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Iron in PDB 3e1o: Crystal Structure of E. Coli Bacterioferritin (Bfr) with Two Zn(II) Ion Sites at the Ferroxidase Centre (Zn-Bfr).

Protein crystallography data

The structure of Crystal Structure of E. Coli Bacterioferritin (Bfr) with Two Zn(II) Ion Sites at the Ferroxidase Centre (Zn-Bfr)., PDB code: 3e1o 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) 44.81 / 2.95
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 207.867, 207.867, 142.432, 90.00, 90.00, 90.00
R / Rfree (%) 22.9 / 25.2

Other elements in 3e1o:

The structure of Crystal Structure of E. Coli Bacterioferritin (Bfr) with Two Zn(II) Ion Sites at the Ferroxidase Centre (Zn-Bfr). also contains other interesting chemical elements:

Zinc (Zn) 24 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of E. Coli Bacterioferritin (Bfr) with Two Zn(II) Ion Sites at the Ferroxidase Centre (Zn-Bfr). (pdb code 3e1o). 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) with Two Zn(II) Ion Sites at the Ferroxidase Centre (Zn-Bfr)., PDB code: 3e1o:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 3e1o

Go back to Iron Binding Sites List in 3e1o
Iron binding site 1 out of 6 in the Crystal Structure of E. Coli Bacterioferritin (Bfr) with Two Zn(II) Ion Sites at the Ferroxidase Centre (Zn-Bfr).


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) with Two Zn(II) Ion Sites at the Ferroxidase Centre (Zn-Bfr). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe200

b:16.4
occ:0.04
FE A:HEM200 0.0 16.4 0.0
NC A:HEM200 2.1 16.2 0.0
NA A:HEM200 2.1 16.7 0.0
NB A:HEM200 2.1 16.2 0.0
ND A:HEM200 2.1 16.7 0.0
SD A:MET52 2.1 11.6 1.0
SD B:MET52 2.2 11.6 1.0
CE A:MET52 3.0 10.0 1.0
C4C A:HEM200 3.1 16.2 0.0
C1C A:HEM200 3.1 16.0 0.0
C1D A:HEM200 3.1 16.8 0.0
C1A A:HEM200 3.1 16.9 0.0
C4A A:HEM200 3.1 16.7 0.0
C4D A:HEM200 3.1 16.9 0.0
C4B A:HEM200 3.1 15.9 0.0
C1B A:HEM200 3.1 16.2 0.0
CE B:MET52 3.1 10.0 1.0
CHD A:HEM200 3.4 16.5 0.0
CHA A:HEM200 3.5 16.8 0.0
CHC A:HEM200 3.5 15.9 0.0
CHB A:HEM200 3.5 16.4 0.0
CG B:MET52 3.6 8.8 1.0
CG A:MET52 3.6 8.8 1.0
C3C A:HEM200 4.3 15.8 0.0
C2C A:HEM200 4.3 15.8 0.0
C3A A:HEM200 4.3 16.9 0.0
C2A A:HEM200 4.3 17.1 0.0
C2D A:HEM200 4.3 16.9 0.0
C3B A:HEM200 4.3 15.7 0.0
C2B A:HEM200 4.3 15.8 0.0
C3D A:HEM200 4.4 17.1 0.0
CB B:MET52 4.4 7.6 1.0
CB A:MET52 4.5 7.6 1.0

Iron binding site 2 out of 6 in 3e1o

Go back to Iron Binding Sites List in 3e1o
Iron binding site 2 out of 6 in the Crystal Structure of E. Coli Bacterioferritin (Bfr) with Two Zn(II) Ion Sites at the Ferroxidase Centre (Zn-Bfr).


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) with Two Zn(II) Ion Sites at the Ferroxidase Centre (Zn-Bfr). within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe200

b:16.4
occ:0.04
FE D:HEM200 0.0 16.4 0.0
NC D:HEM200 2.1 16.2 0.0
NA D:HEM200 2.1 16.7 0.0
NB D:HEM200 2.1 16.2 0.0
ND D:HEM200 2.1 16.7 0.0
SD D:MET52 2.2 11.6 1.0
SD C:MET52 2.2 11.6 1.0
CE C:MET52 3.0 10.0 1.0
C4C D:HEM200 3.1 16.2 0.0
C1C D:HEM200 3.1 16.0 0.0
C1A D:HEM200 3.1 16.9 0.0
CE D:MET52 3.1 10.0 1.0
C1D D:HEM200 3.1 16.8 0.0
C4A D:HEM200 3.1 16.7 0.0
C4B D:HEM200 3.1 15.9 0.0
C4D D:HEM200 3.1 16.9 0.0
C1B D:HEM200 3.1 16.2 0.0
CHD D:HEM200 3.4 16.5 0.0
CHA D:HEM200 3.5 16.8 0.0
CHC D:HEM200 3.5 15.9 0.0
CG D:MET52 3.5 8.8 1.0
CHB D:HEM200 3.5 16.4 0.0
CG C:MET52 3.6 8.8 1.0
C3C D:HEM200 4.3 15.8 0.0
C2C D:HEM200 4.3 15.8 0.0
C2A D:HEM200 4.3 17.1 0.0
C3A D:HEM200 4.3 16.9 0.0
C3B D:HEM200 4.3 15.7 0.0
C2B D:HEM200 4.3 15.8 0.0
C2D D:HEM200 4.3 16.9 0.0
C3D D:HEM200 4.4 17.1 0.0
CB D:MET52 4.4 7.7 1.0
CB C:MET52 4.5 7.7 1.0

