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Iron in PDB 8b9z: Drosophila Melanogaster Complex I in the Active State (DM1)

Enzymatic activity of Drosophila Melanogaster Complex I in the Active State (DM1)

All present enzymatic activity of Drosophila Melanogaster Complex I in the Active State (DM1):
1.6.99.3; 7.1.1.2;

Other elements in 8b9z:

The structure of Drosophila Melanogaster Complex I in the Active State (DM1) also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Sodium (Na) 1 atom

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Iron atom in the Drosophila Melanogaster Complex I in the Active State (DM1) (pdb code 8b9z). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 28 binding sites of Iron where determined in the Drosophila Melanogaster Complex I in the Active State (DM1), PDB code: 8b9z:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 28 in 8b9z

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Iron binding site 1 out of 28 in the Drosophila Melanogaster Complex I in the Active State (DM1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Drosophila Melanogaster Complex I in the Active State (DM1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:65.8
occ:1.00
 FE1 B:SF4301 0.0 65.8 1.0
SG B:CYS161 2.2 67.1 1.0
S3 B:SF4301 2.3 65.8 1.0
S4 B:SF4301 2.3 65.8 1.0
S2 B:SF4301 2.3 65.8 1.0
FE2 B:SF4301 2.7 65.8 1.0
FE4 B:SF4301 2.7 65.8 1.0
FE3 B:SF4301 2.7 65.8 1.0
CB B:CYS161 3.0 67.1 1.0
S1 B:SF4301 3.9 65.8 1.0
OG1 B:THR133 3.9 74.8 1.0
N B:CYS161 4.0 67.1 1.0
CA B:CYS161 4.1 67.1 1.0
CQ1 D:2MR123 4.5 75.0 1.0
SG B:CYS191 4.6 65.5 1.0
SG B:CYS97 4.7 73.7 1.0
SG B:CYS96 4.8 75.5 1.0
CE2 B:TYR168 4.9 69.1 1.0

Iron binding site 2 out of 28 in 8b9z

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Iron binding site 2 out of 28 in the Drosophila Melanogaster Complex I in the Active State (DM1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Drosophila Melanogaster Complex I in the Active State (DM1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:65.8
occ:1.00
 FE2 B:SF4301 0.0 65.8 1.0
SG B:CYS191 2.2 65.5 1.0
S3 B:SF4301 2.3 65.8 1.0
S4 B:SF4301 2.3 65.8 1.0
S1 B:SF4301 2.3 65.8 1.0
FE1 B:SF4301 2.7 65.8 1.0
FE3 B:SF4301 2.7 65.8 1.0
FE4 B:SF4301 2.7 65.8 1.0
CB B:CYS191 3.4 65.5 1.0
CA B:CYS191 3.5 65.5 1.0
C B:CYS191 3.7 65.5 1.0
S2 B:SF4301 3.9 65.8 1.0
NH2 D:ARG143 4.1 72.7 1.0
O B:CYS191 4.1 65.5 1.0
N B:PRO192 4.2 68.9 1.0
NE D:ARG143 4.3 72.7 1.0
CD2 D:HIS228 4.6 76.2 1.0
CA B:PRO192 4.6 68.9 1.0
SG B:CYS161 4.6 67.1 1.0
CZ D:ARG143 4.6 72.7 1.0
SG B:CYS96 4.7 75.5 1.0
NE2 D:HIS228 4.7 76.2 1.0
SG B:CYS97 4.7 73.7 1.0
O B:GLY190 4.9 64.2 1.0
N B:CYS191 4.9 65.5 1.0

