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Iron in PDB 1d3w: Crystal Structure of Ferredoxin 1 D15E Mutant From Azotobacter Vinelandii at 1.7 Angstrom Resolution.

Protein crystallography data

The structure of Crystal Structure of Ferredoxin 1 D15E Mutant From Azotobacter Vinelandii at 1.7 Angstrom Resolution., PDB code: 1d3w was solved by K.Chen, J.Hirst, R.Camba, C.A.Bonagura, C.D.Stout, B.K.Burges, F.A.Armstrong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 1.70
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 55.370, 55.370, 92.535, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 24.7

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Ferredoxin 1 D15E Mutant From Azotobacter Vinelandii at 1.7 Angstrom Resolution. (pdb code 1d3w). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 7 binding sites of Iron where determined in the Crystal Structure of Ferredoxin 1 D15E Mutant From Azotobacter Vinelandii at 1.7 Angstrom Resolution., PDB code: 1d3w:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7;

Iron binding site 1 out of 7 in 1d3w

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Iron binding site 1 out of 7 in the Crystal Structure of Ferredoxin 1 D15E Mutant From Azotobacter Vinelandii at 1.7 Angstrom 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 Ferredoxin 1 D15E Mutant From Azotobacter Vinelandii at 1.7 Angstrom Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe107

b:18.3
occ:1.00
 FE1 A:SF4107 0.0 18.3 1.0
SG A:CYS39 2.3 12.7 1.0
S4 A:SF4107 2.3 15.3 1.0
S3 A:SF4107 2.3 14.1 1.0
S2 A:SF4107 2.3 15.8 1.0
FE3 A:SF4107 2.7 16.6 1.0
FE2 A:SF4107 2.8 16.8 1.0
FE4 A:SF4107 2.8 17.4 1.0
CB A:CYS39 3.3 15.4 1.0
H A:ASP41 3.3 0.0 1.0
H A:ILE40 3.5 0.0 1.0
H A:CYS42 3.8 0.0 1.0
CA A:CYS39 3.8 15.3 1.0
S1 A:SF4107 3.9 14.2 1.0
H2 A:ALA1 3.9 0.0 1.0
H A:PHE2 4.0 0.0 1.0
SG A:CYS24 4.0 13.3 1.0
N A:ILE40 4.1 14.5 1.0
N A:ASP41 4.1 14.3 1.0
C A:CYS39 4.3 15.3 1.0
H A:ALA43 4.5 0.0 1.0
CB A:PHE2 4.5 11.6 1.0
CG2 A:ILE34 4.5 10.2 1.0
CA A:ASP41 4.6 13.9 1.0
N A:CYS42 4.6 12.4 1.0
H1 A:ALA1 4.7 0.0 1.0
N A:PHE2 4.8 15.1 1.0
N A:ALA1 4.8 22.5 1.0
SG A:CYS45 4.8 14.4 1.0
SG A:CYS20 4.9 16.6 1.0
CD1 A:PHE2 4.9 10.5 1.0
CG A:PHE2 4.9 10.3 1.0
SG A:CYS42 5.0 13.8 1.0

Iron binding site 2 out of 7 in 1d3w

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Iron binding site 2 out of 7 in the Crystal Structure of Ferredoxin 1 D15E Mutant From Azotobacter Vinelandii at 1.7 Angstrom 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 Ferredoxin 1 D15E Mutant From Azotobacter Vinelandii at 1.7 Angstrom Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe107

b:16.8
occ:1.00
 FE2 A:SF4107 0.0 16.8 1.0
S1 A:SF4107 2.3 14.2 1.0
S3 A:SF4107 2.3 14.1 1.0
SG A:CYS42 2.3 13.8 1.0
S4 A:SF4107 2.3 15.3 1.0
FE4 A:SF4107 2.7 17.4 1.0
FE3 A:SF4107 2.7 16.6 1.0
FE1 A:SF4107 2.8 18.3 1.0
H A:CYS42 2.8 0.0 1.0
H A:ALA43 3.5 0.0 1.0
H A:LEU44 3.5 0.0 1.0
CB A:CYS42 3.5 12.1 1.0
N A:CYS42 3.6 12.4 1.0
N A:ALA43 3.9 11.1 1.0
CD A:PRO21 3.9 17.0 1.0
H A:CYS45 3.9 0.0 1.0
CA A:CYS42 3.9 12.1 1.0
S2 A:SF4107 3.9 15.8 1.0
C A:CYS42 4.1 11.5 1.0
N A:LEU44 4.3 11.7 1.0
CG A:PRO21 4.3 19.4 1.0
H A:ILE40 4.4 0.0 1.0
H A:ASP41 4.5 0.0 1.0
C A:ASP41 4.6 13.8 1.0
SG A:CYS20 4.7 16.6 1.0
SG A:CYS45 4.7 14.4 1.0
CA A:ALA43 4.8 11.7 1.0
N A:ASP41 4.8 14.3 1.0
SG A:CYS39 4.8 12.7 1.0
N A:CYS45 4.8 12.7 1.0
CB A:LEU44 4.8 13.7 1.0
CG1 A:ILE40 4.9 15.0 1.0
C A:ALA43 4.9 11.2 1.0
CA A:ASP41 5.0 13.9 1.0

