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Iron in PDB 1sof: Crystal Structure of the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution

Protein crystallography data

The structure of Crystal Structure of the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution, PDB code: 1sof was solved by H.L.Liu, J.F.Huang, R.C.Bi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.32 / 2.60
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 124.965, 124.965, 287.406, 90.00, 90.00, 120.00
R / Rfree (%) 19.6 / 24.6

Other elements in 1sof:

The structure of Crystal Structure of the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution also contains other interesting chemical elements:

Magnesium (Mg) 10 atoms
Barium (Ba) 2 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution (pdb code 1sof). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 20 binding sites of Iron where determined in the Crystal Structure of the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution, PDB code: 1sof:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 20 in 1sof

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Iron binding site 1 out of 20 in the Crystal Structure of the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution


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 the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe202

b:36.9
occ:1.00
OE2 A:GLU127 1.9 46.9 1.0
OE1 A:GLU51 2.0 36.1 1.0
ND1 A:HIS54 2.0 28.0 1.0
OE1 A:GLU18 2.2 45.6 1.0
CD A:GLU127 2.8 45.1 1.0
CE1 A:HIS54 3.0 28.9 1.0
CD A:GLU51 3.0 33.3 1.0
CG A:HIS54 3.1 27.9 1.0
CD A:GLU18 3.1 44.5 1.0
OE1 A:GLU127 3.3 46.5 1.0
OE2 A:GLU51 3.4 36.1 1.0
OE2 A:GLU18 3.4 48.3 1.0
CB A:HIS54 3.5 25.9 1.0
O A:HOH417 3.6 50.1 1.0
O A:HOH421 4.0 45.4 1.0
CG A:GLU127 4.0 42.6 1.0
CG2 A:ILE123 4.0 29.0 1.0
NE2 A:HIS54 4.1 29.4 1.0
CA A:GLU51 4.2 28.7 1.0
CD2 A:HIS54 4.2 27.3 1.0
CG A:GLU51 4.3 32.7 1.0
FE A:FE2201 4.4 33.8 0.5
CG A:GLU18 4.5 40.7 1.0
CB A:GLU51 4.5 30.6 1.0
CB A:GLU18 4.8 36.8 1.0
O A:GLU51 4.9 26.0 1.0
N A:GLU51 5.0 28.1 1.0

Iron binding site 2 out of 20 in 1sof

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Iron binding site 2 out of 20 in the Crystal Structure of the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution


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 the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:33.8
occ:0.49
OE2 A:GLU51 2.1 36.1 1.0
OE1 A:GLU127 2.3 46.5 1.0
OE1 A:GLU94 2.4 37.1 1.0
OE2 A:GLU94 2.5 37.2 1.0
CD A:GLU94 2.7 37.1 1.0
O A:HOH421 2.7 45.4 1.0
ND1 A:HIS130 3.0 41.7 1.0
CD A:GLU127 3.3 45.1 1.0
CD A:GLU51 3.3 33.3 1.0
CB A:HIS130 3.5 37.6 1.0
O A:HOH417 3.5 50.1 1.0
CG A:HIS130 3.6 40.4 1.0
OE2 A:GLU127 3.7 46.9 1.0
OE1 A:GLU47 3.9 36.8 1.0
OE1 A:GLU51 4.0 36.1 1.0
CE1 A:HIS130 4.0 41.5 1.0
CG A:GLU94 4.1 37.4 1.0
CE2 A:TYR25 4.2 34.9 1.0
CA A:GLU127 4.3 38.2 1.0
FE A:FE2202 4.4 36.9 1.0
OH A:TYR25 4.4 37.0 1.0
CG A:GLU51 4.4 32.7 1.0
CG A:GLU127 4.5 42.6 1.0
CB A:GLU127 4.6 39.4 1.0
CZ A:TYR25 4.8 35.5 1.0
CD2 A:HIS130 4.8 41.1 1.0
O A:GLU127 4.9 36.4 1.0

Iron binding site 3 out of 20 in 1sof

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Iron binding site 3 out of 20 in the Crystal Structure of the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution


