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Iron in PDB 3w5u: Cross-Linked Complex Between Ferredoxin and Ferredoxin-Nadp+ Reductase

Protein crystallography data

The structure of Cross-Linked Complex Between Ferredoxin and Ferredoxin-Nadp+ Reductase, PDB code: 3w5u was solved by Y.Kimata-Ariga, H.Kubota-Kawai, N.Muraki, T.Hase, G.Kurisu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.46 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.202, 153.634, 100.107, 90.00, 99.42, 90.00
R / Rfree (%) 22.6 / 28

Iron Binding Sites:

The binding sites of Iron atom in the Cross-Linked Complex Between Ferredoxin and Ferredoxin-Nadp+ Reductase (pdb code 3w5u). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Cross-Linked Complex Between Ferredoxin and Ferredoxin-Nadp+ Reductase, PDB code: 3w5u:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 3w5u

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Iron binding site 1 out of 8 in the Cross-Linked Complex Between Ferredoxin and Ferredoxin-Nadp+ Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cross-Linked Complex Between Ferredoxin and Ferredoxin-Nadp+ Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe101

b:20.6
occ:1.00
 FE1 B:FES101 0.0 20.6 1.0
SG B:CYS77 2.2 21.2 1.0
SG B:CYS47 2.2 25.9 1.0
S2 B:FES101 2.2 25.8 1.0
S1 B:FES101 2.2 20.7 1.0
FE2 B:FES101 3.1 19.1 1.0
CB B:CYS77 3.1 21.3 1.0
CB B:CYS47 3.3 27.0 1.0
N B:CYS77 4.1 23.4 1.0
CA B:CYS77 4.2 22.3 1.0
N B:CYS47 4.3 26.4 1.0
SG B:CYS39 4.3 20.6 1.0
CA B:ARG40 4.3 18.6 1.0
N B:GLY42 4.3 19.3 1.0
N B:ARG40 4.4 19.9 1.0
CA B:CYS47 4.4 22.8 1.0
N B:ALA41 4.5 19.2 1.0
CB B:LEU75 4.7 28.5 1.0
CD2 B:LEU75 4.7 27.4 1.0
CA B:GLY42 4.7 19.2 1.0
C B:ARG40 4.7 19.3 1.0
C B:CYS77 4.9 22.2 1.0
O B:CYS44 4.9 22.8 1.0
SG B:CYS44 4.9 17.5 1.0
N B:HIS78 5.0 22.9 1.0

Iron binding site 2 out of 8 in 3w5u

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Iron binding site 2 out of 8 in the Cross-Linked Complex Between Ferredoxin and Ferredoxin-Nadp+ Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cross-Linked Complex Between Ferredoxin and Ferredoxin-Nadp+ Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe101

b:19.1
occ:1.00
 FE2 B:FES101 0.0 19.1 1.0
SG B:CYS44 2.1 17.5 1.0
S2 B:FES101 2.2 25.8 1.0
S1 B:FES101 2.2 20.7 1.0
SG B:CYS39 2.3 20.6 1.0
FE1 B:FES101 3.1 20.6 1.0
CB B:CYS39 3.4 18.3 1.0
CB B:CYS44 3.4 21.1 1.0
N B:CYS39 3.6 21.0 1.0
N B:CYS44 3.6 22.3 1.0
CA B:CYS44 3.8 22.9 1.0
N B:ARG40 3.8 19.9 1.0
O B:CYS44 3.9 22.8 1.0
CA B:CYS39 3.9 20.3 1.0
C B:CYS44 3.9 24.1 1.0
C B:CYS39 4.4 20.3 1.0
N B:SER46 4.4 26.3 1.0
CB B:SER46 4.4 24.2 1.0
N B:SER43 4.5 21.5 1.0
N B:ALA41 4.5 19.2 1.0
N B:GLY42 4.6 19.3 1.0
C B:SER43 4.6 21.6 1.0
C B:SER38 4.6 20.8 1.0
SG B:CYS77 4.7 21.2 1.0
N B:SER38 4.7 18.6 1.0
CA B:ARG40 4.7 18.6 1.0
N B:SER45 4.7 23.0 1.0
SG B:CYS47 4.7 25.9 1.0
CB B:SER38 4.8 18.6 1.0
CA B:SER46 4.9 26.2 1.0
N B:CYS47 4.9 26.4 1.0
CA B:SER38 4.9 20.0 1.0

