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Iron in PDB 3av8: Refined Structure of Plant-Type [2FE-2S] Ferredoxin I From Aphanothece Sacrum at 1.46 A Resolution

Protein crystallography data

The structure of Refined Structure of Plant-Type [2FE-2S] Ferredoxin I From Aphanothece Sacrum at 1.46 A Resolution, PDB code: 3av8 was solved by H.Kameda, K.Hirabayashi, K.Wada, K.Fukuyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.64 / 1.46
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 92.027, 92.027, 46.286, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 22.4

Iron Binding Sites:

The binding sites of Iron atom in the Refined Structure of Plant-Type [2FE-2S] Ferredoxin I From Aphanothece Sacrum at 1.46 A Resolution (pdb code 3av8). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Refined Structure of Plant-Type [2FE-2S] Ferredoxin I From Aphanothece Sacrum at 1.46 A Resolution, PDB code: 3av8:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 3av8

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Iron binding site 1 out of 8 in the Refined Structure of Plant-Type [2FE-2S] Ferredoxin I From Aphanothece Sacrum at 1.46 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Refined Structure of Plant-Type [2FE-2S] Ferredoxin I From Aphanothece Sacrum at 1.46 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe98

b:21.2
occ:1.00
 FE1 A:FES98 0.0 21.2 1.0
S2 A:FES98 2.2 22.1 1.0
S1 A:FES98 2.2 20.5 1.0
SG A:CYS44 2.3 24.6 1.0
SG A:CYS39 2.4 22.7 1.0
FE2 A:FES98 2.8 20.2 1.0
CB A:CYS44 3.4 26.9 1.0
CB A:CYS39 3.6 23.0 1.0
N A:CYS44 3.6 28.0 1.0
N A:CYS39 3.6 17.3 1.0
N A:ARG40 3.8 19.8 1.0
CA A:CYS44 3.9 27.2 1.0
CA A:CYS39 4.0 19.7 1.0
C A:CYS44 4.0 26.2 1.0
N A:ALA43 4.2 25.0 1.0
O A:CYS44 4.3 27.1 1.0
C A:CYS39 4.3 23.7 1.0
OG A:SER38 4.3 27.9 1.0
N A:GLY42 4.4 22.8 1.0
N A:ALA41 4.5 19.2 1.0
SG A:CYS78 4.5 19.2 1.0
C A:ALA43 4.5 30.5 1.0
N A:THR46 4.6 21.7 1.0
SG A:CYS47 4.6 19.2 1.0
C A:SER38 4.6 21.0 1.0
CA A:ARG40 4.6 20.9 1.0
N A:SER45 4.7 26.6 1.0
N A:SER38 4.7 19.2 1.0
CB A:THR46 4.8 24.4 1.0
CA A:ALA43 4.9 25.0 1.0
CA A:GLY42 4.9 23.6 1.0
C A:GLY42 4.9 29.3 1.0
OG1 A:THR46 4.9 25.2 1.0

Iron binding site 2 out of 8 in 3av8

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Iron binding site 2 out of 8 in the Refined Structure of Plant-Type [2FE-2S] Ferredoxin I From Aphanothece Sacrum at 1.46 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Refined Structure of Plant-Type [2FE-2S] Ferredoxin I From Aphanothece Sacrum at 1.46 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe98

b:20.2
occ:1.00
 FE2 A:FES98 0.0 20.2 1.0
S1 A:FES98 2.2 20.5 1.0
S2 A:FES98 2.2 22.1 1.0
SG A:CYS47 2.3 19.2 1.0
SG A:CYS78 2.3 19.2 1.0
FE1 A:FES98 2.8 21.2 1.0
CB A:CYS78 3.2 19.8 1.0
CB A:CYS47 3.3 18.1 1.0
N A:CYS78 4.2 18.1 1.0
N A:CYS47 4.2 21.8 1.0
N A:GLY42 4.3 22.8 1.0
N A:ARG40 4.3 19.8 1.0
CA A:ARG40 4.3 20.9 1.0
CA A:CYS78 4.4 18.9 1.0
CA A:CYS47 4.4 19.4 1.0
SG A:CYS39 4.5 22.7 1.0
CB A:LEU76 4.6 22.2 1.0
N A:ALA41 4.6 19.2 1.0
CA A:GLY42 4.6 23.6 1.0
SG A:CYS44 4.6 24.6 1.0
C A:ARG40 4.8 20.0 1.0
O A:CYS44 5.0 27.1 1.0

