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Iron in PDB 1axq: Ferricyanide Oxidized Fdi

Protein crystallography data

The structure of Ferricyanide Oxidized Fdi, PDB code: 1axq was solved by C.D.Stout, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.10
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 55.600, 55.600, 95.800, 90.00, 90.00, 90.00
R / Rfree (%) 25.5 / n/a

Iron Binding Sites:

The binding sites of Iron atom in the Ferricyanide Oxidized Fdi (pdb code 1axq). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 7 binding sites of Iron where determined in the Ferricyanide Oxidized Fdi, PDB code: 1axq:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7;

Iron binding site 1 out of 7 in 1axq

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Iron binding site 1 out of 7 in the Ferricyanide Oxidized Fdi


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Ferricyanide Oxidized Fdi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe107

b:21.3
occ:1.00
 FE1 A:SF4107 0.0 21.3 1.0
S2 A:SF4107 2.2 22.0 1.0
S4 A:SF4107 2.2 19.4 1.0
SG A:CYS39 2.3 16.1 1.0
S3 A:SF4107 2.5 18.8 1.0
FE3 A:SF4107 2.5 23.1 1.0
FE4 A:SF4107 2.8 23.8 1.0
FE2 A:SF4107 2.8 23.0 1.0
CB A:CYS39 3.5 15.6 1.0
CA A:CYS39 3.8 16.6 1.0
N A:ILE40 4.0 17.0 1.0
N A:ASP41 4.0 18.8 1.0
S1 A:SF4107 4.1 19.8 1.0
SG A:CYS24 4.1 15.1 1.0
C A:CYS39 4.3 17.5 1.0
CB A:PHE2 4.4 13.8 1.0
CA A:ASP41 4.5 20.0 1.0
CG2 A:ILE34 4.5 7.2 1.0
N A:CYS42 4.7 19.1 1.0
CD1 A:PHE2 4.7 16.1 1.0
CG A:PHE2 4.8 15.2 1.0
SG A:CYS20 4.9 17.0 1.0
SG A:CYS42 4.9 16.9 1.0
SG A:CYS45 4.9 18.4 1.0
C A:ILE40 4.9 18.7 1.0
N A:PHE2 5.0 17.3 1.0

Iron binding site 2 out of 7 in 1axq

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Iron binding site 2 out of 7 in the Ferricyanide Oxidized Fdi


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Ferricyanide Oxidized Fdi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe107

b:23.0
occ:1.00
 FE2 A:SF4107 0.0 23.0 1.0
SG A:CYS42 2.1 16.9 1.0
S4 A:SF4107 2.5 19.4 1.0
S3 A:SF4107 2.6 18.8 1.0
S1 A:SF4107 2.7 19.8 1.0
FE3 A:SF4107 2.8 23.1 1.0
FE1 A:SF4107 2.8 21.3 1.0
FE4 A:SF4107 3.0 23.8 1.0
CB A:CYS42 3.5 17.2 1.0
N A:CYS42 3.5 19.1 1.0
N A:ALA43 3.7 17.4 1.0
CA A:CYS42 3.9 18.0 1.0
N A:LEU44 4.0 14.6 1.0
C A:CYS42 4.0 18.0 1.0
S2 A:SF4107 4.1 22.0 1.0
CD A:PRO21 4.2 18.9 1.0
C A:ASP41 4.5 19.8 1.0
CA A:ALA43 4.5 15.1 1.0
N A:ASP41 4.6 18.8 1.0
CG1 A:ILE40 4.7 15.8 1.0
CB A:LEU44 4.7 14.3 1.0
C A:ALA43 4.8 15.7 1.0
CA A:ASP41 4.8 20.0 1.0
SG A:CYS39 4.8 16.1 1.0
N A:CYS45 4.8 16.1 1.0
CG A:PRO21 4.8 20.4 1.0
SG A:CYS45 4.9 18.4 1.0
O A:CYS42 4.9 19.8 1.0
SG A:CYS20 4.9 17.0 1.0
CA A:LEU44 4.9 14.4 1.0

