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Iron in PDB 7arb: Cryo-Em Structure of Arabidopsis Thaliana Complex-I (Complete Composition)

Enzymatic activity of Cryo-Em Structure of Arabidopsis Thaliana Complex-I (Complete Composition)

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

Other elements in 7arb:

The structure of Cryo-Em Structure of Arabidopsis Thaliana Complex-I (Complete Composition) 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 (Complete Composition) (pdb code 7arb). 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 (Complete Composition), PDB code: 7arb:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 29 in 7arb

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


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 (Complete Composition) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe500

b:32.7
occ:1.00
 FE1 B:SF4500 0.0 32.7 1.0
SG B:CYS158 2.3 25.3 1.0
S3 B:SF4500 2.3 32.7 1.0
S2 B:SF4500 2.3 32.7 1.0
S4 B:SF4500 2.3 32.7 1.0
CB B:CYS158 2.7 25.3 1.0
FE4 B:SF4500 2.7 32.7 1.0
FE3 B:SF4500 2.7 32.7 1.0
FE2 B:SF4500 2.7 32.7 1.0
N B:CYS158 3.6 25.3 1.0
CA B:CYS158 3.7 25.3 1.0
S1 B:SF4500 3.9 32.7 1.0
OG1 B:THR130 3.9 28.5 1.0
SG B:CYS188 4.7 29.7 1.0
N B:THR130 4.8 28.5 1.0
C B:SER157 4.8 28.2 1.0
SG B:CYS94 4.8 32.6 1.0
SG B:CYS93 4.9 34.0 1.0
N B:SER157 4.9 28.2 1.0
C B:GLY129 5.0 28.0 1.0
C B:CYS158 5.0 25.3 1.0

Iron binding site 2 out of 29 in 7arb

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


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 (Complete Composition) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe500

b:32.7
occ:1.00
 FE2 B:SF4500 0.0 32.7 1.0
SG B:CYS94 2.3 32.6 1.0
S1 B:SF4500 2.3 32.7 1.0
S4 B:SF4500 2.3 32.7 1.0
S3 B:SF4500 2.3 32.7 1.0
FE4 B:SF4500 2.7 32.7 1.0
FE3 B:SF4500 2.7 32.7 1.0
FE1 B:SF4500 2.7 32.7 1.0
CB B:CYS94 3.7 32.6 1.0
S2 B:SF4500 3.9 32.7 1.0
SG B:CYS93 3.9 34.0 1.0
N B:CYS94 4.0 32.6 1.0
CA B:CYS94 4.3 32.6 1.0
CA B:GLY156 4.4 26.0 1.0
CA B:PRO189 4.5 29.6 1.0
CB B:PRO189 4.7 29.6 1.0
CB B:CYS158 4.7 25.3 1.0
CA B:CYS188 4.7 29.7 1.0
C B:CYS93 4.8 34.0 1.0
SG B:CYS188 4.8 29.7 1.0
N B:SER157 4.8 28.2 1.0
N B:CYS158 4.9 25.3 1.0
CD B:PRO190 4.9 29.2 1.0
SG B:CYS158 4.9 25.3 1.0

Iron binding site 3 out of 29 in 7arb

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


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 (Complete Composition) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe500

b:32.7
occ:1.00
 FE3 B:SF4500 0.0 32.7 1.0
SG B:CYS188 2.3 29.7 1.0
S1 B:SF4500 2.3 32.7 1.0
S2 B:SF4500 2.3 32.7 1.0
S4 B:SF4500 2.3 32.7 1.0
FE1 B:SF4500 2.7 32.7 1.0
FE4 B:SF4500 2.7 32.7 1.0
FE2 B:SF4500 2.7 32.7 1.0
CB B:CYS188 3.3 29.7 1.0
CA B:CYS188 3.5 29.7 1.0
S3 B:SF4500 3.9 32.7 1.0
C B:CYS188 3.9 29.7 1.0
SG B:CYS93 4.2 34.0 1.0
O B:CYS188 4.4 29.7 1.0
N B:PRO189 4.4 29.6 1.0
NE D:ARG69 4.4 30.7 1.0
SG B:CYS158 4.6 25.3 1.0
CD2 D:HIS154 4.7 34.5 1.0
CA B:PRO189 4.7 29.6 1.0
O B:GLY187 4.7 28.8 1.0
SG B:CYS94 4.8 32.6 1.0
N B:CYS188 4.8 29.7 1.0
NE2 D:HIS154 4.8 34.5 1.0
NH2 D:ARG69 4.9 30.7 1.0
N B:SER157 5.0 28.2 1.0