Iron binding site 3 out of 8 in 3av8

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Iron binding site 3 out of 8 in the Refined Structure of Plant-Type [2FE-2S] Ferredoxin I From Aphanothece Sacrum at 1.46 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Refined Structure of Plant-Type [2FE-2S] Ferredoxin I From Aphanothece Sacrum at 1.46 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe98

b:18.8
occ:1.00
 FE1 B:FES98 0.0 18.8 1.0
S2 B:FES98 2.2 19.0 1.0
SG B:CYS44 2.3 19.1 1.0
S1 B:FES98 2.3 18.7 1.0
SG B:CYS39 2.3 19.3 1.0
FE2 B:FES98 2.8 18.1 1.0
CB B:CYS44 3.4 20.5 1.0
CB B:CYS39 3.5 19.2 1.0
N B:CYS39 3.6 18.9 1.0
N B:CYS44 3.7 19.5 1.0
N B:ARG40 3.7 19.4 1.0
CA B:CYS44 3.9 18.3 1.0
CA B:CYS39 4.0 17.7 1.0
C B:CYS44 4.1 21.8 1.0
N B:ALA43 4.2 20.7 1.0
O B:CYS44 4.2 20.9 1.0
C B:CYS39 4.2 19.3 1.0
OG B:SER38 4.3 23.6 1.0
SG B:CYS78 4.4 18.5 1.0
N B:ALA41 4.4 19.8 1.0
N B:GLY42 4.4 18.5 1.0
C B:ALA43 4.5 20.5 1.0
CA B:ARG40 4.6 19.1 1.0
C B:SER38 4.6 17.9 1.0
SG B:CYS47 4.6 18.6 1.0
N B:THR46 4.7 17.9 1.0
N B:SER45 4.7 21.0 1.0
N B:SER38 4.7 18.6 1.0
CB B:THR46 4.8 19.3 1.0
CA B:ALA43 4.9 20.8 1.0
C B:GLY42 4.9 20.6 1.0
CA B:GLY42 4.9 18.4 1.0
OG1 B:THR46 5.0 19.4 1.0

Iron binding site 4 out of 8 in 3av8

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Iron binding site 4 out of 8 in the Refined Structure of Plant-Type [2FE-2S] Ferredoxin I From Aphanothece Sacrum at 1.46 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Refined Structure of Plant-Type [2FE-2S] Ferredoxin I From Aphanothece Sacrum at 1.46 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe98

b:18.1
occ:1.00
 FE2 B:FES98 0.0 18.1 1.0
S1 B:FES98 2.2 18.7 1.0
S2 B:FES98 2.2 19.0 1.0
SG B:CYS47 2.3 18.6 1.0
SG B:CYS78 2.3 18.5 1.0
FE1 B:FES98 2.8 18.8 1.0
CB B:CYS78 3.2 20.6 1.0
CB B:CYS47 3.3 17.4 1.0
N B:CYS47 4.2 17.9 1.0
N B:CYS78 4.2 17.5 1.0
N B:ARG40 4.3 19.4 1.0
CA B:CYS78 4.3 17.9 1.0
N B:GLY42 4.3 18.5 1.0
CA B:ARG40 4.4 19.1 1.0
CA B:CYS47 4.4 19.7 1.0
SG B:CYS39 4.4 19.3 1.0
CB B:LEU76 4.6 17.4 1.0
SG B:CYS44 4.6 19.1 1.0
CA B:GLY42 4.6 18.4 1.0
N B:ALA41 4.7 19.8 1.0
C B:ARG40 4.9 19.2 1.0
O B:CYS44 5.0 20.9 1.0

