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Iron in PDB 7ar8: Cryo-Em Structure of Arabidopsis Thaliana Complex-I (Closed Conformation)

Enzymatic activity of Cryo-Em Structure of Arabidopsis Thaliana Complex-I (Closed Conformation)

All present enzymatic activity of Cryo-Em Structure of Arabidopsis Thaliana Complex-I (Closed Conformation):
7.1.1.2;

Other elements in 7ar8:

The structure of Cryo-Em Structure of Arabidopsis Thaliana Complex-I (Closed Conformation) also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 29;

Binding sites:

The binding sites of Iron atom in the Cryo-Em Structure of Arabidopsis Thaliana Complex-I (Closed Conformation) (pdb code 7ar8). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 29 binding sites of Iron where determined in the Cryo-Em Structure of Arabidopsis Thaliana Complex-I (Closed Conformation), PDB code: 7ar8:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 29 in 7ar8

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Iron binding site 1 out of 29 in the Cryo-Em Structure of Arabidopsis Thaliana Complex-I (Closed Conformation)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryo-Em Structure of Arabidopsis Thaliana Complex-I (Closed Conformation) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe500

b:47.5
occ:1.00
 FE1 B:SF4500 0.0 47.5 1.0
SG B:CYS158 2.3 34.2 1.0
S3 B:SF4500 2.3 47.5 1.0
S2 B:SF4500 2.3 47.5 1.0
S4 B:SF4500 2.3 47.5 1.0
CB B:CYS158 2.7 34.2 1.0
FE4 B:SF4500 2.7 47.5 1.0
FE3 B:SF4500 2.7 47.5 1.0
FE2 B:SF4500 2.7 47.5 1.0
N B:CYS158 3.4 34.2 1.0
CA B:CYS158 3.6 34.2 1.0
S1 B:SF4500 3.9 47.5 1.0
C B:SER157 4.5 35.4 1.0
SG B:CYS188 4.7 39.1 1.0
N B:SER157 4.7 35.4 1.0
N B:THR130 4.8 31.6 1.0
SG B:CYS94 4.8 29.7 1.0
SG B:CYS93 4.9 15.6 1.0
C B:CYS158 4.9 34.2 1.0
CE2 B:TYR165 5.0 47.5 1.0

Iron binding site 2 out of 29 in 7ar8

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Iron binding site 2 out of 29 in the Cryo-Em Structure of Arabidopsis Thaliana Complex-I (Closed Conformation)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryo-Em Structure of Arabidopsis Thaliana Complex-I (Closed Conformation) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe500

b:47.5
occ:1.00
 FE2 B:SF4500 0.0 47.5 1.0
SG B:CYS94 2.3 29.7 1.0
S4 B:SF4500 2.3 47.5 1.0
S1 B:SF4500 2.3 47.5 1.0
S3 B:SF4500 2.3 47.5 1.0
FE4 B:SF4500 2.7 47.5 1.0
FE3 B:SF4500 2.7 47.5 1.0
FE1 B:SF4500 2.7 47.5 1.0
CB B:CYS94 3.4 29.7 1.0
SG B:CYS93 3.7 15.6 1.0
N B:CYS94 3.8 29.7 1.0
S2 B:SF4500 3.9 47.5 1.0
CA B:CYS94 4.1 29.7 1.0
CA B:GLY156 4.5 47.5 1.0
N B:SER157 4.5 35.4 1.0
CA B:PRO189 4.7 47.5 1.0
N B:CYS158 4.7 34.2 1.0
CB B:PRO189 4.7 47.5 1.0
CB B:CYS158 4.8 34.2 1.0
CA B:GLY129 4.8 29.4 1.0
C B:CYS93 4.8 15.6 1.0
SG B:CYS188 4.8 39.1 1.0
CA B:CYS188 4.9 39.1 1.0
SG B:CYS158 4.9 34.2 1.0
N B:GLY129 5.0 29.4 1.0