Iron binding site 3 out of 7 in 1axq

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Iron binding site 3 out of 7 in the Ferricyanide Oxidized Fdi


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Ferricyanide Oxidized Fdi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe107

b:23.1
occ:1.00
 FE3 A:SF4107 0.0 23.1 1.0
S4 A:SF4107 2.1 19.4 1.0
S2 A:SF4107 2.4 22.0 1.0
SG A:CYS45 2.5 18.4 1.0
FE1 A:SF4107 2.5 21.3 1.0
S1 A:SF4107 2.6 19.8 1.0
FE2 A:SF4107 2.8 23.0 1.0
FE4 A:SF4107 3.0 23.8 1.0
CB A:CYS45 3.5 19.3 1.0
S3 A:SF4107 4.0 18.8 1.0
N A:CYS45 4.2 16.1 1.0
CB A:PHE2 4.2 13.8 1.0
CA A:CYS45 4.4 17.5 1.0
CG A:PHE2 4.5 15.2 1.0
SG A:CYS39 4.5 16.1 1.0
CZ A:PHE25 4.6 9.2 1.0
CE2 A:PHE25 4.6 9.3 1.0
CD1 A:ILE34 4.6 7.2 1.0
SG A:CYS42 4.7 16.9 1.0
N A:LEU44 4.8 14.6 1.0
N A:ALA43 4.9 17.4 1.0
CD2 A:PHE2 4.9 12.5 1.0
SG A:CYS20 4.9 17.0 1.0
CD1 A:PHE2 4.9 16.1 1.0
CA A:ALA43 5.0 15.1 1.0

Iron binding site 4 out of 7 in 1axq

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Iron binding site 4 out of 7 in the Ferricyanide Oxidized Fdi


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Ferricyanide Oxidized Fdi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe107

b:23.8
occ:1.00
 FE4 A:SF4107 0.0 23.8 1.0
SG A:CYS20 2.2 17.0 1.0
S3 A:SF4107 2.3 18.8 1.0
S2 A:SF4107 2.3 22.0 1.0
S1 A:SF4107 2.6 19.8 1.0
FE1 A:SF4107 2.8 21.3 1.0
FE3 A:SF4107 3.0 23.1 1.0
FE2 A:SF4107 3.0 23.0 1.0
CB A:CYS20 3.3 19.1 1.0
SG A:CYS24 3.5 15.1 1.0
CA A:CYS20 3.7 19.7 1.0
CD A:PRO21 4.2 18.9 1.0
S4 A:SF4107 4.2 19.4 1.0
CG2 A:VAL22 4.2 15.6 1.0
CE2 A:PHE25 4.2 9.3 1.0
C A:CYS20 4.4 20.6 1.0
N A:PRO21 4.5 19.9 1.0
SG A:CYS42 4.7 16.9 1.0
CD2 A:PHE25 4.8 11.2 1.0
N A:CYS20 4.9 20.7 1.0
SG A:CYS39 5.0 16.1 1.0
N A:CYS24 5.0 17.5 1.0
N A:VAL22 5.0 21.5 1.0

Iron binding site 5 out of 7 in 1axq

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Iron binding site 5 out of 7 in the Ferricyanide Oxidized Fdi


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Ferricyanide Oxidized Fdi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe108

