0
|
0.0
|
CG
|
J:MET52
|
3.5
|
16.2
|
1.0
|
CB
|
J:MET52
|
4.3
|
14.5
|
1.0
|
CB
|
I:MET52
|
4.3
|
14.5
|
1.0
|
C2C
|
I:HEM200
|
4.3
|
2.0
|
0.0
|
C3C
|
I:HEM200
|
4.3
|
2.0
|
0.0
|
C3B
|
I:HEM200
|
4.3
|
2.0
|
0.0
|
C2A
|
I:HEM200
|
4.3
|
2.0
|
0.0
|
C2B
|
I:HEM200
|
4.3
|
2.0
|
0.0
|
C3A
|
I:HEM200
|
4.3
|
2.0
|
0.0
|
C3D
|
I:HEM200
|
4.4
|
2.0
|
0.0
|
C2D
|
I:HEM200
|
4.4
|
2.0
|
0.0
|
CD1
|
I:ILE49
|
5.0
|
16.3
|
1.0
|
CD1
|
J:ILE49
|
5.0
|
16.3
|
1.0
|
|
Iron binding site 6 out
of 6 in 3e1l
Go back to
Iron Binding Sites List in 3e1l
Iron binding site 6 out
of 6 in the Crystal Structure of E. Coli Bacterioferritin (Bfr) Soaked in Phosphate with An Alternative Conformation of the Unoccupied Ferroxidase Centre (Apo-Bfr II).
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Crystal Structure of E. Coli Bacterioferritin (Bfr) Soaked in Phosphate with An Alternative Conformation of the Unoccupied Ferroxidase Centre (Apo-Bfr II). within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:Fe200
b:2.0
occ:0.04
|
FE
|
K:HEM200
|
0.0
|
2.0
|
0.0
|
SD
|
K:MET52
|
2.1
|
19.3
|
1.0
|
SD
|
L:MET52
|
2.1
|
19.3
|
1.0
|
NC
|
K:HEM200
|
2.2
|
2.0
|
0.0
|
NB
|
K:HEM200
|
2.2
|
2.0
|
0.0
|
ND
|
K:HEM200
|
2.2
|
2.0
|
0.0
|
NA
|
K:HEM200
|
2.2
|
2.0
|
0.0
|
CE
|
K:MET52
|
3.1
|
17.9
|
1.0
|
CE
|
L:MET52
|
3.1
|
17.9
|
1.0
|
C1C
|
K:HEM200
|
3.2
|
2.0
|
0.0
|
C4B
|
K:HEM200
|
3.2
|
2.0
|
0.0
|
C4D
|
K:HEM200
|
3.2
|
2.0
|
0.0
|
C4C
|
K:HEM200
|
3.2
|
2.0
|
0.0
|
C1B
|
K:HEM200
|
3.2
|
2.0
|
0.0
|
C1D
|
K:HEM200
|
3.2
|
2.0
|
0.0
|
C4A
|
K:HEM200
|
3.2
|
2.0
|
0.0
|
C1A
|
K:HEM200
|
3.2
|
2.0
|
0.0
|
CHC
|
K:HEM200
|
3.5
|
2.0
|
0.0
|
CG
|
L:MET52
|
3.5
|
16.2
|
1.0
|
CG
|
K:MET52
|
3.5
|
16.2
|
1.0
|
CHD
|
K:HEM200
|
3.6
|
2.0
|
0.0
|
CHB
|
K:HEM200
|
3.6
|
2.0
|
0.0
|
CB
|
L:MET52
|
4.3
|
14.5
|
1.0
|
CB
|
K:MET52
|
4.3
|
14.5
|
1.0
|
C2C
|
K:HEM200
|
4.4
|
2.0
|
0.0
|
C3B
|
K:HEM200
|
4.4
|
2.0
|
0.0
|
C3C
|
K:HEM200
|
4.4
|
2.0
|
0.0
|
C2B
|
K:HEM200
|
4.4
|
2.0
|
0.0
|
C3D
|
K:HEM200
|
4.4
|
2.0
|
0.0
|
C3A
|
K:HEM200
|
4.5
|
2.0
|
0.0
|
C2D
|
K:HEM200
|
4.5
|
2.0
|
0.0
|
C2A
|
K:HEM200
|
4.5
|
2.0
|
0.0
|
CD1
|
K:ILE49
|
4.9
|
16.3
|
1.0
|
CD1
|
L:ILE49
|
5.0
|
16.3
|
1.0
|
|
Reference:
A.Crow,
T.L.Lawson,
A.Lewin,
G.R.Moore,
N.E.Le Brun.
Structural Basis For Iron Mineralization By Bacterioferritin J.Am.Chem.Soc. V. 131 6808 2009.
ISSN: ISSN 0002-7863
PubMed: 19391621
DOI: 10.1021/JA8093444
Page generated: Sun Aug 4 09:17:51 2024
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