Iron binding site 3 out of 8 in 3w5u

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Iron binding site 3 out of 8 in the Cross-Linked Complex Between Ferredoxin and Ferredoxin-Nadp+ Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cross-Linked Complex Between Ferredoxin and Ferredoxin-Nadp+ Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe101

b:23.6
occ:1.00
 FE1 D:FES101 0.0 23.6 1.0
S2 D:FES101 2.1 23.7 1.0
SG D:CYS77 2.2 20.1 1.0
S1 D:FES101 2.2 21.1 1.0
SG D:CYS47 2.2 23.4 1.0
FE2 D:FES101 2.9 21.2 1.0
CB D:CYS47 3.2 22.0 1.0
CB D:CYS77 3.3 19.7 1.0
N D:CYS47 4.1 21.4 1.0
N D:CYS77 4.2 20.3 1.0
CA D:CYS47 4.3 20.9 1.0
CA D:CYS77 4.3 19.4 1.0
SG D:CYS39 4.4 27.1 1.0
CA D:ARG40 4.4 23.4 1.0
N D:GLY42 4.4 22.4 1.0
N D:ARG40 4.4 23.9 1.0
CB D:LEU75 4.5 24.9 1.0
CD2 D:LEU75 4.6 27.2 1.0
N D:ALA41 4.7 21.2 1.0
O D:CYS44 4.7 27.8 1.0
CA D:GLY42 4.7 18.5 1.0
SG D:CYS44 4.7 25.2 1.0
C D:ARG40 4.9 22.9 1.0

Iron binding site 4 out of 8 in 3w5u

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Iron binding site 4 out of 8 in the Cross-Linked Complex Between Ferredoxin and Ferredoxin-Nadp+ Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cross-Linked Complex Between Ferredoxin and Ferredoxin-Nadp+ Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe101

b:21.2
occ:1.00
 FE2 D:FES101 0.0 21.2 1.0
S2 D:FES101 2.2 23.7 1.0
SG D:CYS44 2.2 25.2 1.0
S1 D:FES101 2.3 21.1 1.0
SG D:CYS39 2.3 27.1 1.0
FE1 D:FES101 2.9 23.6 1.0
CB D:CYS39 3.4 25.0 1.0
N D:CYS39 3.5 25.7 1.0
CB D:CYS44 3.6 25.8 1.0
N D:CYS44 3.7 26.0 1.0
N D:ARG40 3.7 23.9 1.0
CA D:CYS39 3.9 24.4 1.0
CA D:CYS44 4.0 27.1 1.0
O D:CYS44 4.0 27.8 1.0
C D:CYS44 4.1 29.0 1.0
C D:CYS39 4.3 24.0 1.0
N D:ALA41 4.4 21.2 1.0
SG D:CYS77 4.4 20.1 1.0
CB D:SER46 4.5 22.1 1.0
N D:SER46 4.5 20.3 1.0
N D:SER43 4.5 18.7 1.0
C D:SER38 4.5 26.8 1.0
CA D:ARG40 4.6 23.4 1.0
N D:SER38 4.6 27.8 1.0
N D:GLY42 4.6 22.4 1.0
CB D:SER38 4.6 23.0 1.0
C D:SER43 4.7 23.9 1.0
SG D:CYS47 4.8 23.4 1.0
CA D:SER38 4.8 25.2 1.0
N D:SER45 4.8 25.0 1.0
N D:CYS47 5.0 21.4 1.0

Iron binding site 5 out of 8 in 3w5u

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Iron binding site 5 out of 8 in the Cross-Linked Complex Between Ferredoxin and Ferredoxin-Nadp+ Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Cross-Linked Complex Between Ferredoxin and Ferredoxin-Nadp+ Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe101

b:23.1
occ:1.00
 FE1 F:FES101 0.0 23.1 1.0
SG F:CYS47 2.1 17.4 1.0
S2 F:FES101 2.2 19.4 1.0
S1 F:FES101 2.2 16.6 1.0
SG F:CYS77 2.3 16.2 1.0
FE2 F:FES101 2.9 17.7 1.0
CB F:CYS47 3.1 15.2 1.0
CB F:CYS77 3.3 16.1 1.0
N F:CYS47 4.0 16.9 1.0
CA F:CYS47 4.2 15.6 1.0
N F:CYS77 4.2 18.8 1.0
CA F:CYS77 4.4 16.7 1.0
N F:ARG40 4.4 17.3 1.0
CA F:ARG40 4.5 16.9 1.0
N F:GLY42 4.5 20.1 1.0
CB F:LEU75 4.6 21.8 1.0
SG F:CYS39 4.6 14.9 1.0
CD2 F:LEU75 4.6 28.3 1.0
CA F:GLY42 4.7 19.2 1.0
SG F:CYS44 4.7 24.5 1.0
N F:ALA41 4.7 16.9 1.0
O F:CYS44 4.7 20.2 1.0
C F:ARG40 5.0 15.7 1.0
C F:CYS47 5.0 15.5 1.0

Iron binding site 6 out of 8 in 3w5u

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Iron binding site 6 out of 8 in the Cross-Linked Complex Between Ferredoxin and Ferredoxin-Nadp+ Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Cross-Linked Complex Between Ferredoxin and Ferredoxin-Nadp+ Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe101