Iron binding site 3 out of 7 in 1d3w

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Iron binding site 3 out of 7 in the Crystal Structure of Ferredoxin 1 D15E Mutant From Azotobacter Vinelandii at 1.7 Angstrom 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 Ferredoxin 1 D15E Mutant From Azotobacter Vinelandii at 1.7 Angstrom Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe107

b:16.6
occ:1.00
 FE3 A:SF4107 0.0 16.6 1.0
SG A:CYS45 2.3 14.4 1.0
S4 A:SF4107 2.3 15.3 1.0
S1 A:SF4107 2.3 14.2 1.0
S2 A:SF4107 2.3 15.8 1.0
FE1 A:SF4107 2.7 18.3 1.0
FE2 A:SF4107 2.7 16.8 1.0
FE4 A:SF4107 2.8 17.4 1.0
H A:CYS45 3.1 0.0 1.0
CB A:CYS45 3.3 13.0 1.0
S3 A:SF4107 3.9 14.1 1.0
N A:CYS45 4.0 12.7 1.0
CA A:CYS45 4.2 13.8 1.0
CZ A:PHE25 4.3 12.3 1.0
CE2 A:PHE25 4.3 12.2 1.0
H A:ALA43 4.5 0.0 1.0
CB A:PHE2 4.5 11.6 1.0
CD1 A:ILE34 4.5 6.7 1.0
H A:LEU44 4.6 0.0 1.0
H A:GLU46 4.6 0.0 1.0
SG A:CYS42 4.7 13.8 1.0
SG A:CYS39 4.7 12.7 1.0
CG A:PHE2 4.8 10.3 1.0
SG A:CYS20 4.8 16.6 1.0
N A:LEU44 4.9 11.7 1.0
N A:ALA43 4.9 11.1 1.0
H A:CYS42 5.0 0.0 1.0

Iron binding site 4 out of 7 in 1d3w

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Iron binding site 4 out of 7 in the Crystal Structure of Ferredoxin 1 D15E Mutant From Azotobacter Vinelandii at 1.7 Angstrom 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 Ferredoxin 1 D15E Mutant From Azotobacter Vinelandii at 1.7 Angstrom Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe107

b:17.4
occ:1.00
 FE4 A:SF4107 0.0 17.4 1.0
SG A:CYS20 2.3 16.6 1.0
S1 A:SF4107 2.3 14.2 1.0
S3 A:SF4107 2.3 14.1 1.0
S2 A:SF4107 2.3 15.8 1.0
FE2 A:SF4107 2.7 16.8 1.0
FE3 A:SF4107 2.8 16.6 1.0
FE1 A:SF4107 2.8 18.3 1.0
CB A:CYS20 3.3 17.2 1.0
SG A:CYS24 3.5 13.3 1.0
CA A:CYS20 3.7 17.7 1.0
S4 A:SF4107 3.9 15.3 1.0
CE2 A:PHE25 4.0 12.2 1.0
H A:VAL22 4.1 0.0 1.0
CD A:PRO21 4.1 17.0 1.0
H A:CYS24 4.1 0.0 1.0
CG2 A:VAL22 4.4 12.4 1.0
C A:CYS20 4.5 17.8 1.0
N A:PRO21 4.5 18.0 1.0
CD2 A:PHE25 4.6 13.1 1.0
SG A:CYS42 4.7 13.8 1.0
H A:ILE40 4.7 0.0 1.0
CG A:PRO21 4.8 19.4 1.0
SG A:CYS45 4.8 14.4 1.0
CZ A:PHE25 4.8 12.3 1.0
N A:CYS20 4.9 18.0 1.0
SG A:CYS39 4.9 12.7 1.0

Iron binding site 5 out of 7 in 1d3w

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Iron binding site 5 out of 7 in the Crystal Structure of Ferredoxin 1 D15E Mutant From Azotobacter Vinelandii at 1.7 Angstrom 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 Ferredoxin 1 D15E Mutant From Azotobacter Vinelandii at 1.7 Angstrom Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe108