Iron binding site 3 out of 6 in 3e1o

Go back to Iron Binding Sites List in 3e1o
Iron binding site 3 out of 6 in the Crystal Structure of E. Coli Bacterioferritin (Bfr) with Two Zn(II) Ion Sites at the Ferroxidase Centre (Zn-Bfr).


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) with Two Zn(II) Ion Sites at the Ferroxidase Centre (Zn-Bfr). within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe200

b:16.4
occ:0.04
FE E:HEM200 0.0 16.4 0.0
NC E:HEM200 2.1 16.2 0.0
NA E:HEM200 2.1 16.6 0.0
NB E:HEM200 2.1 16.2 0.0
ND E:HEM200 2.1 16.7 0.0
SD E:MET52 2.1 11.6 1.0
SD F:MET52 2.2 11.6 1.0
CE E:MET52 3.0 10.0 1.0
C4C E:HEM200 3.1 16.2 0.0
CE F:MET52 3.1 10.0 1.0
C1C E:HEM200 3.1 16.0 0.0
C1A E:HEM200 3.1 16.9 0.0
C1D E:HEM200 3.1 16.8 0.0
C4A E:HEM200 3.1 16.7 0.0
C4D E:HEM200 3.1 16.9 0.0
C4B E:HEM200 3.1 15.9 0.0
C1B E:HEM200 3.1 16.2 0.0
CHD E:HEM200 3.4 16.5 0.0
CHA E:HEM200 3.5 16.8 0.0
CHC E:HEM200 3.5 15.9 0.0
CHB E:HEM200 3.5 16.4 0.0
CG F:MET52 3.6 8.8 1.0
CG E:MET52 3.6 8.8 1.0
C3C E:HEM200 4.3 15.8 0.0
C2C E:HEM200 4.3 15.8 0.0
C3A E:HEM200 4.3 16.9 0.0
C2A E:HEM200 4.3 17.1 0.0
C3B E:HEM200 4.3 15.7 0.0
C2B E:HEM200 4.3 15.8 0.0
C2D E:HEM200 4.3 16.9 0.0
C3D E:HEM200 4.4 17.1 0.0
CB F:MET52 4.4 7.7 1.0
CB E:MET52 4.4 7.6 1.0
CD1 E:ILE49 5.0 7.7 1.0

Iron binding site 4 out of 6 in 3e1o

Go back to Iron Binding Sites List in 3e1o
Iron binding site 4 out of 6 in the Crystal Structure of E. Coli Bacterioferritin (Bfr) with Two Zn(II) Ion Sites at the Ferroxidase Centre (Zn-Bfr).


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) with Two Zn(II) Ion Sites at the Ferroxidase Centre (Zn-Bfr). within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe200

b:16.4
occ:0.04
FE H:HEM200 0.0 16.4 0.0
NC H:HEM200 2.1 16.2 0.0
NB H:HEM200 2.1 16.2 0.0
NA H:HEM200 2.1 16.7 0.0
ND H:HEM200 2.1 16.7 0.0
SD H:MET52 2.2 11.6 1.0
SD G:MET52 2.2 11.6 1.0
CE G:MET52 3.0 10.0 1.0
C4C H:HEM200 3.1 16.2 0.0
C1C H:HEM200 3.1 16.0 0.0
C1A H:HEM200 3.1 16.9 0.0
C4A H:HEM200 3.1 16.7 0.0
C4B H:HEM200 3.1 15.9 0.0
C1D H:HEM200 3.1 16.8 0.0
C1B H:HEM200 3.1 16.2 0.0
C4D H:HEM200 3.1 16.9 0.0
CE H:MET52 3.1 10.0 1.0
CG H:MET52 3.4 8.8 1.0
CHD H:HEM200 3.4 16.5 0.0
CHC H:HEM200 3.5 15.9 0.0
CHA H:HEM200 3.5 16.8 0.0
CHB H:HEM200 3.5 16.4 0.0
CG G:MET52 3.6 8.8 1.0
CB H:MET52 4.3 7.6 1.0
C3C H:HEM200 4.3 15.8 0.0
C2C H:HEM200 4.3 15.8 0.0
C3A H:HEM200 4.3 16.9 0.0
C2A H:HEM200 4.3 17.1 0.0
C3B H:HEM200 4.3 15.7 0.0
C2B H:HEM200 4.3 15.8 0.0
C2D H:HEM200 4.3 16.9 0.0
C3D H:HEM200 4.4 17.1 0.0
CB G:MET52 4.6 7.7 1.0

Iron binding site 5 out of 6 in 3e1o

Go back to Iron Binding Sites List in 3e1o
Iron binding site 5 out of 6 in the Crystal Structure of E. Coli Bacterioferritin (Bfr) with Two Zn(II) Ion Sites at the Ferroxidase Centre (Zn-Bfr).