Iron binding site 3 out of 28 in 8b9z

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Iron binding site 3 out of 28 in the Drosophila Melanogaster Complex I in the Active State (DM1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Drosophila Melanogaster Complex I in the Active State (DM1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:65.8
occ:1.00
 FE3 B:SF4301 0.0 65.8 1.0
SG B:CYS96 2.2 75.5 1.0
S2 B:SF4301 2.3 65.8 1.0
S1 B:SF4301 2.3 65.8 1.0
S4 B:SF4301 2.3 65.8 1.0
FE4 B:SF4301 2.7 65.8 1.0
FE1 B:SF4301 2.7 65.8 1.0
FE2 B:SF4301 2.7 65.8 1.0
CB B:CYS96 3.5 75.5 1.0
NE2 D:HIS228 3.8 76.2 1.0
N B:CYS97 3.9 73.7 1.0
S3 B:SF4301 3.9 65.8 1.0
C B:CYS96 3.9 75.5 1.0
CA B:CYS96 3.9 75.5 1.0
N B:CYS96 4.0 75.5 1.0
O B:CYS96 4.5 75.5 1.0
CG D:ARG143 4.5 72.7 1.0
CD2 D:HIS228 4.5 76.2 1.0
CQ1 D:2MR123 4.7 75.0 1.0
NE D:ARG143 4.7 72.7 1.0
SG B:CYS161 4.7 67.1 1.0
SG B:CYS97 4.8 73.7 1.0
SG B:CYS191 4.8 65.5 1.0
CE1 D:HIS228 4.8 76.2 1.0
CA B:CYS97 4.9 73.7 1.0

Iron binding site 4 out of 28 in 8b9z

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Iron binding site 4 out of 28 in the Drosophila Melanogaster Complex I in the Active State (DM1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Drosophila Melanogaster Complex I in the Active State (DM1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:65.8
occ:1.00
 FE4 B:SF4301 0.0 65.8 1.0
SG B:CYS97 2.2 73.7 1.0
S2 B:SF4301 2.3 65.8 1.0
S1 B:SF4301 2.3 65.8 1.0
S3 B:SF4301 2.3 65.8 1.0
FE3 B:SF4301 2.7 65.8 1.0
FE1 B:SF4301 2.7 65.8 1.0
FE2 B:SF4301 2.7 65.8 1.0
N B:CYS97 3.4 73.7 1.0
CB B:CYS97 3.4 73.7 1.0
CA B:CYS97 3.8 73.7 1.0
S4 B:SF4301 3.9 65.8 1.0
C B:CYS96 4.2 75.5 1.0
CA B:PRO192 4.4 68.9 1.0
CB B:PRO192 4.6 68.9 1.0
CA B:GLY159 4.6 65.7 1.0
CB B:CYS161 4.7 67.1 1.0
SG B:CYS161 4.7 67.1 1.0
SG B:CYS96 4.7 75.5 1.0
O B:CYS96 4.8 75.5 1.0
SG B:CYS191 4.8 65.5 1.0
CA B:CYS191 4.8 65.5 1.0
N B:PRO192 4.8 68.9 1.0
CA B:GLY132 5.0 71.9 1.0
N B:CYS96 5.0 75.5 1.0

Iron binding site 5 out of 28 in 8b9z

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Iron binding site 5 out of 28 in the Drosophila Melanogaster Complex I in the Active State (DM1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Drosophila Melanogaster Complex I in the Active State (DM1) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe301

b:103.9
occ:1.00
 FE1 E:FES301 0.0 103.9 1.0
SG E:CYS133 2.2 95.5 1.0
SG E:CYS128 2.2 95.3 1.0
S2 E:FES301 2.2 103.9 1.0
S1 E:FES301 2.2 103.9 1.0
FE2 E:FES301 2.6 103.9 1.0
CB E:CYS133 3.2 95.5 1.0
CB E:CYS128 3.2 95.3 1.0
N E:CYS133 4.2 95.5 1.0
CA E:CYS133 4.3 95.5 1.0
O E:THR130 4.3 92.7 1.0
CA E:CYS169 4.3 94.8 1.0
SG E:CYS169 4.4 94.8 1.0
OG1 E:THR130 4.5 92.7 1.0
N E:LEU170 4.5 97.1 1.0
CA E:CYS173 4.6 99.0 1.0
SG E:CYS173 4.6 99.0 1.0
CA E:CYS128 4.6 95.3 1.0
CB E:CYS169 4.6 94.8 1.0
O E:GLU168 4.7 93.4 1.0
SD E:MET178 4.7 102.1 1.0
CG E:MET178 4.8 102.1 1.0
CB E:CYS173 4.9 99.0 1.0
C E:CYS128 4.9 95.3 1.0
N E:CYS173 4.9 99.0 1.0
C E:CYS169 5.0 94.8 1.0

