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Iron in PDB 7ak6: Cryo-Em Structure of ND6-P25L Mutant Respiratory Complex I From Mus Musculus at 3.8 A

Enzymatic activity of Cryo-Em Structure of ND6-P25L Mutant Respiratory Complex I From Mus Musculus at 3.8 A

All present enzymatic activity of Cryo-Em Structure of ND6-P25L Mutant Respiratory Complex I From Mus Musculus at 3.8 A:
7.1.1.2;

Other elements in 7ak6:

The structure of Cryo-Em Structure of ND6-P25L Mutant Respiratory Complex I From Mus Musculus at 3.8 A also contains other interesting chemical elements:

Zinc (Zn) 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 Cryo-Em Structure of ND6-P25L Mutant Respiratory Complex I From Mus Musculus at 3.8 A (pdb code 7ak6). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 28 binding sites of Iron where determined in the Cryo-Em Structure of ND6-P25L Mutant Respiratory Complex I From Mus Musculus at 3.8 A, PDB code: 7ak6:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 28 in 7ak6

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Iron binding site 1 out of 28 in the Cryo-Em Structure of ND6-P25L Mutant Respiratory Complex I From Mus Musculus at 3.8 A


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 ND6-P25L Mutant Respiratory Complex I From Mus Musculus at 3.8 A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:55.4
occ:1.00
 FE1 B:SF4201 0.0 55.4 1.0
SG B:CYS129 2.2 35.9 1.0
S2 B:SF4201 2.3 55.4 1.0
S3 B:SF4201 2.3 55.4 1.0
S4 B:SF4201 2.3 55.4 1.0
FE4 B:SF4201 2.7 55.4 1.0
FE3 B:SF4201 2.7 55.4 1.0
FE2 B:SF4201 2.7 55.4 1.0
CB B:CYS129 3.1 35.9 1.0
S1 B:SF4201 3.9 55.4 1.0
N B:CYS129 4.0 35.9 1.0
CA B:CYS129 4.1 35.9 1.0
OG1 B:THR101 4.5 35.1 1.0
SG B:CYS159 4.5 35.6 1.0
SG B:CYS64 4.7 37.4 1.0
SG B:CYS65 4.8 36.3 1.0
N B:THR101 5.0 35.1 1.0

Iron binding site 2 out of 28 in 7ak6

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Iron binding site 2 out of 28 in the Cryo-Em Structure of ND6-P25L Mutant Respiratory Complex I From Mus Musculus at 3.8 A


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 ND6-P25L Mutant Respiratory Complex I From Mus Musculus at 3.8 A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:55.4
occ:1.00
 FE2 B:SF4201 0.0 55.4 1.0
SG B:CYS65 2.3 36.3 1.0
S4 B:SF4201 2.3 55.4 1.0
S3 B:SF4201 2.3 55.4 1.0
S1 B:SF4201 2.3 55.4 1.0
FE3 B:SF4201 2.7 55.4 1.0
FE4 B:SF4201 2.7 55.4 1.0
FE1 B:SF4201 2.7 55.4 1.0
CB B:CYS65 3.3 36.3 1.0
N B:CYS65 3.7 36.3 1.0
CA B:CYS65 3.9 36.3 1.0
S2 B:SF4201 3.9 55.4 1.0
C B:CYS64 4.3 37.4 1.0
CA B:CYS159 4.4 35.6 1.0
CA B:PRO160 4.5 35.6 1.0
CA B:GLY127 4.6 33.5 1.0
O B:CYS64 4.6 37.4 1.0
O B:GLY158 4.6 32.7 1.0
SG B:CYS129 4.8 35.9 1.0
SG B:CYS159 4.8 35.6 1.0
SG B:CYS64 4.8 37.4 1.0
CB B:CYS129 4.9 35.9 1.0
CB B:PRO160 4.9 35.6 1.0
N B:SER128 4.9 31.4 1.0

Iron binding site 3 out of 28 in 7ak6

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Iron binding site 3 out of 28 in the Cryo-Em Structure of ND6-P25L Mutant Respiratory Complex I From Mus Musculus at 3.8 A


