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Iron in PDB 1fd2: Site-Directed Mutagenesis of Azotobacter Vinelandii Ferredoxin I. (Fe-S) Cluster-Driven Protein Rearrangement

Protein crystallography data

The structure of Site-Directed Mutagenesis of Azotobacter Vinelandii Ferredoxin I. (Fe-S) Cluster-Driven Protein Rearrangement, PDB code: 1fd2 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 / 1.90
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 55.000, 55.000, 95.400, 90.00, 90.00, 90.00
R / Rfree (%) 23.2 / n/a

Iron Binding Sites:

The binding sites of Iron atom in the Site-Directed Mutagenesis of Azotobacter Vinelandii Ferredoxin I. (Fe-S) Cluster-Driven Protein Rearrangement (pdb code 1fd2). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 7 binding sites of Iron where determined in the Site-Directed Mutagenesis of Azotobacter Vinelandii Ferredoxin I. (Fe-S) Cluster-Driven Protein Rearrangement, PDB code: 1fd2:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7;

Iron binding site 1 out of 7 in 1fd2

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Iron binding site 1 out of 7 in the Site-Directed Mutagenesis of Azotobacter Vinelandii Ferredoxin I. (Fe-S) Cluster-Driven Protein Rearrangement


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Site-Directed Mutagenesis of Azotobacter Vinelandii Ferredoxin I. (Fe-S) Cluster-Driven Protein Rearrangement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe107

b:15.4
occ:1.00
 FE1 A:SF4107 0.0 15.4 1.0
S4 A:SF4107 2.2 9.7 1.0
S2 A:SF4107 2.3 14.9 1.0
SG A:CYS39 2.3 10.5 1.0
S3 A:SF4107 2.3 10.1 1.0
FE3 A:SF4107 2.6 16.2 1.0
FE4 A:SF4107 2.6 14.1 1.0
FE2 A:SF4107 2.7 13.9 1.0
CB A:CYS39 3.3 11.6 1.0
CA A:CYS39 3.7 13.6 1.0
S1 A:SF4107 3.9 12.6 1.0
N A:ASP41 3.9 13.0 1.0
N A:ILE40 4.1 13.2 1.0
CB A:PHE2 4.3 9.9 1.0
C A:CYS39 4.3 14.1 1.0
CA A:ASP41 4.3 14.3 1.0
CB A:CYS24 4.4 12.8 1.0
CG2 A:ILE34 4.5 4.4 1.0
CD1 A:PHE2 4.5 11.6 1.0
N A:CYS42 4.5 14.2 1.0
SG A:CYS24 4.5 12.6 1.0
CG A:PHE2 4.6 9.4 1.0
SG A:CYS45 4.7 11.1 1.0
C A:ILE40 4.8 15.6 1.0
N A:PHE2 4.9 13.7 1.0
SG A:CYS42 4.9 10.2 1.0
C A:ASP41 4.9 14.9 1.0
N A:CYS39 5.0 14.3 1.0

Iron binding site 2 out of 7 in 1fd2

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Iron binding site 2 out of 7 in the Site-Directed Mutagenesis of Azotobacter Vinelandii Ferredoxin I. (Fe-S) Cluster-Driven Protein Rearrangement


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Site-Directed Mutagenesis of Azotobacter Vinelandii Ferredoxin I. (Fe-S) Cluster-Driven Protein Rearrangement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe107

b:13.9
occ:1.00
 FE2 A:SF4107 0.0 13.9 1.0
S1 A:SF4107 2.3 12.6 1.0
S3 A:SF4107 2.3 10.1 1.0
SG A:CYS42 2.3 10.2 1.0
S4 A:SF4107 2.4 9.7 1.0
FE3 A:SF4107 2.6 16.2 1.0
FE4 A:SF4107 2.6 14.1 1.0
FE1 A:SF4107 2.7 15.4 1.0
CB A:CYS42 3.4 9.0 1.0
N A:CYS42 3.6 14.2 1.0
S2 A:SF4107 3.9 14.9 1.0
N A:ALA43 3.9 12.6 1.0
CD A:PRO21 4.0 14.7 1.0
CA A:CYS42 4.0 13.1 1.0
C A:CYS42 4.3 12.7 1.0
CG A:PRO21 4.4 14.0 1.0
N A:LEU44 4.4 13.1 1.0
SG A:CYS45 4.6 11.1 1.0
C A:ASP41 4.7 14.9 1.0
SG A:CYS39 4.7 10.5 1.0
CG1 A:ILE40 4.7 14.4 1.0
N A:ASP41 4.7 13.0 1.0
SG A:CYS24 4.8 12.6 1.0
CA A:ALA43 4.8 10.4 1.0
CA A:ASP41 4.9 14.3 1.0
N A:CYS45 5.0 13.9 1.0
N A:ILE40 5.0 13.2 1.0