Iron binding site 6 out of 28 in 8b9z

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Iron binding site 6 out of 28 in the Drosophila Melanogaster Complex I in the Active State (DM1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Drosophila Melanogaster Complex I in the Active State (DM1) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe301

b:103.9
occ:1.00
 FE2 E:FES301 0.0 103.9 1.0
S2 E:FES301 2.2 103.9 1.0
S1 E:FES301 2.2 103.9 1.0
SG E:CYS173 2.3 99.0 1.0
SG E:CYS169 2.3 94.8 1.0
FE1 E:FES301 2.6 103.9 1.0
CB E:CYS173 3.4 99.0 1.0
CB E:CYS169 3.4 94.8 1.0
CA E:CYS173 3.7 99.0 1.0
N E:CYS173 3.8 99.0 1.0
CA E:CYS169 3.9 94.8 1.0
N E:GLY171 4.0 99.0 1.0
N E:LEU170 4.2 97.1 1.0
SG E:CYS128 4.2 95.3 1.0
C E:CYS169 4.3 94.8 1.0
N F:GLY138 4.3 98.1 1.0
N E:ALA172 4.4 101.1 1.0
SG E:CYS133 4.4 95.5 1.0
CA E:GLY171 4.5 99.0 1.0
C E:ALA172 4.6 101.1 1.0
CA F:PRO137 4.7 92.7 1.0
OG1 E:THR130 4.8 92.7 1.0
CD E:PRO132 4.8 96.6 1.0
C E:GLY171 4.8 99.0 1.0
C E:LEU170 4.9 97.1 1.0
O E:THR131 5.0 93.9 1.0

Iron binding site 7 out of 28 in 8b9z

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Iron binding site 7 out of 28 in the Drosophila Melanogaster Complex I in the Active State (DM1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Drosophila Melanogaster Complex I in the Active State (DM1) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe502

b:68.2
occ:1.00
 FE1 F:SF4502 0.0 68.2 1.0
SG F:CYS397 2.3 67.5 1.0
S3 F:SF4502 2.3 68.2 1.0
S4 F:SF4502 2.3 68.2 1.0
S2 F:SF4502 2.3 68.2 1.0
FE2 F:SF4502 2.7 68.2 1.0
FE3 F:SF4502 2.7 68.2 1.0
FE4 F:SF4502 2.7 68.2 1.0
CB F:CYS397 3.4 67.5 1.0
N F:CYS397 3.7 67.5 1.0
S1 F:SF4502 3.9 68.2 1.0
CB F:CYS400 4.0 69.6 1.0
CA F:CYS397 4.0 67.5 1.0
O F:CYS397 4.2 67.5 1.0
N F:ILE439 4.2 68.3 1.0
SG F:CYS400 4.4 69.6 1.0
CB F:THR438 4.4 70.8 1.0
C F:CYS397 4.4 67.5 1.0
CB F:ILE439 4.5 68.3 1.0
N F:CYS440 4.6 73.1 1.0
CG2 F:THR438 4.7 70.8 1.0
SG F:CYS394 4.7 72.9 1.0
SG F:CYS440 4.8 73.1 1.0
CG1 F:ILE439 4.8 68.3 1.0
C F:GLN396 4.9 70.2 1.0
N F:GLN396 4.9 70.2 1.0
CA F:ILE439 4.9 68.3 1.0
CB F:GLN396 4.9 70.2 1.0
CD1 F:ILE439 5.0 68.3 1.0

Iron binding site 8 out of 28 in 8b9z

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Iron binding site 8 out of 28 in the Drosophila Melanogaster Complex I in the Active State (DM1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Drosophila Melanogaster Complex I in the Active State (DM1) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe502

b:68.2
occ:1.00
 FE2 F:SF4502 0.0 68.2 1.0
SG F:CYS400 2.2 69.6 1.0
S4 F:SF4502 2.3 68.2 1.0
S3 F:SF4502 2.3 68.2 1.0
S1 F:SF4502 2.3 68.2 1.0
FE1 F:SF4502 2.7 68.2 1.0
FE4 F:SF4502 2.7 68.2 1.0
FE3 F:SF4502 2.7 68.2 1.0
CB F:CYS400 2.9 69.6 1.0
S2 F:SF4502 3.9 68.2 1.0
CB F:SER393 4.1 73.7 1.0
CA F:CYS400 4.2 69.6 1.0
N F:CYS394 4.2 72.9 1.0
CA F:SER393 4.3 73.7 1.0
C F:CYS400 4.4 69.6 1.0
CD2 F:LEU442 4.5 79.2 1.0
CB F:LEU442 4.5 79.2 1.0
SG F:CYS440 4.5 73.1 1.0
SG F:CYS397 4.6 67.5 1.0
O F:CYS400 4.7 69.6 1.0
C F:SER393 4.7 73.7 1.0
N F:GLY395 4.7 70.1 1.0
SG F:CYS394 4.7 72.9 1.0
N F:ARG401 4.8 69.1 1.0
N F:GLY443 4.8 78.4 1.0
CG F:LEU442 4.9 79.2 1.0
N F:CYS400 5.0 69.6 1.0