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 ND6-P25L Mutant Respiratory Complex I From Mus Musculus at 3.8 A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:55.4
occ:1.00
 FE3 B:SF4201 0.0 55.4 1.0
SG B:CYS64 2.3 37.4 1.0
S2 B:SF4201 2.3 55.4 1.0
S1 B:SF4201 2.3 55.4 1.0
S4 B:SF4201 2.3 55.4 1.0
FE2 B:SF4201 2.7 55.4 1.0
FE4 B:SF4201 2.7 55.4 1.0
FE1 B:SF4201 2.7 55.4 1.0
CB B:CYS64 3.4 37.4 1.0
C B:CYS64 3.7 37.4 1.0
N B:CYS65 3.8 36.3 1.0
CA B:CYS64 3.8 37.4 1.0
S3 B:SF4201 3.9 55.4 1.0
N B:CYS64 4.0 37.4 1.0
O B:CYS64 4.2 37.4 1.0
CE1 D:HIS190 4.3 36.6 1.0
CG D:ARG105 4.6 35.5 1.0
SG B:CYS65 4.7 36.3 1.0
SG B:CYS129 4.7 35.9 1.0
SG B:CYS159 4.8 35.6 1.0
CA B:CYS65 4.8 36.3 1.0
NE2 D:HIS190 4.8 36.6 1.0
CB B:CYS65 4.9 36.3 1.0
C B:ALA63 4.9 36.0 1.0
ND1 D:HIS190 5.0 36.6 1.0

Iron binding site 4 out of 28 in 7ak6

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Iron binding site 4 out of 28 in the Cryo-Em Structure of ND6-P25L Mutant Respiratory Complex I From Mus Musculus at 3.8 A


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 ND6-P25L Mutant Respiratory Complex I From Mus Musculus at 3.8 A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:55.4
occ:1.00
 FE4 B:SF4201 0.0 55.4 1.0
SG B:CYS159 2.3 35.6 1.0
S2 B:SF4201 2.3 55.4 1.0
S3 B:SF4201 2.3 55.4 1.0
S1 B:SF4201 2.3 55.4 1.0
FE1 B:SF4201 2.7 55.4 1.0
FE3 B:SF4201 2.7 55.4 1.0
FE2 B:SF4201 2.7 55.4 1.0
CB B:CYS159 3.1 35.6 1.0
CA B:CYS159 3.2 35.6 1.0
C B:CYS159 3.7 35.6 1.0
S4 B:SF4201 3.9 55.4 1.0
O B:CYS159 4.1 35.6 1.0
NE D:ARG105 4.1 35.5 1.0
N B:PRO160 4.3 35.6 1.0
NH1 D:ARG105 4.5 35.5 1.0
N B:CYS159 4.5 35.6 1.0
O B:GLY158 4.6 32.7 1.0
CA B:PRO160 4.6 35.6 1.0
SG B:CYS129 4.7 35.9 1.0
SG B:CYS64 4.7 37.4 1.0
CZ D:ARG105 4.8 35.5 1.0
ND1 D:HIS190 4.8 36.6 1.0
SG B:CYS65 4.8 36.3 1.0
CE1 D:HIS190 4.8 36.6 1.0
CG D:ARG105 4.8 35.5 1.0
C B:GLY158 4.9 32.7 1.0

Iron binding site 5 out of 28 in 7ak6

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Iron binding site 5 out of 28 in the Cryo-Em Structure of ND6-P25L Mutant Respiratory Complex I From Mus Musculus at 3.8 A


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 ND6-P25L Mutant Respiratory Complex I From Mus Musculus at 3.8 A within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe301

b:66.5
occ:1.00
 FE1 E:FES301 0.0 66.5 1.0
S2 E:FES301 2.2 66.5 1.0
S1 E:FES301 2.2 66.5 1.0
SG E:CYS108 2.3 64.9 1.0
SG E:CYS103 2.3 61.6 1.0
FE2 E:FES301 2.7 66.5 1.0
CB E:CYS103 3.3 61.6 1.0
CB E:CYS108 3.3 64.9 1.0
SG E:CYS144 4.1 58.7 1.0
N E:CYS108 4.1 64.9 1.0
CA E:CYS108 4.3 64.9 1.0
CA E:CYS144 4.5 58.7 1.0
O E:ALA151 4.5 68.5 1.0
CA E:CYS148 4.5 67.9 1.0
CA E:CYS103 4.7 61.6 1.0
CB E:THR105 4.7 59.0 1.0
SG E:CYS148 4.7 67.9 1.0
O E:ALA147 4.8 67.8 1.0
OG1 E:THR105 4.9 59.0 1.0
CB E:CYS144 4.9 58.7 1.0
N E:CYS148 4.9 67.9 1.0
O E:THR105 4.9 59.0 1.0
C E:ALA147 5.0 67.8 1.0

