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Iron in PDB 3e1m: Crystal Structure of E. Coli Bacterioferritin (Bfr) Obtained After Soaking Apo-Bfr Crystals For 2.5 Minutes in FE2+ (2.5M Fe(II)-Bfr)

Protein crystallography data

The structure of Crystal Structure of E. Coli Bacterioferritin (Bfr) Obtained After Soaking Apo-Bfr Crystals For 2.5 Minutes in FE2+ (2.5M Fe(II)-Bfr), PDB code: 3e1m 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) 32.04 / 2.70
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 207.972, 207.972, 142.878, 90.00, 90.00, 90.00
R / Rfree (%) 24.1 / 25.9

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 42;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of E. Coli Bacterioferritin (Bfr) Obtained After Soaking Apo-Bfr Crystals For 2.5 Minutes in FE2+ (2.5M Fe(II)-Bfr) (pdb code 3e1m). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 42 binding sites of Iron where determined in the Crystal Structure of E. Coli Bacterioferritin (Bfr) Obtained After Soaking Apo-Bfr Crystals For 2.5 Minutes in FE2+ (2.5M Fe(II)-Bfr), PDB code: 3e1m:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 42 in 3e1m

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Iron binding site 1 out of 42 in the Crystal Structure of E. Coli Bacterioferritin (Bfr) Obtained After Soaking Apo-Bfr Crystals For 2.5 Minutes in FE2+ (2.5M Fe(II)-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) Obtained After Soaking Apo-Bfr Crystals For 2.5 Minutes in FE2+ (2.5M Fe(II)-Bfr) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe300

b:20.8
occ:1.00
 OE1 A:GLU127 2.0 12.1 1.0
OE1 A:GLU18 2.2 15.7 1.0
OE2 A:GLU51 2.2 14.2 1.0
ND1 A:HIS54 2.3 12.6 1.0
OE2 A:GLU18 2.4 15.5 1.0
CD A:GLU18 2.6 14.8 1.0
CD A:GLU51 3.0 12.4 1.0
CD A:GLU127 3.0 12.7 1.0
CE1 A:HIS54 3.2 13.4 1.0
OE2 A:GLU127 3.3 14.6 1.0
CG A:HIS54 3.4 10.5 1.0
OE1 A:GLU51 3.5 13.5 1.0
FE A:FE2301 3.7 30.6 1.0
CB A:HIS54 3.7 7.8 1.0
CG A:GLU51 4.1 11.2 1.0
CG A:GLU18 4.1 12.7 1.0
O A:HOH413 4.2 2.5 1.0
CA A:GLU51 4.3 7.7 1.0
NE2 A:HIS54 4.3 10.9 1.0
O A:HOH403 4.3 2.0 1.0
CG A:GLU127 4.4 12.1 1.0
CD2 A:HIS54 4.4 12.2 1.0
CG2 A:ILE123 4.6 2.4 1.0
CB A:GLU51 4.6 8.7 1.0
CE1 A:HIS130 4.7 15.6 1.0
CB A:GLU18 4.8 9.8 1.0
CA A:GLU18 4.9 9.6 1.0
O A:GLU51 4.9 6.7 1.0

Iron binding site 2 out of 42 in 3e1m

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Iron binding site 2 out of 42 in the Crystal Structure of E. Coli Bacterioferritin (Bfr) Obtained After Soaking Apo-Bfr Crystals For 2.5 Minutes in FE2+ (2.5M Fe(II)-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) Obtained After Soaking Apo-Bfr Crystals For 2.5 Minutes in FE2+ (2.5M Fe(II)-Bfr) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:30.6
occ:1.00
 OE2 A:GLU127 2.0 14.6 1.0
OE1 A:GLU51 2.1 13.5 1.0
OE2 A:GLU94 2.2 15.9 1.0
ND1 A:HIS130 2.3 14.7 1.0
OE1 A:GLU94 2.5 16.1 1.0
O A:HOH413 2.5 2.5 1.0
CD A:GLU94 2.7 14.0 1.0
CE1 A:HIS130 3.0 15.6 1.0
CD A:GLU127 3.1 12.7 1.0
CD A:GLU51 3.1 12.4 1.0
OE2 A:GLU51 3.4 14.2 1.0
CG A:HIS130 3.5 13.1 1.0
OE1 A:GLU127 3.6 12.1 1.0
FE A:FE2300 3.7 20.8 1.0
CB A:HIS130 4.0 8.8 1.0
CG A:GLU94 4.1 10.1 1.0
NE2 A:HIS130 4.2 15.7 1.0
O A:HOH406 4.3 7.4 1.0
CG A:GLU127 4.3 12.1 1.0
CE2 A:TYR25 4.4 9.6 1.0
CG A:GLU51 4.4 11.2 1.0
CA A:GLU127 4.4 7.8 1.0
OH A:TYR25 4.4 10.2 1.0
CD2 A:HIS130 4.5 15.2 1.0
CB A:GLU127 4.5 8.0 1.0
O A:HOH412 4.7 2.0 1.0
CZ A:TYR25 4.9 10.9 1.0
CB A:GLU94 5.0 7.1 1.0