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 the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe202

b:32.7
occ:1.00
ND1 B:HIS54 2.0 25.9 1.0
OE2 B:GLU18 2.0 35.0 1.0
OE2 B:GLU127 2.0 37.0 1.0
OE2 B:GLU51 2.1 36.0 1.0
CD B:GLU18 2.8 33.6 1.0
CE1 B:HIS54 2.8 24.6 1.0
OE1 B:GLU18 3.0 34.6 1.0
CD B:GLU127 3.0 37.9 1.0
CG B:HIS54 3.1 26.3 1.0
CD B:GLU51 3.2 34.7 1.0
OE1 B:GLU127 3.4 40.9 1.0
O B:HOH1204 3.4 25.4 1.0
CB B:HIS54 3.5 25.9 1.0
OE1 B:GLU51 3.6 35.7 1.0
FE B:FE2201 3.9 34.1 0.5
CG2 B:ILE123 4.0 27.0 1.0
NE2 B:HIS54 4.0 24.6 1.0
CD2 B:HIS54 4.1 26.2 1.0
CG B:GLU18 4.2 33.4 1.0
CA B:GLU51 4.3 30.4 1.0
CG B:GLU127 4.3 37.0 1.0
CG B:GLU51 4.5 33.3 1.0
CB B:GLU51 4.8 31.4 1.0
O B:HOH1203 4.9 38.4 1.0
O B:GLU51 5.0 27.8 1.0

Iron binding site 4 out of 20 in 1sof

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Iron binding site 4 out of 20 in the Crystal Structure of the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution


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 the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:34.1
occ:0.50
OE1 B:GLU51 2.0 35.7 1.0
OE1 B:GLU127 2.2 40.9 1.0
O B:HOH1203 2.4 38.4 1.0
OE1 B:GLU94 2.5 48.5 1.0
OE2 B:GLU94 2.7 50.9 1.0
O B:HOH1204 2.7 25.4 1.0
CD B:GLU94 2.7 48.5 1.0
CD B:GLU51 3.1 34.7 1.0
CD B:GLU127 3.3 37.9 1.0
OE2 B:GLU51 3.5 36.0 1.0
OE2 B:GLU127 3.7 37.0 1.0
ND1 B:HIS130 3.8 40.8 1.0
FE B:FE2202 3.9 32.7 1.0
CG B:GLU94 4.0 47.5 1.0
CB B:HIS130 4.2 35.8 1.0
CE2 B:TYR25 4.3 32.8 1.0
CG B:GLU51 4.3 33.3 1.0
CG B:HIS130 4.4 39.1 1.0
CA B:GLU127 4.4 35.9 1.0
CG B:GLU127 4.5 37.0 1.0
OH B:TYR25 4.6 35.4 1.0
CB B:GLU127 4.7 36.2 1.0
CE1 B:HIS130 4.8 39.8 1.0
CZ B:TYR25 5.0 34.0 1.0

Iron binding site 5 out of 20 in 1sof

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Iron binding site 5 out of 20 in the Crystal Structure of the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution


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 the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1200

b:28.3
occ:1.00
FE B:HEM1200 0.0 28.3 1.0
ND B:HEM1200 2.1 28.5 1.0
NB B:HEM1200 2.1 28.5 1.0
NC B:HEM1200 2.1 28.5 1.0
NA B:HEM1200 2.1 28.5 1.0
SD B:MET52 2.3 31.9 1.0
SD A:MET52 2.5 35.9 1.0
C1D B:HEM1200 3.1 39.2 1.0
C4D B:HEM1200 3.1 39.8 1.0
C4C B:HEM1200 3.1 37.7 1.0
C4B B:HEM1200 3.1 37.3 1.0
C1C B:HEM1200 3.1 36.5 1.0
C1A B:HEM1200 3.1 40.4 1.0
C1B B:HEM1200 3.1 38.4 1.0
C4A B:HEM1200 3.1 40.0 1.0
CHD B:HEM1200 3.4 38.3 1.0
CHA B:HEM1200 3.4 39.7 1.0
CE B:MET52 3.5 31.4 1.0
CHC B:HEM1200 3.5 36.8 1.0
CHB B:HEM1200 3.5 39.1 1.0
CG B:MET52 3.5 28.8 1.0
CG A:MET52 3.7 31.1 1.0
CE A:MET52 3.8 33.0 1.0
C3D B:HEM1200 4.3 40.6 1.0
C2D B:HEM1200 4.3 40.1 1.0
CB B:MET52 4.4 26.0 1.0
C3B B:HEM1200 4.4 37.4 1.0
C2C B:HEM1200 4.4 37.2 1.0
C3C B:HEM1200 4.4 38.5 1.0
C2B B:HEM1200 4.4 38.8 1.0
C2A B:HEM1200 4.4 41.2 1.0
C3A B:HEM1200 4.4 40.9 1.0
CB A:MET52 4.5 26.6 1.0