b:20.6
occ:1.00
 FE1 A:F3S108 0.0 20.6 1.0
S2 A:F3S108 2.0 17.8 1.0
SG A:CYS16 2.2 18.5 1.0
S3 A:F3S108 2.4 18.3 1.0
S1 A:F3S108 2.5 16.7 1.0
FE4 A:F3S108 2.8 20.6 1.0
CB A:CYS16 3.1 19.6 1.0
FE3 A:F3S108 3.1 20.2 1.0
N A:CYS16 3.8 21.0 1.0
CA A:THR14 3.9 20.1 1.0
N A:THR14 3.9 18.1 1.0
CA A:CYS16 4.1 19.8 1.0
CD2 A:LEU32 4.2 10.0 1.0
C A:THR14 4.2 20.3 1.0
N A:ASP15 4.3 21.9 1.0
S4 A:F3S108 4.3 16.9 1.0
CD1 A:ILE54 4.7 8.4 1.0
SG A:CYS49 4.8 13.1 1.0
O A:THR14 4.8 21.5 1.0
CB A:LEU32 4.9 12.0 1.0
CE1 A:PHE25 5.0 10.6 1.0
C A:ASP15 5.0 23.2 1.0

Iron binding site 6 out of 7 in 1axq

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Iron binding site 6 out of 7 in the Ferricyanide Oxidized Fdi


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Ferricyanide Oxidized Fdi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe108

b:20.2
occ:1.00
 FE3 A:F3S108 0.0 20.2 1.0
SG A:CYS8 2.2 12.7 1.0
S3 A:F3S108 2.3 18.3 1.0
S1 A:F3S108 2.4 16.7 1.0
S4 A:F3S108 2.4 16.9 1.0
FE4 A:F3S108 2.9 20.6 1.0
CB A:CYS8 2.9 15.8 1.0
FE1 A:F3S108 3.1 20.6 1.0
CA A:CYS8 3.7 16.4 1.0
S2 A:F3S108 3.8 17.8 1.0
CA A:LYS12 4.0 13.8 1.0
N A:LYS12 4.3 14.6 1.0
N A:TYR13 4.4 15.4 1.0
CG1 A:VAL4 4.4 6.0 1.0
O A:CYS8 4.4 16.7 1.0
C A:CYS8 4.5 16.0 1.0
CB A:LEU32 4.6 12.0 1.0
C A:LYS12 4.6 14.2 1.0
SG A:CYS49 4.7 13.1 1.0
N A:CYS8 4.9 16.4 1.0
N A:LEU32 4.9 12.7 1.0

Iron binding site 7 out of 7 in 1axq

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Iron binding site 7 out of 7 in the Ferricyanide Oxidized Fdi


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Ferricyanide Oxidized Fdi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe108

b:20.6
occ:1.00
 FE4 A:F3S108 0.0 20.6 1.0
S2 A:F3S108 2.1 17.8 1.0
SG A:CYS49 2.2 13.1 1.0
S3 A:F3S108 2.3 18.3 1.0
S4 A:F3S108 2.4 16.9 1.0
FE1 A:F3S108 2.8 20.6 1.0
FE3 A:F3S108 2.9 20.2 1.0
CB A:CYS49 3.2 14.5 1.0
CA A:CYS49 3.7 15.9 1.0
S1 A:F3S108 4.0 16.7 1.0
CD A:PRO50 4.3 14.6 1.0
C A:CYS49 4.4 15.4 1.0
N A:PRO50 4.6 15.5 1.0
CD2 A:TYR13 4.6 15.7 1.0
CB A:ALA51 4.7 13.0 1.0
CB A:ALA53 4.7 14.3 1.0
N A:ALA51 4.8 17.3 1.0
SG A:CYS16 4.8 18.5 1.0
CB A:CYS8 4.8 15.8 1.0
CB A:CYS16 4.8 19.6 1.0
CB A:TYR13 4.9 15.4 1.0
CD1 A:ILE54 4.9 8.4 1.0
SG A:CYS8 4.9 12.7 1.0
CG1 A:ILE54 4.9 9.4 1.0
N A:CYS49 5.0 17.6 1.0

Reference:

V.Sridhar, G.S.Prasad, B.K.Burgess, C.D.Stout. Crystal Structures of Ferricyanide-Oxidized [Fe-S] Clusters in Azotobacter Vinelandii Ferredoxin I. J.Biol.Inorg.Chem. V. 3 140 1998.
ISSN: ISSN 0949-8257
Page generated: Sat Aug 3 02:22:22 2024

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