Iron binding site 5 out of 8 in 3av8

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Iron binding site 5 out of 8 in the Refined Structure of Plant-Type [2FE-2S] Ferredoxin I From Aphanothece Sacrum at 1.46 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Refined Structure of Plant-Type [2FE-2S] Ferredoxin I From Aphanothece Sacrum at 1.46 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe98

b:18.7
occ:1.00
 FE1 C:FES98 0.0 18.7 1.0
S2 C:FES98 2.2 19.1 1.0
S1 C:FES98 2.2 17.3 1.0
SG C:CYS44 2.3 20.9 1.0
SG C:CYS39 2.4 19.4 1.0
FE2 C:FES98 2.7 17.5 1.0
CB C:CYS44 3.4 21.7 1.0
CB C:CYS39 3.6 20.8 1.0
N C:CYS44 3.6 19.3 1.0
N C:CYS39 3.6 17.1 1.0
N C:ARG40 3.8 18.9 1.0
CA C:CYS44 3.8 21.3 1.0
CA C:CYS39 4.0 16.2 1.0
C C:CYS44 4.0 20.0 1.0
O C:CYS44 4.2 24.9 1.0
C C:CYS39 4.2 16.8 1.0
N C:ALA43 4.3 18.8 1.0
OG C:SER38 4.3 24.6 1.0
N C:ALA41 4.4 19.1 1.0
SG C:CYS78 4.4 18.4 1.0
N C:GLY42 4.5 17.8 1.0
C C:ALA43 4.5 25.9 1.0
N C:SER45 4.5 21.6 1.0
N C:THR46 4.6 18.1 1.0
CA C:ARG40 4.7 18.4 1.0
C C:SER38 4.7 18.9 1.0
SG C:CYS47 4.7 17.8 1.0
N C:SER38 4.7 15.9 1.0
CB C:THR46 4.9 19.6 1.0
C C:GLY42 4.9 20.3 1.0
CA C:ALA43 4.9 20.9 1.0
CA C:GLY42 5.0 20.3 1.0

Iron binding site 6 out of 8 in 3av8

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Iron binding site 6 out of 8 in the Refined Structure of Plant-Type [2FE-2S] Ferredoxin I From Aphanothece Sacrum at 1.46 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Refined Structure of Plant-Type [2FE-2S] Ferredoxin I From Aphanothece Sacrum at 1.46 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe98

b:17.5
occ:1.00
 FE2 C:FES98 0.0 17.5 1.0
S1 C:FES98 2.2 17.3 1.0
S2 C:FES98 2.2 19.1 1.0
SG C:CYS78 2.3 18.4 1.0
SG C:CYS47 2.4 17.8 1.0
FE1 C:FES98 2.7 18.7 1.0
CB C:CYS78 3.3 16.4 1.0
CB C:CYS47 3.4 15.9 1.0
N C:CYS47 4.3 17.5 1.0
N C:CYS78 4.3 16.0 1.0
N C:ARG40 4.3 18.9 1.0
N C:GLY42 4.3 17.8 1.0
CA C:CYS78 4.4 15.8 1.0
CA C:ARG40 4.4 18.4 1.0
SG C:CYS39 4.4 19.4 1.0
CA C:CYS47 4.5 15.7 1.0
CB C:LEU76 4.5 18.2 1.0
N C:ALA41 4.6 19.1 1.0
SG C:CYS44 4.6 20.9 1.0
CA C:GLY42 4.7 20.3 1.0
C C:ARG40 4.9 19.0 1.0
O C:CYS44 4.9 24.9 1.0