Iron binding site 6 out of 28 in 7ak6

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Iron binding site 6 out of 28 in the Cryo-Em Structure of ND6-P25L Mutant Respiratory Complex I From Mus Musculus at 3.8 A


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 ND6-P25L Mutant Respiratory Complex I From Mus Musculus at 3.8 A within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe301

b:66.5
occ:1.00
 FE2 E:FES301 0.0 66.5 1.0
S2 E:FES301 2.2 66.5 1.0
S1 E:FES301 2.2 66.5 1.0
SG E:CYS144 2.3 58.7 1.0
SG E:CYS148 2.3 67.9 1.0
FE1 E:FES301 2.7 66.5 1.0
CB E:CYS144 3.2 58.7 1.0
CB E:CYS148 3.3 67.9 1.0
CA E:CYS148 3.5 67.9 1.0
CA E:CYS144 3.7 58.7 1.0
N E:CYS148 3.9 67.9 1.0
N E:LEU145 4.2 63.1 1.0
SG E:CYS103 4.2 61.6 1.0
N F:GLY103 4.4 64.2 1.0
CA F:PRO102 4.5 58.5 1.0
C E:CYS144 4.5 58.7 1.0
C E:ALA147 4.6 67.8 1.0
N E:GLY146 4.8 63.9 1.0
N E:CYS144 4.8 58.7 1.0
SG E:CYS108 4.8 64.9 1.0
N E:ALA147 4.8 67.8 1.0
CB F:PRO102 4.9 58.5 1.0
CG E:PRO107 4.9 64.3 1.0
C E:CYS148 4.9 67.9 1.0
CB E:THR105 5.0 59.0 1.0
C F:PRO102 5.0 58.5 1.0

Iron binding site 7 out of 28 in 7ak6

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Iron binding site 7 out of 28 in the Cryo-Em Structure of ND6-P25L Mutant Respiratory Complex I From Mus Musculus at 3.8 A


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 ND6-P25L Mutant Respiratory Complex I From Mus Musculus at 3.8 A within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe502

b:55.4
occ:1.00
 FE1 F:SF4502 0.0 55.4 1.0
SG F:CYS362 2.2 38.8 1.0
S3 F:SF4502 2.3 55.4 1.0
S4 F:SF4502 2.3 55.4 1.0
S2 F:SF4502 2.3 55.4 1.0
FE4 F:SF4502 2.7 55.4 1.0
FE2 F:SF4502 2.7 55.4 1.0
FE3 F:SF4502 2.7 55.4 1.0
CB F:CYS362 3.1 38.8 1.0
N F:CYS362 3.8 38.8 1.0
S1 F:SF4502 3.9 55.4 1.0
CA F:CYS362 4.0 38.8 1.0
CB F:CYS365 4.4 39.7 1.0
CD1 F:ILE404 4.5 40.5 1.0
SG F:CYS359 4.5 42.1 1.0
CB F:ILE404 4.5 40.5 1.0
CG1 F:ILE404 4.6 40.5 1.0
CG F:GLN361 4.6 39.9 1.0
N F:ILE404 4.6 40.5 1.0
SG F:CYS365 4.7 39.7 1.0
N F:CYS405 4.8 43.5 1.0
SG F:CYS405 4.8 43.5 1.0
C F:GLN361 4.9 39.9 1.0
N F:GLN361 4.9 39.9 1.0

Iron binding site 8 out of 28 in 7ak6

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Iron binding site 8 out of 28 in the Cryo-Em Structure of ND6-P25L Mutant Respiratory Complex I From Mus Musculus at 3.8 A


