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Iron in PDB 1frm: Azotobacter Vinelandii Ferredoxin I: Alteration of Individual Surface Charges and the [4FE-4S] Cluster Reduction Potential

Protein crystallography data

The structure of Azotobacter Vinelandii Ferredoxin I: Alteration of Individual Surface Charges and the [4FE-4S] Cluster Reduction Potential, PDB code: 1frm 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 / 2.30
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 55.260, 55.260, 95.340, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / n/a

Iron Binding Sites:

The binding sites of Iron atom in the Azotobacter Vinelandii Ferredoxin I: Alteration of Individual Surface Charges and the [4FE-4S] Cluster Reduction Potential (pdb code 1frm). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 7 binding sites of Iron where determined in the Azotobacter Vinelandii Ferredoxin I: Alteration of Individual Surface Charges and the [4FE-4S] Cluster Reduction Potential, PDB code: 1frm:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7;

Iron binding site 1 out of 7 in 1frm

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Iron binding site 1 out of 7 in the Azotobacter Vinelandii Ferredoxin I: Alteration of Individual Surface Charges and the [4FE-4S] Cluster Reduction Potential


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Azotobacter Vinelandii Ferredoxin I: Alteration of Individual Surface Charges and the [4FE-4S] Cluster Reduction Potential 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 2.3 15.5 1.0
S2 A:SF4107 2.3 17.7 1.0
S3 A:SF4107 2.3 15.3 1.0
SG A:CYS39 2.3 15.7 1.0
FE3 A:SF4107 2.6 14.9 1.0
FE4 A:SF4107 2.7 15.7 1.0
FE2 A:SF4107 2.7 15.5 1.0
CB A:CYS39 3.4 14.1 1.0
S1 A:SF4107 3.8 17.0 1.0
CA A:CYS39 3.8 16.3 1.0
N A:ILE40 4.1 15.3 1.0
N A:ASP41 4.1 16.4 1.0
SG A:CYS24 4.1 14.8 1.0
C A:CYS39 4.4 15.7 1.0
CB A:PHE2 4.5 11.2 1.0
CG2 A:ILE34 4.5 9.4 1.0
CA A:ASP41 4.6 16.5 1.0
SG A:CYS45 4.7 16.9 1.0
SG A:CYS20 4.8 17.3 1.0
N A:CYS42 4.8 15.0 1.0
CD1 A:PHE2 4.9 11.0 1.0
N A:PHE2 4.9 11.8 1.0
CG A:PHE2 4.9 11.3 1.0
SG A:CYS42 5.0 15.8 1.0
C A:ILE40 5.0 16.3 1.0

Iron binding site 2 out of 7 in 1frm

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Iron binding site 2 out of 7 in the Azotobacter Vinelandii Ferredoxin I: Alteration of Individual Surface Charges and the [4FE-4S] Cluster Reduction Potential


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Azotobacter Vinelandii Ferredoxin I: Alteration of Individual Surface Charges and the [4FE-4S] Cluster Reduction Potential within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe107

b:15.5
occ:1.00
 FE2 A:SF4107 0.0 15.5 1.0
S1 A:SF4107 2.2 17.0 1.0
S3 A:SF4107 2.3 15.3 1.0
S4 A:SF4107 2.3 15.5 1.0
SG A:CYS42 2.3 15.8 1.0
FE4 A:SF4107 2.6 15.7 1.0
FE3 A:SF4107 2.7 14.9 1.0
FE1 A:SF4107 2.7 15.4 1.0
CB A:CYS42 3.6 13.6 1.0
N A:CYS42 3.6 15.0 1.0
N A:ALA43 3.9 13.1 1.0
S2 A:SF4107 3.9 17.7 1.0
CA A:CYS42 4.0 13.9 1.0
C A:CYS42 4.2 13.9 1.0
CD A:PRO21 4.3 16.2 1.0
N A:LEU44 4.3 13.3 1.0
N A:ASP41 4.5 16.4 1.0
C A:ASP41 4.6 15.3 1.0
SG A:CYS39 4.6 15.7 1.0
SG A:CYS45 4.6 16.9 1.0
SG A:CYS20 4.6 17.3 1.0
CG A:PRO21 4.7 14.7 1.0
CA A:ALA43 4.7 12.2 1.0
CA A:ASP41 4.8 16.5 1.0
CG1 A:ILE40 4.8 10.7 1.0
CB A:LEU44 4.9 13.2 1.0
N A:ILE40 4.9 15.3 1.0
N A:CYS45 5.0 15.7 1.0
C A:ALA43 5.0 12.9 1.0