Iron binding site 6 out of 20 in 1sof

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Iron binding site 6 out of 20 in the Crystal Structure of the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution


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 the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe202

b:23.3
occ:1.00
OE1 C:GLU18 1.8 32.2 1.0
OE2 C:GLU127 1.9 32.4 1.0
OE1 C:GLU51 2.0 23.7 1.0
ND1 C:HIS54 2.1 21.7 1.0
CD C:GLU18 2.7 29.1 1.0
OE2 C:GLU18 3.0 29.4 1.0
CD C:GLU51 3.0 24.3 1.0
CE1 C:HIS54 3.0 19.8 1.0
CD C:GLU127 3.1 30.6 1.0
CG C:HIS54 3.1 22.8 1.0
OE2 C:GLU51 3.4 25.2 1.0
CB C:HIS54 3.5 19.6 1.0
CG2 C:ILE123 3.7 21.1 1.0
OE1 C:GLU127 3.7 32.9 1.0
CG C:GLU18 4.0 27.4 1.0
NE2 C:HIS54 4.2 22.0 1.0
CG C:GLU127 4.2 29.6 1.0
CD2 C:HIS54 4.3 22.1 1.0
CG C:GLU51 4.3 24.3 1.0
FE C:FE2201 4.4 31.2 0.5
CA C:GLU51 4.5 22.3 1.0
CB C:GLU51 4.6 24.1 1.0
CB C:GLU18 4.9 24.4 1.0

Iron binding site 7 out of 20 in 1sof

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Iron binding site 7 out of 20 in the Crystal Structure of the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution


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 the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:31.2
occ:0.52
OE2 C:GLU94 1.9 41.5 1.0
OE2 C:GLU51 2.2 25.2 1.0
OE1 C:GLU127 2.2 32.9 1.0
CD C:GLU94 2.8 35.9 1.0
CD C:GLU51 3.0 24.3 1.0
OE1 C:GLU94 3.2 38.0 1.0
ND1 C:HIS130 3.3 23.4 1.0
CD C:GLU127 3.3 30.6 1.0
OE1 C:GLU51 3.6 23.7 1.0
OE2 C:GLU127 3.7 32.4 1.0
CE2 C:TYR25 3.9 21.5 1.0
CG C:GLU51 4.0 24.3 1.0
OE2 C:GLU47 4.0 32.3 1.0
CG C:HIS130 4.1 25.0 1.0
CG C:GLU94 4.1 34.4 1.0
CB C:HIS130 4.1 24.5 1.0
OH C:TYR25 4.1 23.1 1.0
CE1 C:HIS130 4.2 23.7 1.0
FE C:FE2202 4.4 23.3 1.0
CZ C:TYR25 4.6 20.8 1.0
CA C:GLU127 4.6 26.8 1.0
CG C:GLU127 4.6 29.6 1.0
CG C:GLU47 4.7 30.4 1.0
CD C:GLU47 4.8 31.8 1.0
CB C:GLU127 4.8 26.6 1.0
CD2 C:TYR25 5.0 20.4 1.0

Iron binding site 8 out of 20 in 1sof

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Iron binding site 8 out of 20 in the Crystal Structure of the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution


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 the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe2200

b:28.3
occ:1.00
FE C:HEM2200 0.0 28.3 1.0
ND C:HEM2200 2.1 28.5 1.0
NA C:HEM2200 2.1 28.5 1.0
NB C:HEM2200 2.1 28.5 1.0
NC C:HEM2200 2.1 28.5 1.0
SD D:MET52 2.2 17.0 1.0
SD C:MET52 2.3 20.9 1.0
C1D C:HEM2200 3.1 20.9 1.0
C4C C:HEM2200 3.1 21.8 1.0
C4D C:HEM2200 3.1 20.4 1.0
C4A C:HEM2200 3.1 19.3 1.0
C4B C:HEM2200 3.1 22.5 1.0
C1C C:HEM2200 3.1 22.1 1.0
C1A C:HEM2200 3.1 21.8 1.0
C1B C:HEM2200 3.1 21.7 1.0
CHD C:HEM2200 3.4 21.4 1.0
CE C:MET52 3.4 16.5 1.0
CE D:MET52 3.4 12.7 1.0
CHA C:HEM2200 3.4 20.5 1.0
CHC C:HEM2200 3.5 21.3 1.0
CHB C:HEM2200 3.5 21.1 1.0
CG D:MET52 3.6 15.2 1.0
CG C:MET52 3.6 19.1 1.0
CB D:MET52 4.2 14.2 1.0
CB C:MET52 4.2 18.2 1.0
C2D C:HEM2200 4.3 20.7 1.0
C3D C:HEM2200 4.3 22.6 1.0
C3B C:HEM2200 4.3 23.9 1.0
C3A C:HEM2200 4.4 19.8 1.0
C2C C:HEM2200 4.4 23.1 1.0
C3C C:HEM2200 4.4 22.2 1.0
C2A C:HEM2200 4.4 20.5 1.0
C2B C:HEM2200 4.4 22.8 1.0