Iron binding site 3 out of 29 in 7ar8

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Iron binding site 3 out of 29 in the Cryo-Em Structure of Arabidopsis Thaliana Complex-I (Closed Conformation)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cryo-Em Structure of Arabidopsis Thaliana Complex-I (Closed Conformation) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe500

b:47.5
occ:1.00
 FE3 B:SF4500 0.0 47.5 1.0
SG B:CYS188 2.3 39.1 1.0
S1 B:SF4500 2.3 47.5 1.0
S2 B:SF4500 2.3 47.5 1.0
S4 B:SF4500 2.3 47.5 1.0
FE2 B:SF4500 2.7 47.5 1.0
FE1 B:SF4500 2.7 47.5 1.0
FE4 B:SF4500 2.7 47.5 1.0
CB B:CYS188 3.3 39.1 1.0
CA B:CYS188 3.6 39.1 1.0
S3 B:SF4500 3.9 47.5 1.0
C B:CYS188 4.1 39.1 1.0
SG B:CYS93 4.1 15.6 1.0
NE D:ARG69 4.4 35.7 1.0
CD2 D:HIS154 4.5 28.5 1.0
NH2 D:ARG69 4.5 35.7 1.0
N B:PRO189 4.5 47.5 1.0
O B:CYS188 4.6 39.1 1.0
SG B:CYS158 4.6 34.2 1.0
SG B:CYS94 4.6 29.7 1.0
NE2 D:HIS154 4.7 28.5 1.0
CA B:PRO189 4.8 47.5 1.0
O B:GLY187 4.8 47.5 1.0
N B:CYS188 4.9 39.1 1.0
CZ D:ARG69 5.0 35.7 1.0
N B:SER157 5.0 35.4 1.0

Iron binding site 4 out of 29 in 7ar8

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Iron binding site 4 out of 29 in the Cryo-Em Structure of Arabidopsis Thaliana Complex-I (Closed Conformation)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cryo-Em Structure of Arabidopsis Thaliana Complex-I (Closed Conformation) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe500

b:47.5
occ:1.00
 FE4 B:SF4500 0.0 47.5 1.0
SG B:CYS93 2.2 15.6 1.0
S3 B:SF4500 2.3 47.5 1.0
S2 B:SF4500 2.3 47.5 1.0
S1 B:SF4500 2.3 47.5 1.0
FE1 B:SF4500 2.7 47.5 1.0
FE2 B:SF4500 2.7 47.5 1.0
FE3 B:SF4500 2.7 47.5 1.0
S4 B:SF4500 3.9 47.5 1.0
CB B:CYS93 4.0 15.6 1.0
CG D:ARG69 4.3 35.7 1.0
NE2 D:HIS154 4.3 28.5 1.0
N B:CYS93 4.4 15.6 1.0
SG B:CYS158 4.5 34.2 1.0
N B:CYS94 4.6 29.7 1.0
CB B:ALA92 4.6 29.2 1.0
CA B:CYS93 4.6 15.6 1.0
SG B:CYS188 4.7 39.1 1.0
SG B:CYS94 4.8 29.7 1.0
CD2 D:HIS154 4.8 28.5 1.0
NE D:ARG69 4.8 35.7 1.0

Iron binding site 5 out of 29 in 7ar8

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Iron binding site 5 out of 29 in the Cryo-Em Structure of Arabidopsis Thaliana Complex-I (Closed Conformation)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Cryo-Em Structure of Arabidopsis Thaliana Complex-I (Closed Conformation) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe500

b:122.0
occ:1.00
 FE1 E:FES500 0.0 122.0 1.0
S1 E:FES500 2.2 122.0 1.0
S2 E:FES500 2.2 122.0 1.0
SG E:CYS135 2.3 99.6 1.0
CB E:CYS135 2.4 99.6 1.0
FE2 E:FES500 2.7 122.0 1.0
CE E:MET180 3.1 86.7 1.0
N E:GLY131 3.3 88.8 1.0
CB E:CYS130 3.6 85.8 1.0
CA E:CYS135 3.7 99.6 1.0
SG E:CYS171 3.8 107.0 1.0
CB E:CYS171 3.9 107.0 1.0
SG E:CYS175 4.0 100.0 1.0
CA E:CYS130 4.0 85.8 1.0
CA E:GLY131 4.1 88.8 1.0
C E:CYS130 4.1 85.8 1.0
SG E:CYS130 4.2 85.8 1.0
O E:GLY131 4.2 88.8 1.0
O E:ALA178 4.3 90.5 1.0
N E:CYS135 4.4 99.6 1.0
C E:GLY131 4.6 88.8 1.0
CB E:CYS175 4.7 100.0 1.0
SD E:MET180 4.8 86.7 1.0
C E:CYS135 4.9 99.6 1.0
CA E:CYS171 4.9 107.0 1.0
CB E:MET180 4.9 86.7 1.0