Iron binding site 3 out of 7 in 1frm

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Iron binding site 3 out of 7 in the Azotobacter Vinelandii Ferredoxin I: Alteration of Individual Surface Charges and the [4FE-4S] Cluster Reduction Potential


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Azotobacter Vinelandii Ferredoxin I: Alteration of Individual Surface Charges and the [4FE-4S] Cluster Reduction Potential within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe107

b:14.9
occ:1.00
 FE3 A:SF4107 0.0 14.9 1.0
S4 A:SF4107 2.2 15.5 1.0
S2 A:SF4107 2.3 17.7 1.0
SG A:CYS45 2.3 16.9 1.0
S1 A:SF4107 2.3 17.0 1.0
FE1 A:SF4107 2.6 15.4 1.0
FE2 A:SF4107 2.7 15.5 1.0
FE4 A:SF4107 2.7 15.7 1.0
CB A:CYS45 3.4 16.7 1.0
S3 A:SF4107 3.9 15.3 1.0
N A:CYS45 4.1 15.7 1.0
CA A:CYS45 4.3 16.5 1.0
CB A:PHE2 4.5 11.2 1.0
CZ A:PHE25 4.5 9.9 1.0
CD1 A:ILE34 4.5 9.7 1.0
CE1 A:PHE25 4.6 11.4 1.0
SG A:CYS42 4.6 15.8 1.0
SG A:CYS39 4.6 15.7 1.0
CG A:PHE2 4.7 11.3 1.0
N A:LEU44 4.8 13.3 1.0
SG A:CYS20 4.8 17.3 1.0
N A:ALA43 4.9 13.1 1.0

Iron binding site 4 out of 7 in 1frm

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Iron binding site 4 out of 7 in the Azotobacter Vinelandii Ferredoxin I: Alteration of Individual Surface Charges and the [4FE-4S] Cluster Reduction Potential


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Azotobacter Vinelandii Ferredoxin I: Alteration of Individual Surface Charges and the [4FE-4S] Cluster Reduction Potential within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe107

b:15.7
occ:1.00
 FE4 A:SF4107 0.0 15.7 1.0
S1 A:SF4107 2.3 17.0 1.0
S3 A:SF4107 2.3 15.3 1.0
SG A:CYS20 2.3 17.3 1.0
S2 A:SF4107 2.3 17.7 1.0
FE2 A:SF4107 2.6 15.5 1.0
FE1 A:SF4107 2.7 15.4 1.0
FE3 A:SF4107 2.7 14.9 1.0
CB A:CYS20 3.4 15.4 1.0
SG A:CYS24 3.7 14.8 1.0
CA A:CYS20 3.7 18.0 1.0
S4 A:SF4107 3.9 15.5 1.0
CE1 A:PHE25 4.3 11.4 1.0
CD A:PRO21 4.4 16.2 1.0
C A:CYS20 4.5 17.7 1.0
N A:PRO21 4.5 16.8 1.0
CG2 A:VAL22 4.5 13.9 1.0
SG A:CYS42 4.6 15.8 1.0
SG A:CYS45 4.7 16.9 1.0
SG A:CYS39 4.9 15.7 1.0
N A:CYS20 4.9 18.6 1.0
CZ A:PHE25 5.0 9.9 1.0
CD1 A:PHE25 5.0 9.7 1.0

Iron binding site 5 out of 7 in 1frm

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Iron binding site 5 out of 7 in the Azotobacter Vinelandii Ferredoxin I: Alteration of Individual Surface Charges and the [4FE-4S] Cluster Reduction Potential


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Azotobacter Vinelandii Ferredoxin I: Alteration of Individual Surface Charges and the [4FE-4S] Cluster Reduction Potential within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe108

