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Iron in PDB 5ffi: [2FE:2S] Ferredoxin Fesii From Azotobacter Vinelandii

Protein crystallography data

The structure of [2FE:2S] Ferredoxin Fesii From Azotobacter Vinelandii, PDB code: 5ffi was solved by J.Schlesier, M.Rohde, S.Gerhardt, O.Einsle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 94.66 / 2.17
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 133.271, 134.480, 36.769, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 22.9

Iron Binding Sites:

The binding sites of Iron atom in the [2FE:2S] Ferredoxin Fesii From Azotobacter Vinelandii (pdb code 5ffi). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 10 binding sites of Iron where determined in the [2FE:2S] Ferredoxin Fesii From Azotobacter Vinelandii, PDB code: 5ffi:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 5ffi

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Iron binding site 1 out of 10 in the [2FE:2S] Ferredoxin Fesii From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of [2FE:2S] Ferredoxin Fesii From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1001

b:34.4
occ:1.00
 FE1 A:FES1001 0.0 34.4 1.0
S1 A:FES1001 2.2 35.1 1.0
S2 A:FES1001 2.2 30.4 1.0
SG A:CYS42 2.3 36.4 1.0
SG A:CYS47 2.3 36.7 1.0
FE2 A:FES1001 2.7 34.3 1.0
CB A:CYS42 3.4 34.1 1.0
CB A:CYS47 3.5 34.2 1.0
N A:CYS47 3.6 35.1 1.0
N A:CYS42 3.7 36.5 1.0
N A:GLY48 3.9 34.9 1.0
CA A:CYS42 3.9 35.9 1.0
CA A:CYS47 4.0 34.7 1.0
O A:HOH1117 4.1 30.3 1.0
O A:CYS42 4.1 39.6 1.0
OG A:SER49 4.2 44.2 1.0
C A:CYS42 4.3 41.6 1.0
N A:ASN46 4.3 38.0 1.0
C A:CYS47 4.3 39.1 1.0
N A:SER49 4.4 32.3 1.0
CA A:GLY45 4.4 39.4 1.0
C A:GLU41 4.4 40.0 1.0
SG A:CYS102 4.4 36.2 1.0
N A:GLU41 4.6 31.6 1.0
N A:GLY45 4.6 40.8 1.0
SG A:CYS50 4.7 30.7 1.0
C A:GLY45 4.7 42.4 1.0
C A:ASN46 4.8 40.0 1.0
CA A:GLY48 4.8 32.8 1.0
CB A:SER49 4.9 36.1 1.0
CA A:GLU41 4.9 33.5 1.0

Iron binding site 2 out of 10 in 5ffi

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Iron binding site 2 out of 10 in the [2FE:2S] Ferredoxin Fesii From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of [2FE:2S] Ferredoxin Fesii From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1001

b:34.3
occ:1.00
 FE2 A:FES1001 0.0 34.3 1.0
S2 A:FES1001 2.2 30.4 1.0
S1 A:FES1001 2.2 35.1 1.0
SG A:CYS50 2.2 30.7 1.0
SG A:CYS102 2.4 36.2 1.0
FE1 A:FES1001 2.7 34.4 1.0
CB A:CYS50 3.4 27.1 1.0
CB A:CYS102 3.4 32.7 1.0
O A:HOH1117 4.0 30.3 1.0
N A:CYS50 4.1 27.8 1.0
N A:CYS102 4.3 32.4 1.0
CA A:CYS50 4.4 26.9 1.0
SG A:CYS42 4.4 36.4 1.0
CA A:CYS102 4.5 32.8 1.0
CB A:LEU100 4.5 30.3 1.0
CA A:GLY45 4.6 39.4 1.0
SG A:CYS47 4.6 36.7 1.0
OG A:SER49 4.8 44.2 1.0
N A:SER49 4.8 32.3 1.0
N A:GLY48 4.9 34.9 1.0
CD1 A:LEU100 5.0 30.8 1.0