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 ND6-P25L Mutant Respiratory Complex I From Mus Musculus at 3.8 A within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe502

b:55.4
occ:1.00
 FE2 F:SF4502 0.0 55.4 1.0
SG F:CYS365 2.2 39.7 1.0
S3 F:SF4502 2.3 55.4 1.0
S1 F:SF4502 2.3 55.4 1.0
S4 F:SF4502 2.3 55.4 1.0
FE1 F:SF4502 2.7 55.4 1.0
FE3 F:SF4502 2.7 55.4 1.0
FE4 F:SF4502 2.7 55.4 1.0
CB F:CYS365 2.9 39.7 1.0
OG F:SER358 3.0 43.2 1.0
S2 F:SF4502 3.9 55.4 1.0
CB F:SER358 4.4 43.2 1.0
CA F:CYS365 4.4 39.7 1.0
CD2 F:LEU407 4.6 46.2 1.0
SG F:CYS405 4.6 43.5 1.0
CB F:CYS362 4.7 38.8 1.0
N F:CYS359 4.7 42.1 1.0
SG F:CYS362 4.7 38.8 1.0
SG F:CYS359 4.7 42.1 1.0
N F:GLY360 4.8 39.3 1.0
CA F:SER358 4.9 43.2 1.0
CB F:LEU407 5.0 46.2 1.0

Iron binding site 9 out of 28 in 7ak6

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Iron binding site 9 out of 28 in the Cryo-Em Structure of ND6-P25L Mutant Respiratory Complex I From Mus Musculus at 3.8 A


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 ND6-P25L Mutant Respiratory Complex I From Mus Musculus at 3.8 A within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe502

b:55.4
occ:1.00
 FE3 F:SF4502 0.0 55.4 1.0
S4 F:SF4502 2.3 55.4 1.0
S2 F:SF4502 2.3 55.4 1.0
SG F:CYS405 2.3 43.5 1.0
S1 F:SF4502 2.3 55.4 1.0
FE2 F:SF4502 2.7 55.4 1.0
FE1 F:SF4502 2.7 55.4 1.0
FE4 F:SF4502 2.7 55.4 1.0
CB F:CYS405 3.4 43.5 1.0
S3 F:SF4502 3.9 55.4 1.0
N F:CYS405 4.0 43.5 1.0
CA F:CYS405 4.2 43.5 1.0
CB F:LEU407 4.3 46.2 1.0
CD1 F:ILE185 4.5 47.9 1.0
O F:CYS405 4.5 43.5 1.0
C F:CYS405 4.7 43.5 1.0
CG F:PRO203 4.7 44.9 1.0
SG F:CYS365 4.8 39.7 1.0
SG F:CYS362 4.8 38.8 1.0
SG F:CYS359 4.9 42.1 1.0

Iron binding site 10 out of 28 in 7ak6

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Iron binding site 10 out of 28 in the Cryo-Em Structure of ND6-P25L Mutant Respiratory Complex I From Mus Musculus at 3.8 A


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 ND6-P25L Mutant Respiratory Complex I From Mus Musculus at 3.8 A within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe502

b:55.4
occ:1.00
 FE4 F:SF4502 0.0 55.4 1.0
SG F:CYS359 2.3 42.1 1.0
S3 F:SF4502 2.3 55.4 1.0
S2 F:SF4502 2.3 55.4 1.0
S1 F:SF4502 2.3 55.4 1.0
FE1 F:SF4502 2.7 55.4 1.0
FE2 F:SF4502 2.7 55.4 1.0
FE3 F:SF4502 2.7 55.4 1.0
CB F:CYS359 3.3 42.1 1.0
N F:GLY360 3.6 39.3 1.0
N F:CYS359 3.7 42.1 1.0
S4 F:SF4502 3.9 55.4 1.0
CA F:CYS359 3.9 42.1 1.0
C F:CYS359 4.3 42.1 1.0
CD F:PRO203 4.4 44.9 1.0
OG F:SER358 4.4 43.2 1.0
N F:GLN361 4.4 39.9 1.0
CA F:GLY360 4.6 39.3 1.0
SG F:CYS362 4.7 38.8 1.0
CG F:PRO203 4.7 44.9 1.0
C F:SER358 4.7 43.2 1.0
CG F:GLN361 4.7 39.9 1.0
SG F:CYS365 4.8 39.7 1.0
SG F:CYS405 4.8 43.5 1.0
C F:GLY360 4.9 39.3 1.0
N F:CYS362 4.9 38.8 1.0

Reference:

Z.Yin, N.Burger, D.Kula-Alwar, D.Aksentijevic, H.R.Bridges, H.Prag, D.Grba, C.Viscomi, A.James, A.Mottahedin, T.Krieg, M.P.Murphy, J.Hirst. Structural Basis For A Complex I Mutation That Blocks Pathological Ros Production To Be Published.
DOI: 10.1038/S41467-021-20942-W
Page generated: Wed Aug 7 22:30:23 2024

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