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) with Two Zn(II) Ion Sites at the Ferroxidase Centre (Zn-Bfr). within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Fe200

b:16.4
occ:0.04
FE I:HEM200 0.0 16.4 0.0
NC I:HEM200 2.1 16.2 0.0
NA I:HEM200 2.1 16.6 0.0
NB I:HEM200 2.1 16.2 0.0
ND I:HEM200 2.1 16.7 0.0
SD J:MET52 2.1 11.6 1.0
SD I:MET52 2.2 11.6 1.0
CE I:MET52 3.0 10.0 1.0
C4C I:HEM200 3.1 16.2 0.0
C1A I:HEM200 3.1 16.9 0.0
C1C I:HEM200 3.1 16.0 0.0
CE J:MET52 3.1 10.0 1.0
C4A I:HEM200 3.1 16.7 0.0
C1D I:HEM200 3.1 16.8 0.0
C4B I:HEM200 3.1 15.9 0.0
C4D I:HEM200 3.1 16.9 0.0
C1B I:HEM200 3.1 16.2 0.0
CHD I:HEM200 3.4 16.5 0.0
CHA I:HEM200 3.5 16.8 0.0
CHC I:HEM200 3.5 15.9 0.0
CHB I:HEM200 3.5 16.4 0.0
CG J:MET52 3.5 8.8 1.0
CG I:MET52 3.6 8.8 1.0
C3C I:HEM200 4.3 15.8 0.0
C3A I:HEM200 4.3 16.9 0.0
C2C I:HEM200 4.3 15.8 0.0
C2A I:HEM200 4.3 17.1 0.0
C3B I:HEM200 4.3 15.7 0.0
C2B I:HEM200 4.3 15.8 0.0
C2D I:HEM200 4.3 16.9 0.0
C3D I:HEM200 4.4 17.1 0.0
CB J:MET52 4.4 7.7 1.0
CB I:MET52 4.5 7.6 1.0
CD1 I:ILE49 5.0 7.7 1.0

Iron binding site 6 out of 6 in 3e1o

Go back to Iron Binding Sites List in 3e1o
Iron binding site 6 out of 6 in the Crystal Structure of E. Coli Bacterioferritin (Bfr) with Two Zn(II) Ion Sites at the Ferroxidase Centre (Zn-Bfr).


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) with Two Zn(II) Ion Sites at the Ferroxidase Centre (Zn-Bfr). within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Fe200

b:16.4
occ:0.04
FE K:HEM200 0.0 16.4 0.0
NC K:HEM200 2.1 16.2 0.0
NA K:HEM200 2.1 16.7 0.0
NB K:HEM200 2.1 16.2 0.0
ND K:HEM200 2.1 16.7 0.0
SD K:MET52 2.1 11.6 1.0
SD L:MET52 2.2 11.6 1.0
CE K:MET52 3.0 10.0 1.0
C4C K:HEM200 3.1 16.2 0.0
C1C K:HEM200 3.1 16.0 0.0
C1A K:HEM200 3.1 16.9 0.0
C1D K:HEM200 3.1 16.8 0.0
CE L:MET52 3.1 10.0 1.0
C4A K:HEM200 3.1 16.7 0.0
C4D K:HEM200 3.1 16.9 0.0
C4B K:HEM200 3.1 15.9 0.0
C1B K:HEM200 3.1 16.2 0.0
CHD K:HEM200 3.4 16.5 0.0
CHA K:HEM200 3.5 16.8 0.0
CHC K:HEM200 3.5 15.9 0.0
CHB K:HEM200 3.5 16.4 0.0
CG L:MET52 3.6 8.8 1.0
CG K:MET52 3.6 8.8 1.0
C3C K:HEM200 4.3 15.8 0.0
C2C K:HEM200 4.3 15.8 0.0
C2A K:HEM200 4.3 17.1 0.0
C3A K:HEM200 4.3 16.9 0.0
C2D K:HEM200 4.3 16.9 0.0
C3B K:HEM200 4.3 15.7 0.0
C2B K:HEM200 4.3 15.8 0.0
C3D K:HEM200 4.4 17.1 0.0
CB L:MET52 4.4 7.7 1.0
CB K:MET52 4.4 7.7 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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