Iron binding site 3 out of 7 in 1fd2

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Iron binding site 3 out of 7 in the Site-Directed Mutagenesis of Azotobacter Vinelandii Ferredoxin I. (Fe-S) Cluster-Driven Protein Rearrangement


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Site-Directed Mutagenesis of Azotobacter Vinelandii Ferredoxin I. (Fe-S) Cluster-Driven Protein Rearrangement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe107

b:16.2
occ:1.00
 FE3 A:SF4107 0.0 16.2 1.0
S2 A:SF4107 2.3 14.9 1.0
S4 A:SF4107 2.3 9.7 1.0
SG A:CYS45 2.3 11.1 1.0
S1 A:SF4107 2.3 12.6 1.0
FE1 A:SF4107 2.6 15.4 1.0
FE2 A:SF4107 2.6 13.9 1.0
FE4 A:SF4107 2.7 14.1 1.0
CB A:CYS45 3.3 10.5 1.0
S3 A:SF4107 3.8 10.1 1.0
N A:CYS45 4.2 13.9 1.0
CE1 A:PHE25 4.3 11.0 1.0
CZ A:PHE25 4.4 13.2 1.0
CB A:PHE2 4.4 9.9 1.0
CA A:CYS45 4.4 13.9 1.0
SG A:CYS42 4.5 10.2 1.0
CG A:PHE2 4.6 9.4 1.0
CD1 A:ILE34 4.6 2.0 1.0
SG A:CYS39 4.7 10.5 1.0
SG A:CYS24 4.7 12.6 1.0
N A:ALA43 4.8 12.6 1.0
CD2 A:PHE2 4.9 9.2 1.0
N A:LEU44 5.0 13.1 1.0

Iron binding site 4 out of 7 in 1fd2

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Iron binding site 4 out of 7 in the Site-Directed Mutagenesis of Azotobacter Vinelandii Ferredoxin I. (Fe-S) Cluster-Driven Protein Rearrangement


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Site-Directed Mutagenesis of Azotobacter Vinelandii Ferredoxin I. (Fe-S) Cluster-Driven Protein Rearrangement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe107

b:14.1
occ:1.00
 FE4 A:SF4107 0.0 14.1 1.0
S1 A:SF4107 2.3 12.6 1.0
SG A:CYS24 2.3 12.6 1.0
S3 A:SF4107 2.3 10.1 1.0
S2 A:SF4107 2.3 14.9 1.0
FE2 A:SF4107 2.6 13.9 1.0
FE1 A:SF4107 2.6 15.4 1.0
FE3 A:SF4107 2.7 16.2 1.0
CB A:CYS24 3.1 12.8 1.0
S4 A:SF4107 3.9 9.7 1.0
CB A:ALA20 4.1 14.4 1.0
CE1 A:PHE25 4.1 11.0 1.0
CD A:PRO21 4.5 14.7 1.0
CD1 A:PHE25 4.5 13.6 1.0
CA A:CYS24 4.6 13.8 1.0
CA A:ALA20 4.6 12.8 1.0
CG2 A:VAL22 4.7 16.8 1.0
SG A:CYS39 4.7 10.5 1.0
SG A:CYS42 4.7 10.2 1.0
SG A:CYS45 4.7 11.1 1.0
CZ A:PHE25 4.8 13.2 1.0
CA A:CYS39 4.9 13.6 1.0
N A:CYS24 4.9 14.7 1.0
O A:VAL22 5.0 20.4 1.0

Iron binding site 5 out of 7 in 1fd2

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Iron binding site 5 out of 7 in the Site-Directed Mutagenesis of Azotobacter Vinelandii Ferredoxin I. (Fe-S) Cluster-Driven Protein Rearrangement


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Site-Directed Mutagenesis of Azotobacter Vinelandii Ferredoxin I. (Fe-S) Cluster-Driven Protein Rearrangement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe108

b:13.7
occ:1.00
 FE1 A:F3S108 0.0 13.7 1.0
S2 A:F3S108 2.2 13.4 1.0
SG A:CYS16 2.3 14.1 1.0
S1 A:F3S108 2.3 9.5 1.0
S3 A:F3S108 2.3 12.7 1.0
FE4 A:F3S108 2.6 13.7 1.0
FE3 A:F3S108 2.7 10.9 1.0
CB A:CYS16 3.2 12.4 1.0
S4 A:F3S108 3.9 10.5 1.0
N A:CYS16 3.9 13.9 1.0
N A:THR14 4.0 11.9 1.0
CA A:THR14 4.1 14.8 1.0
CA A:CYS16 4.2 12.0 1.0
N A:ASP15 4.5 19.6 1.0
C A:THR14 4.5 17.4 1.0
CD1 A:LEU32 4.5 19.0 1.0
SG A:CYS49 4.6 11.9 1.0
CD1 A:ILE54 4.6 13.8 1.0
CG A:LEU32 4.8 17.6 1.0
SG A:CYS8 4.8 9.4 1.0
CB A:CYS49 4.8 9.1 1.0
N A:TYR13 5.0 13.5 1.0