Iron binding site 6 out of 29 in 7ar8

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Iron binding site 6 out of 29 in the Cryo-Em Structure of Arabidopsis Thaliana Complex-I (Closed Conformation)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Cryo-Em Structure of Arabidopsis Thaliana Complex-I (Closed Conformation) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe500

b:122.0
occ:1.00
 FE2 E:FES500 0.0 122.0 1.0
CB E:CYS171 1.3 107.0 1.0
S2 E:FES500 2.2 122.0 1.0
S1 E:FES500 2.2 122.0 1.0
SG E:CYS171 2.3 107.0 1.0
CA E:CYS171 2.3 107.0 1.0
FE1 E:FES500 2.7 122.0 1.0
N E:CYS171 2.9 107.0 1.0
N E:GLY131 3.5 88.8 1.0
C E:CYS171 3.7 107.0 1.0
CA E:GLY131 3.7 88.8 1.0
C E:GLU170 4.1 100.0 1.0
CE E:MET180 4.2 86.7 1.0
N E:MET172 4.3 88.8 1.0
CB E:CYS135 4.3 99.6 1.0
CG E:PRO134 4.3 91.3 1.0
O E:CYS171 4.4 107.0 1.0
C E:GLY131 4.6 88.8 1.0
CB F:PRO145 4.7 79.7 1.0
O E:GLU170 4.8 100.0 1.0
C E:CYS130 4.8 85.8 1.0
SG E:CYS135 4.9 99.6 1.0
CD E:PRO134 5.0 91.3 1.0
O E:GLY131 5.0 88.8 1.0

Iron binding site 7 out of 29 in 7ar8

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Iron binding site 7 out of 29 in the Cryo-Em Structure of Arabidopsis Thaliana Complex-I (Closed Conformation)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Cryo-Em Structure of Arabidopsis Thaliana Complex-I (Closed Conformation) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:47.5
occ:1.00
 FE1 F:SF4501 0.0 47.5 1.0
SG F:CYS405 2.3 47.5 1.0
S4 F:SF4501 2.3 47.5 1.0
S3 F:SF4501 2.3 47.5 1.0
S2 F:SF4501 2.3 47.5 1.0
FE2 F:SF4501 2.7 47.5 1.0
FE4 F:SF4501 2.7 47.5 1.0
FE3 F:SF4501 2.7 47.5 1.0
CB F:CYS405 3.4 47.5 1.0
N F:CYS405 3.5 47.5 1.0
CB F:CYS408 3.8 34.3 1.0
S1 F:SF4501 3.9 47.5 1.0
CA F:CYS405 4.0 47.5 1.0
N F:ILE447 4.3 24.8 1.0
O F:CYS405 4.3 47.5 1.0
CB F:ILE447 4.3 24.8 1.0
SG F:CYS408 4.5 34.3 1.0
CB F:GLN404 4.5 36.5 1.0
C F:CYS405 4.6 47.5 1.0
C F:GLN404 4.6 36.5 1.0
CB F:THR446 4.7 26.1 1.0
N F:GLN404 4.7 36.5 1.0
OE1 F:GLN404 4.7 36.5 1.0
N F:CYS448 4.7 24.7 1.0
CG1 F:ILE447 4.8 24.8 1.0
O F:SER401 4.8 30.5 1.0
SG F:CYS448 4.8 24.7 1.0
CA F:ILE447 4.9 24.8 1.0
CA F:GLN404 4.9 36.5 1.0
SG F:CYS402 4.9 32.0 1.0
CD1 F:ILE447 4.9 24.8 1.0

Iron binding site 8 out of 29 in 7ar8

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Iron binding site 8 out of 29 in the Cryo-Em Structure of Arabidopsis Thaliana Complex-I (Closed Conformation)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Cryo-Em Structure of Arabidopsis Thaliana Complex-I (Closed Conformation) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:47.5
occ:1.00
 FE2 F:SF4501 0.0 47.5 1.0
SG F:CYS408 2.3 34.3 1.0
S3 F:SF4501 2.3 47.5 1.0
S4 F:SF4501 2.3 47.5 1.0
S1 F:SF4501 2.3 47.5 1.0
FE1 F:SF4501 2.7 47.5 1.0
FE3 F:SF4501 2.7 47.5 1.0
FE4 F:SF4501 2.7 47.5 1.0
CB F:CYS408 2.8 34.3 1.0
O F:SER401 3.2 30.5 1.0
S2 F:SF4501 3.9 47.5 1.0
C F:SER401 4.2 30.5 1.0
CB F:SER401 4.2 30.5 1.0
CA F:CYS408 4.2 34.3 1.0
SG F:CYS405 4.4 47.5 1.0
CA F:SER401 4.4 30.5 1.0
CD2 F:LEU450 4.4 22.6 1.0
CB F:LEU450 4.5 22.6 1.0
SG F:CYS402 4.6 32.0 1.0
C F:CYS408 4.7 34.3 1.0
SG F:CYS448 4.7 24.7 1.0
N F:GLY451 4.8 32.6 1.0
CG F:LEU450 5.0 22.6 1.0