Iron binding site 3 out of 42 in 3e1m

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Iron binding site 3 out of 42 in the Crystal Structure of E. Coli Bacterioferritin (Bfr) Obtained After Soaking Apo-Bfr Crystals For 2.5 Minutes in FE2+ (2.5M Fe(II)-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) Obtained After Soaking Apo-Bfr Crystals For 2.5 Minutes in FE2+ (2.5M Fe(II)-Bfr) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe400

b:23.9
occ:0.38
 NE2 A:HIS46 2.2 13.2 1.0
OD2 A:ASP50 2.7 12.1 1.0
CE1 A:HIS46 3.1 12.9 1.0
OD1 A:ASP50 3.3 8.4 1.0
CD2 A:HIS46 3.3 11.9 1.0
CG A:ASP50 3.4 7.6 1.0
ND1 A:HIS46 4.3 13.6 1.0
CG A:HIS46 4.4 10.0 1.0
CB A:ASP50 4.8 6.6 1.0
O A:HOH414 4.9 3.6 1.0
NE2 A:HIS130 5.0 15.7 1.0

Iron binding site 4 out of 42 in 3e1m

Go back to Iron Binding Sites List in 3e1m
Iron binding site 4 out of 42 in the Crystal Structure of E. Coli Bacterioferritin (Bfr) Obtained After Soaking Apo-Bfr Crystals For 2.5 Minutes in FE2+ (2.5M Fe(II)-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) Obtained After Soaking Apo-Bfr Crystals For 2.5 Minutes in FE2+ (2.5M Fe(II)-Bfr) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe300

b:20.8
occ:1.00
 OE1 B:GLU127 2.1 12.1 1.0
OE1 B:GLU18 2.1 15.7 1.0
OE2 B:GLU51 2.2 14.2 1.0
ND1 B:HIS54 2.4 12.6 1.0
OE2 B:GLU18 2.4 15.5 1.0
CD B:GLU18 2.6 14.8 1.0
CD B:GLU51 3.0 12.4 1.0
CD B:GLU127 3.0 12.7 1.0
CE1 B:HIS54 3.2 13.4 1.0
OE2 B:GLU127 3.3 14.6 1.0
CG B:HIS54 3.4 10.5 1.0
OE1 B:GLU51 3.5 13.6 1.0
FE B:FE2301 3.7 30.7 1.0
CB B:HIS54 3.7 7.8 1.0
CG B:GLU51 4.0 11.2 1.0
CG B:GLU18 4.1 12.7 1.0
CA B:GLU51 4.2 7.7 1.0
NE2 B:HIS54 4.4 10.9 1.0
CG B:GLU127 4.4 12.1 1.0
O B:HOH425 4.5 5.4 1.0
CD2 B:HIS54 4.5 12.2 1.0
CG2 B:ILE123 4.6 2.4 1.0
CB B:GLU51 4.6 8.7 1.0
CE1 B:HIS130 4.7 15.5 1.0
CB B:GLU18 4.8 9.8 1.0
CA B:GLU18 4.9 9.6 1.0
O B:GLU51 4.9 6.7 1.0

Iron binding site 5 out of 42 in 3e1m

Go back to Iron Binding Sites List in 3e1m
Iron binding site 5 out of 42 in the Crystal Structure of E. Coli Bacterioferritin (Bfr) Obtained After Soaking Apo-Bfr Crystals For 2.5 Minutes in FE2+ (2.5M Fe(II)-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) Obtained After Soaking Apo-Bfr Crystals For 2.5 Minutes in FE2+ (2.5M Fe(II)-Bfr) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:30.7
occ:1.00
 OE2 B:GLU127 2.0 14.6 1.0
OE1 B:GLU51 2.1 13.6 1.0
OE2 B:GLU94 2.3 15.9 1.0
ND1 B:HIS130 2.3 14.7 1.0
OE1 B:GLU94 2.5 16.2 1.0
CD B:GLU94 2.7 14.0 1.0
CE1 B:HIS130 3.0 15.5 1.0
CD B:GLU51 3.1 12.4 1.0
CD B:GLU127 3.1 12.7 1.0
OE2 B:GLU51 3.4 14.2 1.0
CG B:HIS130 3.5 13.1 1.0
OE1 B:GLU127 3.6 12.1 1.0
FE B:FE2300 3.7 20.8 1.0
CB B:HIS130 4.0 8.8 1.0
CG B:GLU94 4.2 10.2 1.0
NE2 B:HIS130 4.2 15.7 1.0
CG B:GLU127 4.3 12.1 1.0
CG B:GLU51 4.3 11.2 1.0
CE2 B:TYR25 4.3 9.6 1.0
OH B:TYR25 4.4 10.2 1.0
CA B:GLU127 4.4 7.9 1.0
CD2 B:HIS130 4.5 15.2 1.0
CB B:GLU127 4.6 8.0 1.0
O B:HOH423 4.7 6.0 1.0
CZ B:TYR25 4.9 10.9 1.0
CB B:GLU94 5.0 7.1 1.0

