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Iron in PDB 3lxf: Crystal Structure of [2FE-2S] Ferredoxin Arx From Novosphingobium Aromaticivorans

Protein crystallography data

The structure of Crystal Structure of [2FE-2S] Ferredoxin Arx From Novosphingobium Aromaticivorans, PDB code: 3lxf was solved by W.Yang, S.G.Bell, H.Wang, M.Bartlam, L.L.Wong, Z.Rao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.16 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 137.554, 78.788, 89.200, 90.00, 125.04, 90.00
R / Rfree (%) 20 / 23.9

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of [2FE-2S] Ferredoxin Arx From Novosphingobium Aromaticivorans (pdb code 3lxf). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 10 binding sites of Iron where determined in the Crystal Structure of [2FE-2S] Ferredoxin Arx From Novosphingobium Aromaticivorans, PDB code: 3lxf:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 3lxf

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Iron binding site 1 out of 10 in the Crystal Structure of [2FE-2S] Ferredoxin Arx From Novosphingobium Aromaticivorans


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Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of [2FE-2S] Ferredoxin Arx From Novosphingobium Aromaticivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:30.8
occ:1.00
 FE1 A:FES500 0.0 30.8 1.0
S2 A:FES500 2.2 29.5 1.0
S1 A:FES500 2.2 26.7 1.0
SG A:CYS49 2.3 25.1 1.0
SG A:CYS86 2.4 27.7 1.0
FE2 A:FES500 2.8 30.7 1.0
CB A:CYS86 3.3 27.0 1.0
CB A:CYS49 3.4 27.0 1.0
CA A:GLY42 4.2 32.4 1.0
N A:CYS86 4.2 27.4 1.0
CA A:CYS86 4.3 27.7 1.0
SG A:CYS40 4.5 29.6 1.0
CA A:CYS49 4.5 28.6 1.0
N A:CYS49 4.5 29.3 1.0
CB A:LEU84 4.5 27.0 1.0
SG A:CYS46 4.5 30.1 1.0
N A:CYS44 4.6 33.0 1.0
N A:GLY42 4.7 33.8 1.0
C A:GLY42 4.7 32.8 1.0
O A:CYS46 4.8 32.0 1.0
CD2 A:LEU84 4.9 24.4 1.0
CA A:CYS44 4.9 32.6 1.0
CD1 A:LEU84 5.0 25.7 1.0
N A:CYS43 5.0 32.4 1.0

Iron binding site 2 out of 10 in 3lxf

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Iron binding site 2 out of 10 in the Crystal Structure of [2FE-2S] Ferredoxin Arx From Novosphingobium Aromaticivorans


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Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of [2FE-2S] Ferredoxin Arx From Novosphingobium Aromaticivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:30.7
occ:1.00
 FE2 A:FES500 0.0 30.7 1.0
SG A:CYS46 2.2 30.1 1.0
S1 A:FES500 2.2 26.7 1.0
S2 A:FES500 2.2 29.5 1.0
SG A:CYS40 2.3 29.6 1.0
FE1 A:FES500 2.8 30.8 1.0
CB A:CYS40 3.4 33.9 1.0
N A:CYS46 3.5 32.1 1.0
CB A:CYS46 3.5 31.0 1.0
N A:CYS40 3.7 36.9 1.0
CA A:CYS46 3.8 31.7 1.0
O A:CYS46 4.0 32.0 1.0
CA A:CYS40 4.0 35.0 1.0
C A:CYS46 4.0 31.4 1.0
N A:SER45 4.1 32.0 1.0
N A:GLY42 4.3 33.8 1.0
N A:CYS44 4.5 33.0 1.0
C A:SER45 4.5 32.7 1.0
C A:CYS40 4.5 35.2 1.0
SG A:CYS49 4.6 25.1 1.0
N A:GLY41 4.6 35.4 1.0
N A:CYS43 4.6 32.4 1.0
CA A:GLY42 4.6 32.4 1.0
SG A:CYS86 4.6 27.7 1.0
OG1 A:THR48 4.8 30.9 1.0
N A:LEU39 4.8 40.8 1.0
C A:ALA38 4.8 41.7 1.0
CA A:CYS44 4.8 32.6 1.0
N A:ALA47 4.9 31.2 1.0
CA A:SER45 4.9 32.5 1.0
N A:THR48 4.9 31.0 1.0
C A:LEU39 5.0 39.1 1.0
CA A:ALA38 5.0 42.6 1.0
C A:CYS44 5.0 32.5 1.0