Iron binding site 3 out of 10 in 5ffi

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Iron binding site 3 out of 10 in the [2FE:2S] Ferredoxin Fesii From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of [2FE:2S] Ferredoxin Fesii From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1001

b:38.4
occ:1.00
 FE1 B:FES1001 0.0 38.4 1.0
S2 B:FES1001 2.2 37.9 1.0
S1 B:FES1001 2.2 33.4 1.0
SG B:CYS42 2.4 41.4 1.0
SG B:CYS47 2.4 41.1 1.0
FE2 B:FES1001 2.7 36.4 1.0
CB B:CYS42 3.5 38.6 1.0
CB B:CYS47 3.6 38.3 1.0
N B:CYS47 3.6 40.7 1.0
N B:CYS42 3.7 39.3 1.0
N B:GLY48 3.8 35.8 1.0
O B:HOH1125 3.9 36.2 1.0
CA B:CYS47 4.0 38.5 1.0
CA B:CYS42 4.0 39.5 1.0
OG B:SER49 4.2 48.2 1.0
O B:CYS42 4.3 43.3 1.0
C B:CYS47 4.3 40.3 1.0
N B:SER49 4.3 34.5 1.0
N B:ASN46 4.3 45.0 1.0
C B:CYS42 4.4 46.0 1.0
CA B:GLY45 4.4 47.0 1.0
SG B:CYS102 4.5 39.7 1.0
C B:GLU41 4.5 44.5 1.0
N B:GLU41 4.5 39.1 1.0
C B:GLY45 4.6 49.0 1.0
SG B:CYS50 4.6 32.2 1.0
N B:GLY45 4.7 48.6 1.0
CA B:GLY48 4.8 34.6 1.0
C B:ASN46 4.8 47.6 1.0
CB B:SER49 4.9 37.4 1.0
CA B:GLU41 5.0 39.4 1.0

Iron binding site 4 out of 10 in 5ffi

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Iron binding site 4 out of 10 in the [2FE:2S] Ferredoxin Fesii From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of [2FE:2S] Ferredoxin Fesii From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1001

b:36.4
occ:1.00
 FE2 B:FES1001 0.0 36.4 1.0
S2 B:FES1001 2.2 37.9 1.0
S1 B:FES1001 2.2 33.4 1.0
SG B:CYS50 2.2 32.2 1.0
SG B:CYS102 2.4 39.7 1.0
FE1 B:FES1001 2.7 38.4 1.0
CB B:CYS50 3.4 29.3 1.0
CB B:CYS102 3.4 35.5 1.0
O B:HOH1125 3.9 36.2 1.0
N B:CYS50 4.2 31.8 1.0
N B:CYS102 4.4 32.8 1.0
CA B:CYS50 4.4 29.8 1.0
CA B:CYS102 4.5 34.4 1.0
SG B:CYS42 4.5 41.4 1.0
CB B:LEU100 4.6 29.1 1.0
CA B:GLY45 4.6 47.0 1.0
SG B:CYS47 4.7 41.1 1.0
N B:GLY48 4.8 35.8 1.0
OG B:SER49 4.9 48.2 1.0
N B:SER49 4.9 34.5 1.0

Iron binding site 5 out of 10 in 5ffi

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Iron binding site 5 out of 10 in the [2FE:2S] Ferredoxin Fesii From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of [2FE:2S] Ferredoxin Fesii From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1001

b:88.7
occ:1.00
 FE1 C:FES1001 0.0 88.7 1.0
S1 C:FES1001 2.2 85.1 1.0
S2 C:FES1001 2.2 85.3 1.0
SG C:CYS42 2.3 0.1 1.0
SG C:CYS47 2.4 97.0 1.0
FE2 C:FES1001 2.7 80.7 1.0
CB C:CYS42 3.4 0.5 1.0
CB C:CYS47 3.6 96.9 1.0
N C:CYS47 3.7 95.1 1.0
N C:CYS42 3.7 0.2 1.0
N C:GLY48 3.8 85.6 1.0
CA C:CYS42 4.0 0.3 1.0
CA C:CYS47 4.0 94.7 1.0
OG C:SER49 4.2 95.5 1.0
O C:CYS42 4.2 0.3 1.0
N C:SER49 4.3 81.0 1.0
C C:CYS47 4.3 93.2 1.0
N C:ASN46 4.4 98.6 1.0
C C:CYS42 4.4 0.8 1.0
CA C:GLY45 4.4 99.8 1.0
SG C:CYS102 4.5 87.7 1.0
C C:GLU41 4.5 0.6 1.0
N C:GLU41 4.5 96.4 1.0
C C:GLY45 4.6 0.5 1.0
N C:GLY45 4.7 0.2 1.0
SG C:CYS50 4.8 73.3 1.0
CA C:GLY48 4.8 81.0 1.0
C C:ASN46 4.8 99.8 1.0
CB C:SER49 4.9 87.2 1.0
CA C:GLU41 5.0 0.7 1.0
N C:CYS50 5.0 73.2 1.0