Iron binding site 6 out of 7 in 1fd2

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Iron binding site 6 out of 7 in the Site-Directed Mutagenesis of Azotobacter Vinelandii Ferredoxin I. (Fe-S) Cluster-Driven Protein Rearrangement


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Site-Directed Mutagenesis of Azotobacter Vinelandii Ferredoxin I. (Fe-S) Cluster-Driven Protein Rearrangement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe108

b:10.9
occ:1.00
 FE3 A:F3S108 0.0 10.9 1.0
SG A:CYS8 2.3 9.4 1.0
S3 A:F3S108 2.3 12.7 1.0
S1 A:F3S108 2.3 9.5 1.0
S4 A:F3S108 2.3 10.5 1.0
FE4 A:F3S108 2.6 13.7 1.0
FE1 A:F3S108 2.7 13.7 1.0
CB A:CYS8 3.2 6.8 1.0
CA A:CYS8 3.8 9.2 1.0
S2 A:F3S108 3.9 13.4 1.0
CA A:LYS12 4.0 9.5 1.0
N A:TYR13 4.3 13.5 1.0
CG1 A:VAL4 4.3 2.0 1.0
N A:LYS12 4.4 9.4 1.0
C A:LYS12 4.5 12.3 1.0
SG A:CYS49 4.6 11.9 1.0
O A:CYS8 4.6 10.2 1.0
C A:CYS8 4.7 10.4 1.0
SG A:CYS16 4.8 14.1 1.0
N A:THR14 4.9 11.9 1.0
CG A:LEU32 4.9 17.6 1.0
CB A:LEU32 4.9 12.5 1.0
N A:LEU32 4.9 6.4 1.0
CB A:ALA53 4.9 8.5 1.0
N A:CYS8 4.9 11.0 1.0

Iron binding site 7 out of 7 in 1fd2

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Iron binding site 7 out of 7 in the Site-Directed Mutagenesis of Azotobacter Vinelandii Ferredoxin I. (Fe-S) Cluster-Driven Protein Rearrangement


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Site-Directed Mutagenesis of Azotobacter Vinelandii Ferredoxin I. (Fe-S) Cluster-Driven Protein Rearrangement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe108

b:13.7
occ:1.00
 FE4 A:F3S108 0.0 13.7 1.0
S3 A:F3S108 2.2 12.7 1.0
SG A:CYS49 2.3 11.9 1.0
S4 A:F3S108 2.3 10.5 1.0
S2 A:F3S108 2.3 13.4 1.0
FE3 A:F3S108 2.6 10.9 1.0
FE1 A:F3S108 2.6 13.7 1.0
CB A:CYS49 3.3 9.1 1.0
S1 A:F3S108 3.8 9.5 1.0
CA A:CYS49 3.8 10.0 1.0
CD A:PRO50 4.2 11.5 1.0
C A:CYS49 4.5 9.6 1.0
CB A:ALA53 4.5 8.5 1.0
N A:PRO50 4.6 12.2 1.0
CB A:ALA51 4.6 12.0 1.0
SG A:CYS16 4.6 14.1 1.0
SG A:CYS8 4.6 9.4 1.0
N A:ALA51 4.7 17.1 1.0
N A:TYR13 4.8 13.5 1.0
CB A:CYS8 4.8 6.8 1.0
CB A:CYS16 4.8 12.4 1.0
CD2 A:TYR13 4.9 12.4 1.0
CB A:TYR13 4.9 12.4 1.0
N A:CYS49 5.0 11.1 1.0

Reference:

A.E.Martin, B.K.Burgess, C.D.Stout, V.L.Cash, D.R.Dean, G.M.Jensen, P.J.Stephens. Site-Directed Mutagenesis of Azotobacter Vinelandii Ferredoxin I: [Fe-S] Cluster-Driven Protein Rearrangement. Proc.Natl.Acad.Sci.Usa V. 87 598 1990.
ISSN: ISSN 0027-8424
PubMed: 2153958
DOI: 10.1073/PNAS.87.2.598
Page generated: Sat Aug 3 04:50:22 2024

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