Iron binding site 9 out of 20 in 1sof

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Iron binding site 9 out of 20 in the Crystal Structure of the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution


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 the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe202

b:26.1
occ:1.00
OE2 D:GLU18 1.8 29.6 1.0
ND1 D:HIS54 1.9 20.2 1.0
OE1 D:GLU127 1.9 24.7 1.0
OE1 D:GLU51 2.0 25.1 1.0
CD D:GLU18 2.7 25.8 1.0
CE1 D:HIS54 2.8 19.2 1.0
CD D:GLU127 2.9 23.5 1.0
OE1 D:GLU18 2.9 27.5 1.0
CG D:HIS54 2.9 20.2 1.0
CD D:GLU51 3.1 24.7 1.0
OE2 D:GLU127 3.3 26.6 1.0
CB D:HIS54 3.4 18.0 1.0
OE2 D:GLU51 3.6 27.1 1.0
O D:HOH512 3.7 30.2 1.0
NE2 D:HIS54 3.9 18.6 1.0
CG2 D:ILE123 3.9 20.8 1.0
CD2 D:HIS54 4.0 18.4 1.0
CG D:GLU18 4.1 25.1 1.0
FE D:FE2201 4.1 27.8 0.5
CG D:GLU127 4.1 24.2 1.0
CA D:GLU51 4.3 19.9 1.0
CG D:GLU51 4.4 24.8 1.0
CB D:GLU51 4.6 22.3 1.0
O D:HOH526 4.8 45.4 1.0
O D:HOH514 4.8 29.5 1.0
CB D:GLU18 4.9 23.0 1.0
CA D:HIS54 4.9 17.9 1.0

Iron binding site 10 out of 20 in 1sof

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Iron binding site 10 out of 20 in the Crystal Structure of the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution


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 the Azotobacter Vinelandii Bacterioferritin at 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:27.8
occ:0.51
OE2 D:GLU51 1.9 27.1 1.0
OE2 D:GLU127 2.1 26.6 1.0
O D:HOH514 2.5 29.5 1.0
O D:HOH512 2.6 30.2 1.0
OE1 D:GLU94 2.6 24.8 1.0
OE2 D:GLU94 2.7 24.4 1.0
CD D:GLU94 2.9 22.7 1.0
CD D:GLU51 2.9 24.7 1.0
CD D:GLU127 3.2 23.5 1.0
ND1 D:HIS130 3.4 29.1 1.0
OE1 D:GLU51 3.4 25.1 1.0
OE1 D:GLU127 3.6 24.7 1.0
CG D:GLU51 4.0 24.8 1.0
FE D:FE2202 4.1 26.1 1.0
CE2 D:TYR25 4.1 27.2 1.0
CB D:HIS130 4.2 22.7 1.0
CG D:HIS130 4.2 26.0 1.0
CG D:GLU94 4.3 20.6 1.0
CE1 D:HIS130 4.4 28.2 1.0
OH D:TYR25 4.4 29.8 1.0
CG D:GLU127 4.4 24.2 1.0
CA D:GLU127 4.5 23.2 1.0
CB D:GLU127 4.5 23.1 1.0
CZ D:TYR25 4.7 28.1 1.0
OE1 D:GLU18 4.9 27.5 1.0
OE2 D:GLU47 4.9 38.0 1.0

Reference:

H.L.Liu, H.N.Zhou, W.M.Xing, J.F.Zhao, S.X.Li, J.F.Huang, R.C.Bi. 2.6 A Resolution Crystal Structure of the Bacterioferritin From Azotobacter Vinelandii Febs Lett. V. 573 93 2004.
ISSN: ISSN 0014-5793
PubMed: 15327981
DOI: 10.1016/J.FEBSLET.2004.07.054
Page generated: Sun Dec 13 14:31:42 2020

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