Iron binding site 7 out of 8 in 3av8

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Iron binding site 7 out of 8 in the Refined Structure of Plant-Type [2FE-2S] Ferredoxin I From Aphanothece Sacrum at 1.46 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Refined Structure of Plant-Type [2FE-2S] Ferredoxin I From Aphanothece Sacrum at 1.46 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe98

b:20.4
occ:1.00
 FE1 D:FES98 0.0 20.4 1.0
S2 D:FES98 2.2 20.7 1.0
S1 D:FES98 2.2 20.1 1.0
SG D:CYS44 2.3 20.6 1.0
SG D:CYS39 2.3 20.9 1.0
FE2 D:FES98 2.7 19.6 1.0
CB D:CYS44 3.4 23.7 1.0
N D:CYS39 3.5 21.4 1.0
CB D:CYS39 3.5 16.9 1.0
N D:CYS44 3.6 19.0 1.0
N D:ARG40 3.8 22.1 1.0
CA D:CYS44 3.8 17.4 1.0
CA D:CYS39 3.9 18.0 1.0
C D:CYS44 4.0 18.9 1.0
O D:CYS44 4.1 21.6 1.0
N D:ALA43 4.2 19.7 1.0
C D:CYS39 4.3 25.6 1.0
SG D:CYS78 4.3 21.7 1.0
N D:GLY42 4.4 19.5 1.0
C D:ALA43 4.4 21.2 1.0
N D:ALA41 4.5 18.9 1.0
SG D:CYS47 4.5 18.4 1.0
C D:SER38 4.6 18.9 1.0
N D:SER38 4.6 18.7 1.0
CA D:ARG40 4.6 21.6 1.0
N D:THR46 4.7 20.0 1.0
N D:SER45 4.7 19.8 1.0
CA D:GLY42 4.9 23.1 1.0
CA D:ALA43 4.9 20.4 1.0
CB D:SER38 4.9 22.0 1.0
CA D:SER38 4.9 20.3 1.0
C D:GLY42 5.0 22.3 1.0
N D:CYS47 5.0 18.0 1.0

Iron binding site 8 out of 8 in 3av8

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Iron binding site 8 out of 8 in the Refined Structure of Plant-Type [2FE-2S] Ferredoxin I From Aphanothece Sacrum at 1.46 A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Refined Structure of Plant-Type [2FE-2S] Ferredoxin I From Aphanothece Sacrum at 1.46 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe98

b:19.6
occ:1.00
 FE2 D:FES98 0.0 19.6 1.0
S2 D:FES98 2.2 20.7 1.0
S1 D:FES98 2.2 20.1 1.0
SG D:CYS78 2.3 21.7 1.0
SG D:CYS47 2.3 18.4 1.0
FE1 D:FES98 2.7 20.4 1.0
CB D:CYS78 3.2 21.5 1.0
CB D:CYS47 3.3 19.6 1.0
N D:CYS78 4.1 16.0 1.0
CA D:CYS78 4.3 17.0 1.0
N D:GLY42 4.3 19.5 1.0
N D:CYS47 4.3 18.0 1.0
N D:ARG40 4.4 22.1 1.0
SG D:CYS39 4.4 20.9 1.0
CA D:ARG40 4.4 21.6 1.0
CA D:CYS47 4.5 17.5 1.0
CB D:LEU76 4.5 17.7 1.0
SG D:CYS44 4.6 20.6 1.0
CA D:GLY42 4.6 23.1 1.0
N D:ALA41 4.7 18.9 1.0
O D:CYS44 4.9 21.6 1.0
C D:ARG40 4.9 19.0 1.0

Reference:

H.Kameda, K.Hirabayashi, K.Wada, K.Fukuyama. Mapping of Protein-Protein Interaction Sites in the Plant-Type [2FE-2S] Ferredoxin. Plos One V. 6 21947 2011.
ISSN: ESSN 1932-6203
PubMed: 21760931
DOI: 10.1371/JOURNAL.PONE.0021947
Page generated: Sun Dec 13 15:01:14 2020

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