Iron binding site 4 out of 29 in 7arb

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


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 (Complete Composition) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe500

b:32.7
occ:1.00
 FE4 B:SF4500 0.0 32.7 1.0
SG B:CYS93 2.2 34.0 1.0
S2 B:SF4500 2.3 32.7 1.0
S3 B:SF4500 2.3 32.7 1.0
S1 B:SF4500 2.3 32.7 1.0
FE1 B:SF4500 2.7 32.7 1.0
FE3 B:SF4500 2.7 32.7 1.0
FE2 B:SF4500 2.7 32.7 1.0
S4 B:SF4500 3.9 32.7 1.0
CB B:CYS93 3.9 34.0 1.0
NE2 D:HIS154 4.1 34.5 1.0
N B:CYS93 4.2 34.0 1.0
CG D:ARG69 4.4 30.7 1.0
CA B:CYS93 4.5 34.0 1.0
CB B:ALA92 4.5 32.4 1.0
N B:CYS94 4.6 32.6 1.0
SG B:CYS158 4.6 25.3 1.0
SG B:CYS94 4.7 32.6 1.0
SG B:CYS188 4.7 29.7 1.0
CD2 D:HIS154 4.8 34.5 1.0
C B:CYS93 4.8 34.0 1.0
CB D:ARG69 5.0 30.7 1.0
NH1 D:ARG49 5.0 27.4 1.0

Iron binding site 5 out of 29 in 7arb

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


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 (Complete Composition) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe500

b:96.8
occ:1.00
 FE1 E:FES500 0.0 96.8 1.0
S2 E:FES500 2.2 96.8 1.0
S1 E:FES500 2.2 96.8 1.0
SD E:MET169 2.3 73.8 1.0
SG E:CYS171 2.3 74.0 1.0
CE E:MET169 2.4 73.8 1.0
FE2 E:FES500 2.7 96.8 1.0
CG E:MET169 3.4 73.8 1.0
CB E:CYS171 3.6 74.0 1.0
CA E:GLY131 4.1 87.5 1.0
CA E:CYS171 4.1 74.0 1.0
O E:MET180 4.1 76.7 1.0
SG E:CYS135 4.2 87.5 1.0
CB E:MET180 4.3 76.7 1.0
CE E:MET180 4.3 76.7 1.0
N E:CYS171 4.6 74.0 1.0
CB E:MET169 4.7 73.8 1.0
O E:VAL129 4.7 72.6 1.0
CB E:CYS135 4.8 87.5 1.0
C E:MET180 4.8 76.7 1.0
C E:GLY131 4.8 87.5 1.0
O E:ALA178 4.8 83.7 1.0
O E:CYS130 4.9 80.3 1.0
N E:GLY131 4.9 87.5 1.0
CA E:MET180 5.0 76.7 1.0
SG E:CYS175 5.0 82.4 1.0

Iron binding site 6 out of 29 in 7arb

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


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 (Complete Composition) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe500

b:96.8
occ:1.00
 FE2 E:FES500 0.0 96.8 1.0
S1 E:FES500 2.2 96.8 1.0
S2 E:FES500 2.2 96.8 1.0
CE E:MET180 2.5 76.7 1.0
FE1 E:FES500 2.7 96.8 1.0
SG E:CYS175 2.7 82.4 1.0
CB E:CYS135 3.0 87.5 1.0
SG E:CYS135 3.1 87.5 1.0
SG E:CYS171 3.3 74.0 1.0
CB E:CYS175 3.4 82.4 1.0
CB E:CYS171 3.7 74.0 1.0
O E:ALA178 4.0 83.7 1.0
SD E:MET180 4.2 76.7 1.0
CB E:MET180 4.4 76.7 1.0
CE E:MET169 4.4 73.8 1.0
CA E:CYS135 4.4 87.5 1.0
CG E:MET180 4.5 76.7 1.0
CA E:CYS175 4.5 82.4 1.0
CA E:CYS171 4.7 74.0 1.0
SD E:MET169 4.8 73.8 1.0
O E:ASN177 4.9 81.6 1.0
C E:ALA178 4.9 83.7 1.0

Iron binding site 7 out of 29 in 7arb

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


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 (Complete Composition) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:50.0
occ:1.00
 FE1 F:SF4501 0.0 50.0 1.0
SG F:CYS405 2.3 34.0 1.0
S4 F:SF4501 2.3 50.0 1.0
S3 F:SF4501 2.3 50.0 1.0
S2 F:SF4501 2.3 50.0 1.0
FE2 F:SF4501 2.7 50.0 1.0
FE3 F:SF4501 2.7 50.0 1.0
FE4 F:SF4501 2.7 50.0 1.0
CB F:CYS405 3.5 34.0 1.0
N F:CYS405 3.6 34.0 1.0
CB F:CYS408 3.8 38.8 1.0
S1 F:SF4501 3.9 50.0 1.0
CA F:CYS405 4.1 34.0 1.0
N F:ILE447 4.2 29.9 1.0
CB F:ILE447 4.4 29.9 1.0
SG F:CYS408 4.4 38.8 1.0
O F:CYS405 4.5 34.0 1.0
CB F:THR446 4.6 32.9 1.0
CB F:GLN404 4.6 29.9 1.0
N F:GLN404 4.6 29.9 1.0
C F:CYS405 4.7 34.0 1.0
C F:GLN404 4.7 29.9 1.0
CG1 F:ILE447 4.7 29.9 1.0
N F:CYS448 4.8 33.8 1.0
SG F:CYS448 4.8 33.8 1.0
SG F:CYS402 4.8 33.1 1.0
CA F:ILE447 4.9 29.9 1.0
CA F:GLN404 4.9 29.9 1.0
CD1 F:ILE447 5.0 29.9 1.0