Iron binding site 9 out of 28 in 8b9z

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Iron binding site 9 out of 28 in the Drosophila Melanogaster Complex I in the Active State (DM1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Drosophila Melanogaster Complex I in the Active State (DM1) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe502

b:68.2
occ:1.00
 FE3 F:SF4502 0.0 68.2 1.0
SG F:CYS440 2.2 73.1 1.0
S4 F:SF4502 2.3 68.2 1.0
S2 F:SF4502 2.3 68.2 1.0
S1 F:SF4502 2.3 68.2 1.0
FE4 F:SF4502 2.7 68.2 1.0
FE2 F:SF4502 2.7 68.2 1.0
FE1 F:SF4502 2.7 68.2 1.0
CB F:CYS440 3.4 73.1 1.0
N F:CYS440 3.8 73.1 1.0
S3 F:SF4502 3.9 68.2 1.0
CA F:CYS440 4.0 73.1 1.0
CB F:LEU442 4.1 79.2 1.0
CG F:PRO238 4.2 74.8 1.0
CD1 F:ILE220 4.4 80.0 1.0
C F:CYS440 4.4 73.1 1.0
O F:CYS440 4.6 73.1 1.0
SG F:CYS394 4.7 72.9 1.0
SG F:CYS400 4.7 69.6 1.0
N F:LEU442 4.7 79.2 1.0
CD F:PRO238 4.7 74.8 1.0
SG F:CYS397 4.8 67.5 1.0
N F:GLY443 4.8 78.4 1.0
CA F:LEU442 4.9 79.2 1.0
C F:ILE439 5.0 68.3 1.0

Iron binding site 10 out of 28 in 8b9z

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Iron binding site 10 out of 28 in the Drosophila Melanogaster Complex I in the Active State (DM1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Drosophila Melanogaster Complex I in the Active State (DM1) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe502

b:68.2
occ:1.00
 FE4 F:SF4502 0.0 68.2 1.0
SG F:CYS394 2.2 72.9 1.0
S3 F:SF4502 2.3 68.2 1.0
S1 F:SF4502 2.3 68.2 1.0
S2 F:SF4502 2.3 68.2 1.0
FE3 F:SF4502 2.7 68.2 1.0
FE2 F:SF4502 2.7 68.2 1.0
FE1 F:SF4502 2.7 68.2 1.0
CB F:CYS394 3.3 72.9 1.0
N F:CYS394 3.6 72.9 1.0
N F:GLN396 3.8 70.2 1.0
N F:GLY395 3.8 70.1 1.0
CA F:CYS394 3.8 72.9 1.0
S4 F:SF4502 3.9 68.2 1.0
CB F:GLN396 4.1 70.2 1.0
C F:CYS394 4.1 72.9 1.0
CD F:PRO238 4.3 74.8 1.0
N F:CYS397 4.4 67.5 1.0
CA F:GLN396 4.5 70.2 1.0
CG F:PRO238 4.6 74.8 1.0
C F:GLY395 4.7 70.1 1.0
C F:SER393 4.7 73.7 1.0
SG F:CYS400 4.7 69.6 1.0
SG F:CYS440 4.7 73.1 1.0
CA F:GLY395 4.8 70.1 1.0
NE2 F:GLN396 4.8 70.2 1.0
SG F:CYS397 4.8 67.5 1.0
CD1 F:ILE220 4.9 80.0 1.0

Reference:

A.A.Agip, I.Chung, A.Sanchez-Martinez, A.J.Whitworth, J.Hirst. Cryo-Em Structures of Mitochondrial Respiratory Complex I From Drosophila Melanogaster. Elife V. 12 2023.
ISSN: ESSN 2050-084X
PubMed: 36622099
DOI: 10.7554/ELIFE.84424
Page generated: Fri Aug 9 18:52:31 2024

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