b:17.7
occ:1.00
 FE2 F:FES101 0.0 17.7 1.0
SG F:CYS44 2.2 24.5 1.0
S2 F:FES101 2.2 19.4 1.0
S1 F:FES101 2.3 16.6 1.0
SG F:CYS39 2.3 14.9 1.0
FE1 F:FES101 2.9 23.1 1.0
CB F:CYS39 3.4 17.8 1.0
N F:CYS39 3.5 20.5 1.0
CB F:CYS44 3.5 22.2 1.0
N F:CYS44 3.6 23.2 1.0
N F:ARG40 3.7 17.3 1.0
CA F:CYS39 3.9 19.0 1.0
CA F:CYS44 3.9 22.4 1.0
O F:CYS44 4.0 20.2 1.0
C F:CYS44 4.0 22.0 1.0
C F:CYS39 4.2 18.7 1.0
N F:SER46 4.4 17.1 1.0
CB F:SER46 4.4 19.2 1.0
N F:SER43 4.5 21.5 1.0
N F:ALA41 4.5 16.9 1.0
SG F:CYS77 4.5 16.2 1.0
C F:SER38 4.6 21.4 1.0
CA F:ARG40 4.6 16.9 1.0
C F:SER43 4.6 24.3 1.0
SG F:CYS47 4.6 17.4 1.0
N F:SER38 4.6 22.0 1.0
N F:GLY42 4.7 20.1 1.0
CB F:SER38 4.7 20.1 1.0
N F:SER45 4.7 20.3 1.0
CA F:SER38 4.9 20.7 1.0
N F:CYS47 5.0 16.9 1.0
CA F:SER46 5.0 17.4 1.0

Iron binding site 7 out of 8 in 3w5u

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Iron binding site 7 out of 8 in the Cross-Linked Complex Between Ferredoxin and Ferredoxin-Nadp+ Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Cross-Linked Complex Between Ferredoxin and Ferredoxin-Nadp+ Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe101

b:20.1
occ:1.00
 FE1 H:FES101 0.0 20.1 1.0
SG H:CYS47 2.1 20.7 1.0
S2 H:FES101 2.2 24.1 1.0
S1 H:FES101 2.2 18.5 1.0
SG H:CYS77 2.3 19.3 1.0
FE2 H:FES101 3.0 19.4 1.0
CB H:CYS77 3.2 19.8 1.0
CB H:CYS47 3.3 21.9 1.0
N H:CYS47 4.1 22.0 1.0
N H:CYS77 4.2 19.0 1.0
SG H:CYS39 4.3 13.9 1.0
CA H:CYS77 4.3 19.7 1.0
CA H:CYS47 4.3 19.0 1.0
CA H:ARG40 4.4 15.6 1.0
N H:GLY42 4.4 16.6 1.0
N H:ARG40 4.5 15.6 1.0
CB H:LEU75 4.6 27.9 1.0
N H:ALA41 4.6 17.6 1.0
CD2 H:LEU75 4.6 28.0 1.0
O H:CYS44 4.7 25.3 1.0
CA H:GLY42 4.8 17.2 1.0
C H:ARG40 4.9 15.9 1.0
SG H:CYS44 4.9 16.7 1.0

Iron binding site 8 out of 8 in 3w5u

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Iron binding site 8 out of 8 in the Cross-Linked Complex Between Ferredoxin and Ferredoxin-Nadp+ Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Cross-Linked Complex Between Ferredoxin and Ferredoxin-Nadp+ Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe101

b:19.4
occ:1.00
 FE2 H:FES101 0.0 19.4 1.0
S1 H:FES101 2.2 18.5 1.0
S2 H:FES101 2.2 24.1 1.0
SG H:CYS44 2.2 16.7 1.0
SG H:CYS39 2.2 13.9 1.0
FE1 H:FES101 3.0 20.1 1.0
CB H:CYS39 3.3 15.0 1.0
CB H:CYS44 3.4 19.9 1.0
N H:CYS39 3.5 17.3 1.0
N H:CYS44 3.5 23.4 1.0
CA H:CYS44 3.8 24.2 1.0
N H:ARG40 3.8 15.6 1.0
O H:CYS44 3.8 25.3 1.0
C H:CYS44 3.9 26.4 1.0
CA H:CYS39 3.9 15.8 1.0
N H:SER46 4.3 25.6 1.0
C H:CYS39 4.3 15.8 1.0
CB H:SER46 4.4 26.0 1.0
N H:SER43 4.4 22.0 1.0
N H:ALA41 4.5 17.6 1.0
C H:SER43 4.6 24.4 1.0
N H:GLY42 4.6 16.6 1.0
C H:SER38 4.6 18.0 1.0
N H:SER38 4.7 17.8 1.0
CA H:ARG40 4.7 15.6 1.0
N H:SER45 4.7 27.6 1.0
SG H:CYS77 4.7 19.3 1.0
SG H:CYS47 4.8 20.7 1.0
CB H:SER38 4.8 18.9 1.0
CA H:SER46 4.9 23.6 1.0
CA H:SER38 4.9 18.2 1.0
N H:CYS47 5.0 22.0 1.0

Reference:

Y.Kimata-Ariga, H.Kubota-Kawai, Y.-H.Lee, N.Muraki, T.Ikegami, G.Kurisu, T.Hase. Concentration-Dependent Oligomerization of Cross-Linked Complexes Between Ferredoxin and Ferredoxin-Nadp(+) Reductase Biochem.Biophys.Res.Commun. V. 434 867 2013.
ISSN: ISSN 0006-291X
PubMed: 23618857
DOI: 10.1016/J.BBRC.2013.04.033
Page generated: Sun Aug 4 22:30:41 2024

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