Iron binding site 9 out of 29 in 7ar8

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Iron binding site 9 out of 29 in the Cryo-Em Structure of Arabidopsis Thaliana Complex-I (Closed Conformation)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Cryo-Em Structure of Arabidopsis Thaliana Complex-I (Closed Conformation) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:47.5
occ:1.00
 FE3 F:SF4501 0.0 47.5 1.0
SG F:CYS402 2.3 32.0 1.0
S2 F:SF4501 2.3 47.5 1.0
S1 F:SF4501 2.3 47.5 1.0
S4 F:SF4501 2.3 47.5 1.0
FE4 F:SF4501 2.7 47.5 1.0
FE2 F:SF4501 2.7 47.5 1.0
FE1 F:SF4501 2.7 47.5 1.0
O F:SER401 2.9 30.5 1.0
S3 F:SF4501 3.9 47.5 1.0
CB F:CYS402 3.9 32.0 1.0
C F:SER401 3.9 30.5 1.0
N F:GLN404 4.0 36.5 1.0
CB F:GLN404 4.0 36.5 1.0
C F:CYS402 4.4 32.0 1.0
N F:GLY403 4.4 47.5 1.0
CD F:PRO246 4.5 22.5 1.0
CA F:CYS402 4.5 32.0 1.0
CA F:GLN404 4.5 36.5 1.0
OE1 F:GLN404 4.6 36.5 1.0
N F:CYS402 4.6 32.0 1.0
N F:CYS405 4.7 47.5 1.0
SG F:CYS448 4.7 24.7 1.0
O F:CYS402 4.8 32.0 1.0
CG1 F:ILE228 4.9 28.3 1.0
SG F:CYS408 4.9 34.3 1.0
SG F:CYS405 4.9 47.5 1.0
CD1 F:ILE228 4.9 28.3 1.0
CA F:SER401 4.9 30.5 1.0
C F:GLY403 5.0 47.5 1.0
CG F:PRO246 5.0 22.5 1.0

Iron binding site 10 out of 29 in 7ar8

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Iron binding site 10 out of 29 in the Cryo-Em Structure of Arabidopsis Thaliana Complex-I (Closed Conformation)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Cryo-Em Structure of Arabidopsis Thaliana Complex-I (Closed Conformation) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:47.5
occ:1.00
 FE4 F:SF4501 0.0 47.5 1.0
SG F:CYS448 2.3 24.7 1.0
S1 F:SF4501 2.3 47.5 1.0
S3 F:SF4501 2.3 47.5 1.0
S2 F:SF4501 2.3 47.5 1.0
FE3 F:SF4501 2.7 47.5 1.0
FE1 F:SF4501 2.7 47.5 1.0
FE2 F:SF4501 2.7 47.5 1.0
CB F:CYS448 3.5 24.7 1.0
N F:CYS448 3.8 24.7 1.0
S4 F:SF4501 3.9 47.5 1.0
CA F:CYS448 4.1 24.7 1.0
CB F:LEU450 4.2 22.6 1.0
C F:CYS448 4.4 24.7 1.0
CD1 F:ILE228 4.5 28.3 1.0
O F:CYS448 4.6 24.7 1.0
SG F:CYS402 4.6 32.0 1.0
N F:LEU450 4.6 22.6 1.0
CG F:PRO246 4.7 22.5 1.0
SG F:CYS405 4.7 47.5 1.0
SG F:CYS408 4.8 34.3 1.0
O F:SER401 4.8 30.5 1.0
N F:GLY451 4.9 32.6 1.0
CB F:CYS408 4.9 34.3 1.0
C F:ILE447 4.9 24.8 1.0
CA F:LEU450 5.0 22.6 1.0
CD F:PRO246 5.0 22.5 1.0

Reference:

N.Klusch, J.Senkler, O.Yildiz, W.Kuehlbrandt, H.P.Braun. A Ferredoxin Bridge Connects the Two Arms of Plant Mitochondrial Complex I. Plant Cell V. 33 2072 2021.
ISSN: ESSN 1532-298X
PubMed: 33768254
DOI: 10.1093/PLCELL/KOAB092
Page generated: Wed Aug 7 22:34:06 2024

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