Iron binding site 6 out of 42 in 3e1m

Go back to Iron Binding Sites List in 3e1m
Iron binding site 6 out of 42 in the Crystal Structure of E. Coli Bacterioferritin (Bfr) Obtained After Soaking Apo-Bfr Crystals For 2.5 Minutes in FE2+ (2.5M Fe(II)-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) Obtained After Soaking Apo-Bfr Crystals For 2.5 Minutes in FE2+ (2.5M Fe(II)-Bfr) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe400

b:23.9
occ:0.38
 NE2 B:HIS46 2.2 13.2 1.0
OD2 B:ASP50 2.7 12.1 1.0
CE1 B:HIS46 3.1 12.9 1.0
OD1 B:ASP50 3.3 8.4 1.0
CD2 B:HIS46 3.3 11.9 1.0
CG B:ASP50 3.4 7.7 1.0
ND1 B:HIS46 4.3 13.6 1.0
CG B:HIS46 4.4 10.0 1.0
CB B:ASP50 4.8 6.6 1.0
NE2 B:HIS130 5.0 15.7 1.0

Iron binding site 7 out of 42 in 3e1m

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Iron binding site 7 out of 42 in the Crystal Structure of E. Coli Bacterioferritin (Bfr) Obtained After Soaking Apo-Bfr Crystals For 2.5 Minutes in FE2+ (2.5M Fe(II)-Bfr)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of E. Coli Bacterioferritin (Bfr) Obtained After Soaking Apo-Bfr Crystals For 2.5 Minutes in FE2+ (2.5M Fe(II)-Bfr) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe200

b:15.5
occ:0.04
 FE B:HEM200 0.0 15.5 0.0
NC B:HEM200 2.1 15.1 0.0
NA B:HEM200 2.1 15.9 0.0
NB B:HEM200 2.1 15.0 0.0
ND B:HEM200 2.1 16.0 0.0
SD B:MET52 2.2 8.5 1.0
SD A:MET52 2.2 8.5 1.0
C1A B:HEM200 3.1 16.3 0.0
C4C B:HEM200 3.1 14.9 0.0
C4A B:HEM200 3.1 15.9 0.0
C1D B:HEM200 3.1 16.1 0.0
C1C B:HEM200 3.1 14.6 0.0
C4D B:HEM200 3.1 16.4 0.0
C1B B:HEM200 3.1 14.8 0.0
C4B B:HEM200 3.1 14.4 0.0
CE A:MET52 3.2 7.2 1.0
CE B:MET52 3.2 7.2 1.0
CHA B:HEM200 3.4 16.2 0.0
CHD B:HEM200 3.4 15.5 0.0
CHB B:HEM200 3.5 15.3 0.0
CHC B:HEM200 3.5 14.5 0.0
CG B:MET52 3.6 6.6 1.0
CG A:MET52 3.7 6.6 1.0
C2A B:HEM200 4.3 16.5 0.0
C3A B:HEM200 4.3 16.2 0.0
C3C B:HEM200 4.3 14.2 0.0
C2C B:HEM200 4.3 14.2 0.0
C2B B:HEM200 4.3 14.2 0.0
C3B B:HEM200 4.3 13.8 0.0
C2D B:HEM200 4.3 16.5 0.0
C3D B:HEM200 4.3 16.7 0.0
CB B:MET52 4.4 6.2 1.0
CB A:MET52 4.6 6.2 1.0
CD1 A:ILE49 4.9 6.3 1.0
CD1 B:ILE49 4.9 6.3 1.0