Iron binding site 6 out of 10 in 5ffi

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Iron binding site 6 out of 10 in the [2FE:2S] Ferredoxin Fesii From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of [2FE:2S] Ferredoxin Fesii From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1001

b:80.7
occ:1.00
 FE2 C:FES1001 0.0 80.7 1.0
S2 C:FES1001 2.2 85.3 1.0
S1 C:FES1001 2.2 85.1 1.0
SG C:CYS50 2.3 73.3 1.0
SG C:CYS102 2.4 87.7 1.0
FE1 C:FES1001 2.7 88.7 1.0
CB C:CYS102 3.4 83.8 1.0
CB C:CYS50 3.4 70.3 1.0
N C:CYS50 4.1 73.2 1.0
N C:CYS102 4.4 78.0 1.0
CA C:CYS50 4.4 69.5 1.0
CA C:CYS102 4.5 80.7 1.0
SG C:CYS42 4.5 0.1 1.0
CB C:LEU100 4.6 70.4 1.0
CA C:GLY45 4.6 99.8 1.0
SG C:CYS47 4.7 97.0 1.0
OG C:SER49 4.9 95.5 1.0
N C:SER49 4.9 81.0 1.0
N C:GLY48 4.9 85.6 1.0

Iron binding site 7 out of 10 in 5ffi

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Iron binding site 7 out of 10 in the [2FE:2S] Ferredoxin Fesii From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of [2FE:2S] Ferredoxin Fesii From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1001

b:31.6
occ:1.00
 FE1 D:FES1001 0.0 31.6 1.0
S2 D:FES1001 2.2 31.0 1.0
S1 D:FES1001 2.2 29.1 1.0
SG D:CYS42 2.3 33.7 1.0
SG D:CYS47 2.4 31.2 1.0
FE2 D:FES1001 2.7 30.7 1.0
CB D:CYS42 3.5 31.8 1.0
CB D:CYS47 3.6 29.2 1.0
N D:CYS47 3.7 30.8 1.0
N D:CYS42 3.7 33.4 1.0
N D:GLY48 3.8 31.6 1.0
O D:HOH1118 4.0 32.4 1.0
CA D:CYS47 4.0 29.9 1.0
CA D:CYS42 4.0 32.7 1.0
O D:CYS42 4.2 33.7 1.0
OG D:SER49 4.2 41.6 1.0
N D:SER49 4.3 29.0 1.0
C D:CYS47 4.3 34.6 1.0
C D:CYS42 4.4 34.6 1.0
N D:ASN46 4.4 30.8 1.0
SG D:CYS102 4.4 30.0 1.0
C D:GLU41 4.5 38.0 1.0
N D:GLU41 4.5 34.3 1.0
CA D:GLY45 4.5 29.9 1.0
SG D:CYS50 4.7 28.7 1.0
C D:GLY45 4.7 33.2 1.0
N D:GLY45 4.7 32.0 1.0
CA D:GLY48 4.8 30.1 1.0
C D:ASN46 4.8 36.6 1.0
CA D:GLU41 4.9 34.7 1.0
CB D:SER49 4.9 32.3 1.0

Iron binding site 8 out of 10 in 5ffi

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Iron binding site 8 out of 10 in the [2FE:2S] Ferredoxin Fesii From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of [2FE:2S] Ferredoxin Fesii From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1001