Iron binding site 3 out of 10 in 3lxf

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Iron binding site 3 out of 10 in the Crystal Structure of [2FE-2S] Ferredoxin Arx From Novosphingobium Aromaticivorans


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Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of [2FE-2S] Ferredoxin Arx From Novosphingobium Aromaticivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe500

b:32.6
occ:1.00
 FE1 B:FES500 0.0 32.6 1.0
S2 B:FES500 2.2 31.3 1.0
S1 B:FES500 2.2 28.8 1.0
SG B:CYS86 2.3 30.3 1.0
SG B:CYS49 2.3 27.9 1.0
FE2 B:FES500 2.8 31.8 1.0
CB B:CYS86 3.3 30.5 1.0
CB B:CYS49 3.4 28.4 1.0
CA B:GLY42 4.3 32.0 1.0
N B:CYS86 4.3 29.2 1.0
CA B:CYS86 4.3 29.8 1.0
SG B:CYS40 4.4 31.9 1.0
CB B:LEU84 4.5 27.6 1.0
N B:CYS49 4.5 30.2 1.0
CA B:CYS49 4.5 28.9 1.0
N B:CYS44 4.5 31.3 1.0
SG B:CYS46 4.6 33.1 1.0
N B:GLY42 4.7 32.7 1.0
C B:GLY42 4.8 32.5 1.0
CA B:CYS44 4.8 31.3 1.0
CD2 B:LEU84 4.8 23.6 1.0
O B:CYS46 4.8 32.7 1.0
CD1 B:LEU84 4.9 26.9 1.0
CG B:LEU84 5.0 28.1 1.0

Iron binding site 4 out of 10 in 3lxf

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Iron binding site 4 out of 10 in the Crystal Structure of [2FE-2S] Ferredoxin Arx From Novosphingobium Aromaticivorans


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Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of [2FE-2S] Ferredoxin Arx From Novosphingobium Aromaticivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe500

b:31.8
occ:1.00
 FE2 B:FES500 0.0 31.8 1.0
S1 B:FES500 2.2 28.8 1.0
S2 B:FES500 2.2 31.3 1.0
SG B:CYS40 2.3 31.9 1.0
SG B:CYS46 2.3 33.1 1.0
FE1 B:FES500 2.8 32.6 1.0
CB B:CYS40 3.4 34.7 1.0
N B:CYS46 3.6 32.2 1.0
CB B:CYS46 3.6 32.7 1.0
N B:CYS40 3.7 36.3 1.0
CA B:CYS46 4.0 32.9 1.0
CA B:CYS40 4.0 35.4 1.0
O B:CYS46 4.0 32.7 1.0
C B:CYS46 4.1 32.8 1.0
N B:SER45 4.1 30.9 1.0
N B:GLY42 4.4 32.7 1.0
N B:GLY41 4.5 35.1 1.0
N B:CYS44 4.5 31.3 1.0
C B:CYS40 4.5 35.7 1.0
C B:SER45 4.6 32.3 1.0
SG B:CYS49 4.6 27.9 1.0
SG B:CYS86 4.6 30.3 1.0
N B:CYS43 4.7 32.9 1.0
C B:ALA38 4.7 38.2 1.0
CA B:GLY42 4.7 32.0 1.0
N B:LEU39 4.8 37.7 1.0
OG1 B:THR48 4.8 33.7 1.0
CA B:CYS44 4.8 31.3 1.0
N B:THR48 4.9 32.8 1.0
N B:ALA47 4.9 33.2 1.0
CA B:SER45 4.9 31.7 1.0
C B:LEU39 5.0 38.4 1.0
O B:ALA38 5.0 38.6 1.0
C B:CYS44 5.0 31.1 1.0