b:15.4
occ:1.00
 FE1 A:F3S108 0.0 15.4 1.0
S2 A:F3S108 2.2 16.7 1.0
S3 A:F3S108 2.3 15.9 1.0
SG A:CYS16 2.3 17.6 1.0
S1 A:F3S108 2.3 16.2 1.0
FE4 A:F3S108 2.6 17.2 1.0
FE3 A:F3S108 2.7 19.8 1.0
CB A:CYS16 3.4 19.4 1.0
S4 A:F3S108 4.0 14.8 1.0
N A:CYS16 4.1 20.4 1.0
CA A:THR14 4.1 17.7 1.0
N A:THR14 4.1 16.4 1.0
CD2 A:LEU32 4.3 10.7 1.0
CA A:CYS16 4.3 19.9 1.0
C A:THR14 4.5 18.9 1.0
SG A:CYS49 4.6 15.4 1.0
N A:ASP15 4.7 19.0 1.0
CD1 A:ILE54 4.7 8.4 1.0
SG A:CYS8 4.8 12.7 1.0
CB A:LEU32 4.9 10.7 1.0
N A:TYR13 4.9 16.6 1.0
CE2 A:PHE25 5.0 11.6 1.0
O A:THR14 5.0 19.0 1.0

Iron binding site 6 out of 7 in 1frm

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Iron binding site 6 out of 7 in the Azotobacter Vinelandii Ferredoxin I: Alteration of Individual Surface Charges and the [4FE-4S] Cluster Reduction Potential


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Azotobacter Vinelandii Ferredoxin I: Alteration of Individual Surface Charges and the [4FE-4S] Cluster Reduction Potential within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe108

b:19.8
occ:1.00
 FE3 A:F3S108 0.0 19.8 1.0
S3 A:F3S108 2.3 15.9 1.0
S4 A:F3S108 2.3 14.8 1.0
SG A:CYS8 2.3 12.7 1.0
S1 A:F3S108 2.3 16.2 1.0
FE4 A:F3S108 2.6 17.2 1.0
FE1 A:F3S108 2.7 15.4 1.0
CB A:CYS8 3.3 14.2 1.0
S2 A:F3S108 3.8 16.7 1.0
CA A:CYS8 3.9 14.5 1.0
CA A:LYS12 4.1 14.3 1.0
N A:TYR13 4.3 16.6 1.0
N A:LYS12 4.4 14.6 1.0
CG1 A:VAL4 4.6 8.1 1.0
SG A:CYS49 4.6 15.4 1.0
O A:CYS8 4.6 14.5 1.0
CB A:LEU32 4.7 10.7 1.0
C A:CYS8 4.7 14.1 1.0
C A:LYS12 4.7 15.6 1.0
SG A:CYS16 4.9 17.6 1.0
N A:THR14 5.0 16.4 1.0

Iron binding site 7 out of 7 in 1frm

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Iron binding site 7 out of 7 in the Azotobacter Vinelandii Ferredoxin I: Alteration of Individual Surface Charges and the [4FE-4S] Cluster Reduction Potential


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Azotobacter Vinelandii Ferredoxin I: Alteration of Individual Surface Charges and the [4FE-4S] Cluster Reduction Potential within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe108

b:17.2
occ:1.00
 FE4 A:F3S108 0.0 17.2 1.0
S2 A:F3S108 2.2 16.7 1.0
S3 A:F3S108 2.3 15.9 1.0
SG A:CYS49 2.3 15.4 1.0
S4 A:F3S108 2.3 14.8 1.0
FE3 A:F3S108 2.6 19.8 1.0
FE1 A:F3S108 2.6 15.4 1.0
CB A:CYS49 3.4 16.6 1.0
S1 A:F3S108 3.8 16.2 1.0
CA A:CYS49 3.9 18.0 1.0
CD A:PRO50 4.3 14.9 1.0
C A:CYS49 4.5 17.7 1.0
N A:PRO50 4.6 16.1 1.0
CD2 A:TYR13 4.6 15.0 1.0
CB A:ALA51 4.6 13.5 1.0
SG A:CYS8 4.6 12.7 1.0
CB A:ALA53 4.7 10.8 1.0
SG A:CYS16 4.7 17.6 1.0
N A:ALA51 4.7 16.8 1.0
CB A:TYR13 4.8 15.1 1.0
CB A:CYS8 4.9 14.2 1.0
N A:TYR13 4.9 16.6 1.0

Reference:

B.Shen, D.R.Jollie, C.D.Stout, T.C.Diller, F.A.Armstrong, C.M.Gorst, G.N.La Mar, P.J.Stephens, B.K.Burgess. Azotobacter Vinelandii Ferredoxin I. Alteration of Individual Surface Charges and the [4FE-4S]2+/+ Cluster Reduction Potential. J.Biol.Chem. V. 269 8564 1994.
ISSN: ISSN 0021-9258
PubMed: 8132582
Page generated: Sat Aug 3 05:18:09 2024

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