b:30.7
occ:1.00
 FE2 D:FES1001 0.0 30.7 1.0
S1 D:FES1001 2.2 29.1 1.0
S2 D:FES1001 2.2 31.0 1.0
SG D:CYS50 2.3 28.7 1.0
SG D:CYS102 2.4 30.0 1.0
FE1 D:FES1001 2.7 31.6 1.0
CB D:CYS102 3.3 26.3 1.0
CB D:CYS50 3.4 24.8 1.0
O D:HOH1118 3.9 32.4 1.0
N D:CYS50 4.2 26.6 1.0
N D:CYS102 4.3 26.6 1.0
CA D:CYS102 4.4 27.1 1.0
CA D:CYS50 4.4 24.8 1.0
SG D:CYS42 4.5 33.7 1.0
CB D:LEU100 4.6 27.1 1.0
SG D:CYS47 4.7 31.2 1.0
CA D:GLY45 4.7 29.9 1.0
N D:SER49 4.9 29.0 1.0
N D:GLY48 4.9 31.6 1.0
OG D:SER49 4.9 41.6 1.0
CD1 D:LEU100 5.0 29.8 1.0

Iron binding site 9 out of 10 in 5ffi

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Iron binding site 9 out of 10 in the [2FE:2S] Ferredoxin Fesii From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of [2FE:2S] Ferredoxin Fesii From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe1001

b:43.8
occ:1.00
 FE1 E:FES1001 0.0 43.8 1.0
S1 E:FES1001 2.2 43.6 1.0
S2 E:FES1001 2.2 38.0 1.0
SG E:CYS42 2.3 49.5 1.0
SG E:CYS47 2.4 48.6 1.0
FE2 E:FES1001 2.7 39.2 1.0
CB E:CYS42 3.5 51.0 1.0
CB E:CYS47 3.6 47.8 1.0
N E:CYS42 3.6 54.9 1.0
N E:CYS47 3.6 46.4 1.0
N E:GLY48 3.8 47.5 1.0
CA E:CYS47 4.0 47.5 1.0
CA E:CYS42 4.1 54.0 1.0
O E:HOH1126 4.1 43.5 1.0
C E:CYS47 4.3 53.0 1.0
N E:ASN46 4.3 44.6 1.0
CA E:GLY45 4.4 44.9 1.0
N E:SER49 4.4 46.3 1.0
SG E:CYS102 4.4 37.6 1.0
C E:GLY45 4.6 46.2 1.0
SG E:CYS50 4.6 38.0 1.0
O E:CYS42 4.7 60.1 1.0
C E:ASN46 4.7 50.9 1.0
C E:GLU41 4.7 62.4 1.0
C E:CYS42 4.7 61.9 1.0
N E:GLY45 4.7 48.9 1.0
CA E:GLY48 4.8 46.4 1.0
CA E:GLU41 4.8 59.9 1.0

Iron binding site 10 out of 10 in 5ffi

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Iron binding site 10 out of 10 in the [2FE:2S] Ferredoxin Fesii From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of [2FE:2S] Ferredoxin Fesii From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe1001

b:39.2
occ:1.00
 FE2 E:FES1001 0.0 39.2 1.0
S2 E:FES1001 2.2 38.0 1.0
S1 E:FES1001 2.2 43.6 1.0
SG E:CYS50 2.3 38.0 1.0
SG E:CYS102 2.4 37.6 1.0
FE1 E:FES1001 2.7 43.8 1.0
CB E:CYS102 3.3 34.0 1.0
CB E:CYS50 3.4 35.1 1.0
O E:HOH1126 4.0 43.5 1.0
N E:CYS50 4.2 39.5 1.0
N E:CYS102 4.3 32.6 1.0
CA E:CYS102 4.4 32.8 1.0
CA E:CYS50 4.4 36.2 1.0
SG E:CYS42 4.5 49.5 1.0
CB E:LEU100 4.5 31.5 1.0
CA E:GLY45 4.6 44.9 1.0
SG E:CYS47 4.7 48.6 1.0
CD2 E:LEU28 4.8 41.3 1.0
N E:GLY48 4.9 47.5 1.0
CD2 E:LEU100 5.0 33.1 1.0
N E:SER49 5.0 46.3 1.0
CD1 E:LEU100 5.0 35.6 1.0

Reference:

J.Schlesier, M.Rohde, S.Gerhardt, O.Einsle. A Conformational Switch Triggers Nitrogenase Protection From Oxygen Damage By Shethna Protein II (Fesii). J.Am.Chem.Soc. V. 138 239 2016.
ISSN: ESSN 1520-5126
PubMed: 26654855
DOI: 10.1021/JACS.5B10341
Page generated: Tue Aug 6 00:55:04 2024

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