Iron binding site 5 out of 10 in 3lxf

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Iron binding site 5 out of 10 in the Crystal Structure of [2FE-2S] Ferredoxin Arx From Novosphingobium Aromaticivorans


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Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of [2FE-2S] Ferredoxin Arx From Novosphingobium Aromaticivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe500

b:36.4
occ:1.00
 FE1 C:FES500 0.0 36.4 1.0
S2 C:FES500 2.2 37.9 1.0
S1 C:FES500 2.2 30.9 1.0
SG C:CYS49 2.3 33.7 1.0
SG C:CYS86 2.4 35.2 1.0
FE2 C:FES500 2.9 37.3 1.0
CB C:CYS49 3.3 34.2 1.0
CB C:CYS86 3.3 33.8 1.0
N C:CYS86 4.2 33.3 1.0
CA C:GLY42 4.2 40.5 1.0
CA C:CYS86 4.3 33.9 1.0
N C:CYS49 4.4 35.2 1.0
CA C:CYS49 4.5 34.6 1.0
CB C:LEU84 4.5 33.7 1.0
SG C:CYS46 4.6 38.0 1.0
N C:GLY42 4.6 41.7 1.0
SG C:CYS40 4.6 38.2 1.0
N C:CYS44 4.7 38.8 1.0
CD2 C:LEU84 4.8 32.1 1.0
O C:CYS46 4.8 39.2 1.0
C C:GLY42 4.8 40.6 1.0
CA C:CYS44 5.0 38.0 1.0

Iron binding site 6 out of 10 in 3lxf

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Iron binding site 6 out of 10 in the Crystal Structure of [2FE-2S] Ferredoxin Arx From Novosphingobium Aromaticivorans


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Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of [2FE-2S] Ferredoxin Arx From Novosphingobium Aromaticivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe500

b:37.3
occ:1.00
 FE2 C:FES500 0.0 37.3 1.0
S1 C:FES500 2.2 30.9 1.0
S2 C:FES500 2.2 37.9 1.0
SG C:CYS46 2.2 38.0 1.0
SG C:CYS40 2.3 38.2 1.0
FE1 C:FES500 2.9 36.4 1.0
N C:CYS46 3.5 38.2 1.0
CB C:CYS46 3.5 39.6 1.0
CB C:CYS40 3.5 42.1 1.0
N C:CYS40 3.8 44.5 1.0
CA C:CYS46 3.8 38.9 1.0
O C:CYS46 3.9 39.2 1.0
C C:CYS46 4.0 38.5 1.0
N C:SER45 4.1 37.7 1.0
CA C:CYS40 4.1 43.2 1.0
N C:GLY42 4.3 41.7 1.0
C C:SER45 4.5 38.1 1.0
N C:CYS44 4.5 38.8 1.0
N C:GLY41 4.5 42.8 1.0
C C:CYS40 4.6 43.3 1.0
SG C:CYS49 4.7 33.7 1.0
OG1 C:THR48 4.7 37.5 1.0
CA C:GLY42 4.7 40.5 1.0
SG C:CYS86 4.7 35.2 1.0
N C:CYS43 4.8 41.2 1.0
N C:ALA47 4.8 37.6 1.0
CA C:CYS44 4.8 38.0 1.0
CA C:SER45 4.8 38.0 1.0
C C:ALA38 4.8 48.9 1.0
N C:THR48 4.9 36.4 1.0
N C:LEU39 4.9 48.2 1.0
C C:CYS44 4.9 37.7 1.0