b:17.7
occ:1.00
 FE1 A:F3S108 0.0 17.7 1.0
SG A:CYS16 2.3 14.9 1.0
S3 A:F3S108 2.3 14.0 1.0
S2 A:F3S108 2.3 14.6 1.0
S1 A:F3S108 2.3 14.6 1.0
FE4 A:F3S108 2.6 15.9 1.0
FE3 A:F3S108 2.7 16.0 1.0
H A:CYS16 3.1 0.0 1.0
H A:THR14 3.3 0.0 1.0
CB A:CYS16 3.3 15.5 1.0
N A:THR14 3.9 15.8 1.0
S4 A:F3S108 3.9 15.2 1.0
N A:CYS16 4.0 16.3 1.0
H A:GLU15 4.0 0.0 1.0
CA A:THR14 4.1 16.9 1.0
CD1 A:LEU32 4.3 12.5 1.0
CA A:CYS16 4.3 15.0 1.0
N A:GLU15 4.3 19.0 1.0
C A:THR14 4.5 18.2 1.0
H A:TYR13 4.6 0.0 1.0
CG A:LEU32 4.6 14.0 1.0
SG A:CYS49 4.7 14.8 1.0
H A:VAL17 4.7 0.0 1.0
CD1 A:ILE54 4.7 14.8 1.0
SG A:CYS8 4.8 12.8 1.0
CB A:CYS49 4.9 14.1 1.0
CB A:LEU32 4.9 10.9 1.0
N A:TYR13 5.0 12.3 1.0

Iron binding site 6 out of 7 in 1d3w

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Iron binding site 6 out of 7 in the Crystal Structure of Ferredoxin 1 D15E Mutant From Azotobacter Vinelandii at 1.7 Angstrom 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 Ferredoxin 1 D15E Mutant From Azotobacter Vinelandii at 1.7 Angstrom Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe108

b:16.0
occ:1.00
 FE3 A:F3S108 0.0 16.0 1.0
S4 A:F3S108 2.3 15.2 1.0
SG A:CYS8 2.3 12.8 1.0
S3 A:F3S108 2.3 14.0 1.0
S1 A:F3S108 2.3 14.6 1.0
FE4 A:F3S108 2.6 15.9 1.0
FE1 A:F3S108 2.7 17.7 1.0
CB A:CYS8 3.2 10.8 1.0
H A:TYR13 3.6 0.0 1.0
H A:THR14 3.9 0.0 1.0
S2 A:F3S108 3.9 14.6 1.0
CA A:CYS8 3.9 10.0 1.0
CA A:LYS12 3.9 11.7 1.0
H A:LYS12 4.0 0.0 1.0
N A:TYR13 4.3 12.3 1.0
H A:LEU32 4.3 0.0 1.0
N A:LYS12 4.4 11.5 1.0
CG1 A:VAL4 4.5 12.1 1.0
O A:CYS8 4.5 9.8 1.0
C A:LYS12 4.5 12.8 1.0
SG A:CYS49 4.6 14.8 1.0
CB A:LEU32 4.6 10.9 1.0
C A:CYS8 4.6 10.9 1.0
CG A:LEU32 4.6 14.0 1.0
SG A:CYS16 4.8 14.9 1.0
N A:THR14 4.8 15.8 1.0

Iron binding site 7 out of 7 in 1d3w

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Iron binding site 7 out of 7 in the Crystal Structure of Ferredoxin 1 D15E Mutant From Azotobacter Vinelandii at 1.7 Angstrom 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 Ferredoxin 1 D15E Mutant From Azotobacter Vinelandii at 1.7 Angstrom Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe108

b:15.9
occ:1.00
 FE4 A:F3S108 0.0 15.9 1.0
SG A:CYS49 2.3 14.8 1.0
S2 A:F3S108 2.3 14.6 1.0
S4 A:F3S108 2.3 15.2 1.0
S3 A:F3S108 2.3 14.0 1.0
FE3 A:F3S108 2.6 16.0 1.0
FE1 A:F3S108 2.6 17.7 1.0
CB A:CYS49 3.2 14.1 1.0
H A:ALA51 3.8 0.0 1.0
CA A:CYS49 3.8 13.6 1.0
S1 A:F3S108 3.9 14.6 1.0
H A:TYR13 4.1 0.0 1.0
H A:ALA53 4.3 0.0 1.0
H A:THR14 4.3 0.0 1.0
CD A:PRO50 4.4 10.3 1.0
C A:CYS49 4.5 12.9 1.0
CB A:ALA51 4.5 10.4 1.0
CD2 A:TYR13 4.6 12.9 1.0
SG A:CYS8 4.6 12.8 1.0
N A:PRO50 4.7 11.5 1.0
SG A:CYS16 4.7 14.9 1.0
N A:ALA51 4.7 11.9 1.0
H A:CYS16 4.7 0.0 1.0
CB A:ALA53 4.8 14.9 1.0
H A:GLU15 4.8 0.0 1.0
CB A:TYR13 4.8 11.7 1.0
CB A:CYS8 4.8 10.8 1.0
N A:TYR13 4.9 12.3 1.0
CB A:CYS16 5.0 15.5 1.0

Reference:

K.Chen, J.Hirst, R.Camba, C.A.Bonagura, C.D.Stout, B.K.Burgess, F.A.Armstrong. Atomically Defined Mechanism For Proton Transfer to A Buried Redox Centre in A Protein. Nature V. 405 814 2000.
ISSN: ISSN 0028-0836
PubMed: 10866206
DOI: 10.1038/35015610
Page generated: Sun Dec 13 14:10:04 2020

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