Iron binding site 8 out of 42 in 3e1m

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Iron binding site 8 out of 42 in the Crystal Structure of E. Coli Bacterioferritin (Bfr) Obtained After Soaking Apo-Bfr Crystals For 2.5 Minutes in FE2+ (2.5M Fe(II)-Bfr)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of E. Coli Bacterioferritin (Bfr) Obtained After Soaking Apo-Bfr Crystals For 2.5 Minutes in FE2+ (2.5M Fe(II)-Bfr) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe300

b:20.8
occ:1.00
 OE1 C:GLU127 2.0 12.1 1.0
OE1 C:GLU18 2.2 15.7 1.0
OE2 C:GLU51 2.2 14.2 1.0
ND1 C:HIS54 2.3 12.6 1.0
O C:HOH418 2.4 4.1 1.0
OE2 C:GLU18 2.4 15.5 1.0
CD C:GLU18 2.6 14.8 1.0
CD C:GLU127 3.0 12.7 1.0
CD C:GLU51 3.0 12.4 1.0
CE1 C:HIS54 3.2 13.4 1.0
OE2 C:GLU127 3.3 14.6 1.0
CG C:HIS54 3.4 10.5 1.0
OE1 C:GLU51 3.5 13.5 1.0
FE C:FE2301 3.7 30.6 1.0
CB C:HIS54 3.7 7.8 1.0
CG C:GLU51 4.1 11.2 1.0
CG C:GLU18 4.1 12.7 1.0
CA C:GLU51 4.3 7.7 1.0
NE2 C:HIS54 4.3 10.9 1.0
CG C:GLU127 4.4 12.1 1.0
CD2 C:HIS54 4.5 12.2 1.0
CG2 C:ILE123 4.5 2.4 1.0
O C:HOH407 4.6 2.0 1.0
CB C:GLU51 4.6 8.7 1.0
CE1 C:HIS130 4.7 15.5 1.0
CB C:GLU18 4.9 9.8 1.0
CA C:GLU18 4.9 9.6 1.0
O C:GLU51 5.0 6.7 1.0
ND1 C:HIS130 5.0 14.8 1.0

Iron binding site 9 out of 42 in 3e1m

Go back to Iron Binding Sites List in 3e1m
Iron binding site 9 out of 42 in the Crystal Structure of E. Coli Bacterioferritin (Bfr) Obtained After Soaking Apo-Bfr Crystals For 2.5 Minutes in FE2+ (2.5M Fe(II)-Bfr)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of E. Coli Bacterioferritin (Bfr) Obtained After Soaking Apo-Bfr Crystals For 2.5 Minutes in FE2+ (2.5M Fe(II)-Bfr) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe301

b:30.6
occ:1.00
 OE2 C:GLU127 1.9 14.6 1.0
OE1 C:GLU51 2.1 13.5 1.0
OE2 C:GLU94 2.3 15.9 1.0
ND1 C:HIS130 2.3 14.8 1.0
OE1 C:GLU94 2.5 16.2 1.0
CD C:GLU94 2.7 14.0 1.0
CE1 C:HIS130 3.0 15.5 1.0
CD C:GLU127 3.0 12.7 1.0
CD C:GLU51 3.1 12.4 1.0
O C:HOH418 3.4 4.1 1.0
OE2 C:GLU51 3.4 14.2 1.0
CG C:HIS130 3.5 13.1 1.0
OE1 C:GLU127 3.5 12.1 1.0
FE C:FE2300 3.7 20.8 1.0
CB C:HIS130 4.0 8.8 1.0
CG C:GLU94 4.2 10.1 1.0
NE2 C:HIS130 4.2 15.7 1.0
CG C:GLU127 4.2 12.1 1.0
CG C:GLU51 4.4 11.2 1.0
CA C:GLU127 4.4 7.9 1.0
CE2 C:TYR25 4.4 9.6 1.0
OH C:TYR25 4.4 10.2 1.0
CD2 C:HIS130 4.5 15.2 1.0
CB C:GLU127 4.5 8.0 1.0
O C:HOH405 4.8 2.0 1.0
CZ C:TYR25 4.9 10.9 1.0
CB C:GLU94 5.0 7.1 1.0

Iron binding site 10 out of 42 in 3e1m

Go back to Iron Binding Sites List in 3e1m
Iron binding site 10 out of 42 in the Crystal Structure of E. Coli Bacterioferritin (Bfr) Obtained After Soaking Apo-Bfr Crystals For 2.5 Minutes in FE2+ (2.5M Fe(II)-Bfr)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of E. Coli Bacterioferritin (Bfr) Obtained After Soaking Apo-Bfr Crystals For 2.5 Minutes in FE2+ (2.5M Fe(II)-Bfr) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe400

b:23.9
occ:0.38
 NE2 C:HIS46 2.2 13.2 1.0
OD2 C:ASP50 2.7 12.0 1.0
CE1 C:HIS46 3.1 12.9 1.0
OD1 C:ASP50 3.3 8.4 1.0
CD2 C:HIS46 3.3 11.9 1.0
CG C:ASP50 3.4 7.7 1.0
ND1 C:HIS46 4.3 13.5 1.0
CG C:HIS46 4.4 9.9 1.0
CB C:ASP50 4.8 6.6 1.0
O C:HOH423 4.9 16.7 1.0
NE2 C:HIS130 5.0 15.7 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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