Iron binding site 7 out of 10 in 3lxf

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Iron binding site 7 out of 10 in the Crystal Structure of [2FE-2S] Ferredoxin Arx From Novosphingobium Aromaticivorans


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Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of [2FE-2S] Ferredoxin Arx From Novosphingobium Aromaticivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe500

b:33.8
occ:1.00
 FE1 D:FES500 0.0 33.8 1.0
S2 D:FES500 2.2 30.6 1.0
S1 D:FES500 2.2 31.2 1.0
SG D:CYS86 2.4 33.1 1.0
SG D:CYS49 2.4 34.0 1.0
FE2 D:FES500 2.8 33.0 1.0
CB D:CYS86 3.2 31.0 1.0
CB D:CYS49 3.4 31.6 1.0
CA D:GLY42 4.1 34.7 1.0
N D:CYS86 4.3 31.1 1.0
CA D:CYS86 4.3 31.6 1.0
SG D:CYS40 4.4 32.2 1.0
SG D:CYS46 4.5 33.9 1.0
N D:GLY42 4.5 35.4 1.0
N D:CYS49 4.6 33.0 1.0
CA D:CYS49 4.6 32.5 1.0
N D:CYS44 4.6 35.7 1.0
CB D:LEU84 4.6 31.1 1.0
C D:GLY42 4.7 35.8 1.0
CA D:CYS44 4.8 35.3 1.0
CD2 D:LEU84 4.9 27.9 1.0
N D:CYS43 5.0 36.0 1.0

Iron binding site 8 out of 10 in 3lxf

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Iron binding site 8 out of 10 in the Crystal Structure of [2FE-2S] Ferredoxin Arx From Novosphingobium Aromaticivorans


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Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of [2FE-2S] Ferredoxin Arx From Novosphingobium Aromaticivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe500

b:33.0
occ:1.00
 FE2 D:FES500 0.0 33.0 1.0
S1 D:FES500 2.2 31.2 1.0
S2 D:FES500 2.2 30.6 1.0
SG D:CYS40 2.2 32.2 1.0
SG D:CYS46 2.3 33.9 1.0
FE1 D:FES500 2.8 33.8 1.0
CB D:CYS40 3.3 36.3 1.0
CB D:CYS46 3.5 38.6 1.0
N D:CYS46 3.6 37.8 1.0
N D:CYS40 3.7 38.9 1.0
CA D:CYS46 3.9 38.2 1.0
CA D:CYS40 3.9 37.2 1.0
C D:CYS46 4.0 38.5 1.0
O D:CYS46 4.1 39.8 1.0
N D:SER45 4.1 34.5 1.0
N D:GLY42 4.3 35.4 1.0
N D:CYS44 4.5 35.7 1.0
C D:CYS40 4.5 37.5 1.0
C D:SER45 4.6 37.1 1.0
N D:GLY41 4.6 36.6 1.0
N D:CYS43 4.6 36.0 1.0
OG1 D:THR48 4.7 32.0 1.0
SG D:CYS49 4.7 34.0 1.0
SG D:CYS86 4.7 33.1 1.0
N D:LEU39 4.7 42.1 1.0
CA D:GLY42 4.7 34.7 1.0
N D:ALA47 4.7 38.0 1.0
C D:ALA38 4.7 42.5 1.0
CA D:CYS44 4.8 35.3 1.0
N D:THR48 4.9 35.4 1.0
C D:LEU39 4.9 41.0 1.0
CA D:SER45 4.9 35.5 1.0
C D:CYS44 4.9 35.0 1.0
CA D:ALA38 5.0 43.0 1.0

Iron binding site 9 out of 10 in 3lxf

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Iron binding site 9 out of 10 in the Crystal Structure of [2FE-2S] Ferredoxin Arx From Novosphingobium Aromaticivorans