Iron binding site 8 out of 29 in 7arb

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


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 (Complete Composition) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:50.0
occ:1.00
 FE2 F:SF4501 0.0 50.0 1.0
SG F:CYS408 2.3 38.8 1.0
S3 F:SF4501 2.3 50.0 1.0
S4 F:SF4501 2.3 50.0 1.0
S1 F:SF4501 2.3 50.0 1.0
FE1 F:SF4501 2.7 50.0 1.0
FE3 F:SF4501 2.7 50.0 1.0
FE4 F:SF4501 2.7 50.0 1.0
CB F:CYS408 2.8 38.8 1.0
OG F:SER401 3.4 35.2 1.0
S2 F:SF4501 3.9 50.0 1.0
CD2 F:LEU450 4.1 37.5 1.0
CA F:CYS408 4.2 38.8 1.0
CB F:SER401 4.3 35.2 1.0
SG F:CYS405 4.4 34.0 1.0
N F:CYS402 4.5 33.1 1.0
CA F:SER401 4.6 35.2 1.0
C F:CYS408 4.6 38.8 1.0
CB F:LEU450 4.6 37.5 1.0
SG F:CYS448 4.7 33.8 1.0
SG F:CYS402 4.7 33.1 1.0
N F:GLY403 4.8 34.1 1.0
N F:GLY451 4.8 37.0 1.0
CG F:LEU450 4.8 37.5 1.0
N F:ARG409 5.0 50.0 1.0
C F:SER401 5.0 35.2 1.0

Iron binding site 9 out of 29 in 7arb

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


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 (Complete Composition) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:50.0
occ:1.00
 FE3 F:SF4501 0.0 50.0 1.0
SG F:CYS402 2.3 33.1 1.0
S4 F:SF4501 2.3 50.0 1.0
S2 F:SF4501 2.3 50.0 1.0
S1 F:SF4501 2.3 50.0 1.0
FE4 F:SF4501 2.7 50.0 1.0
FE1 F:SF4501 2.7 50.0 1.0
FE2 F:SF4501 2.7 50.0 1.0
CB F:CYS402 3.6 33.1 1.0
N F:GLN404 3.8 29.9 1.0
N F:CYS402 3.8 33.1 1.0
S3 F:SF4501 3.9 50.0 1.0
CB F:GLN404 3.9 29.9 1.0
N F:GLY403 3.9 34.1 1.0
CA F:CYS402 4.1 33.1 1.0
C F:CYS402 4.2 33.1 1.0
CD F:PRO246 4.4 29.3 1.0
CA F:GLN404 4.4 29.9 1.0
OG F:SER401 4.6 35.2 1.0
N F:CYS405 4.6 34.0 1.0
OE1 F:GLN404 4.6 29.9 1.0
SG F:CYS448 4.7 33.8 1.0
C F:GLY403 4.7 34.1 1.0
CA F:GLY403 4.8 34.1 1.0
SG F:CYS405 4.9 34.0 1.0
SG F:CYS408 4.9 38.8 1.0
CG F:PRO246 4.9 29.3 1.0
C F:SER401 4.9 35.2 1.0
CG1 F:ILE228 5.0 35.2 1.0

Iron binding site 10 out of 29 in 7arb

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


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 (Complete Composition) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:50.0
occ:1.00
 FE4 F:SF4501 0.0 50.0 1.0
SG F:CYS448 2.3 33.8 1.0
S3 F:SF4501 2.3 50.0 1.0
S1 F:SF4501 2.3 50.0 1.0
S2 F:SF4501 2.3 50.0 1.0
FE3 F:SF4501 2.7 50.0 1.0
FE1 F:SF4501 2.7 50.0 1.0
FE2 F:SF4501 2.7 50.0 1.0
CB F:CYS448 3.6 33.8 1.0
S4 F:SF4501 3.9 50.0 1.0
N F:CYS448 3.9 33.8 1.0
CB F:LEU450 4.2 37.5 1.0
CA F:CYS448 4.2 33.8 1.0
CG F:PRO246 4.4 29.3 1.0
CD1 F:ILE228 4.4 35.2 1.0
C F:CYS448 4.5 33.8 1.0
O F:CYS448 4.7 33.8 1.0
SG F:CYS402 4.7 33.1 1.0
N F:LEU450 4.7 37.5 1.0
SG F:CYS408 4.7 38.8 1.0
CD F:PRO246 4.7 29.3 1.0
SG F:CYS405 4.8 34.0 1.0
N F:GLY451 4.9 37.0 1.0
CB F:CYS408 4.9 38.8 1.0
CA F:LEU450 5.0 37.5 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 22:34:08 2024

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