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Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of [2FE-2S] Ferredoxin Arx From Novosphingobium Aromaticivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe500

b:41.8
occ:1.00
 FE1 E:FES500 0.0 41.8 1.0
S2 E:FES500 2.1 43.1 1.0
S1 E:FES500 2.2 39.3 1.0
SG E:CYS86 2.3 43.5 1.0
SG E:CYS49 2.3 43.5 1.0
FE2 E:FES500 2.9 40.8 1.0
CB E:CYS86 3.1 41.7 1.0
CB E:CYS49 3.3 42.7 1.0
CA E:GLY42 4.2 43.8 1.0
CA E:CYS86 4.2 41.8 1.0
N E:CYS86 4.2 41.3 1.0
N E:CYS49 4.4 42.8 1.0
CA E:CYS49 4.4 43.1 1.0
SG E:CYS40 4.5 42.4 1.0
CB E:LEU84 4.6 39.2 1.0
SG E:CYS46 4.6 41.3 1.0
N E:GLY42 4.7 44.7 1.0
N E:CYS44 4.7 41.0 1.0
C E:GLY42 4.8 43.1 1.0
CA E:CYS44 4.9 39.9 1.0
CD2 E:LEU84 4.9 35.1 1.0
O E:CYS46 5.0 41.5 1.0
CD1 E:LEU84 5.0 37.4 1.0

Iron binding site 10 out of 10 in 3lxf

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Iron binding site 10 out of 10 in the Crystal Structure of [2FE-2S] Ferredoxin Arx From Novosphingobium Aromaticivorans


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 [2FE-2S] Ferredoxin Arx From Novosphingobium Aromaticivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe500

b:40.8
occ:1.00
 FE2 E:FES500 0.0 40.8 1.0
S1 E:FES500 2.2 39.3 1.0
S2 E:FES500 2.2 43.1 1.0
SG E:CYS40 2.2 42.4 1.0
SG E:CYS46 2.3 41.3 1.0
FE1 E:FES500 2.9 41.8 1.0
CB E:CYS40 3.4 45.0 1.0
N E:CYS46 3.4 40.0 1.0
CB E:CYS46 3.5 41.6 1.0
N E:CYS40 3.8 46.8 1.0
CA E:CYS46 3.8 40.9 1.0
C E:CYS46 4.0 40.8 1.0
O E:CYS46 4.0 41.5 1.0
CA E:CYS40 4.1 46.1 1.0
N E:SER45 4.1 39.0 1.0
N E:GLY42 4.4 44.7 1.0
N E:CYS44 4.4 41.0 1.0
C E:SER45 4.5 40.0 1.0
C E:CYS40 4.5 46.1 1.0
CA E:GLY42 4.6 43.8 1.0
SG E:CYS86 4.6 43.5 1.0
OG1 E:THR48 4.7 42.1 1.0
N E:GLY41 4.7 46.3 1.0
SG E:CYS49 4.7 43.5 1.0
CA E:CYS44 4.7 39.9 1.0
N E:LEU39 4.7 50.8 1.0
N E:CYS43 4.8 42.9 1.0
N E:ALA47 4.8 41.0 1.0
N E:THR48 4.8 41.8 1.0
C E:ALA38 4.8 52.0 1.0
CA E:SER45 4.9 39.7 1.0
C E:CYS44 4.9 39.7 1.0
C E:LEU39 5.0 49.0 1.0

Reference:

W.Yang, S.G.Bell, H.Wang, W.Zhou, N.Hoskins, A.Dale, M.Bartlam, L.L.Wong, Z.Rao. Molecular Characterization of A Class I P450 Electron Transfer System From Novosphingobium Aromaticivorans DSM12444 J.Biol.Chem. V. 285 27372 2010.
ISSN: ISSN 0021-9258
PubMed: 20576606
DOI: 10.1074/JBC.M110.118349
Page generated: Sun Aug 4 14:33:51 2024

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