Iron in PDB 8ca3: Cryo-Em Structure NDUFS4 Knockout Complex I From Mus Musculus Heart (Class 2).

Enzymatic activity of Cryo-Em Structure NDUFS4 Knockout Complex I From Mus Musculus Heart (Class 2).

All present enzymatic activity of Cryo-Em Structure NDUFS4 Knockout Complex I From Mus Musculus Heart (Class 2).:
7.1.1.2;

Other elements in 8ca3:

The structure of Cryo-Em Structure NDUFS4 Knockout Complex I From Mus Musculus Heart (Class 2). 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 NDUFS4 Knockout Complex I From Mus Musculus Heart (Class 2). (pdb code 8ca3). 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 NDUFS4 Knockout Complex I From Mus Musculus Heart (Class 2)., PDB code: 8ca3:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 28 in 8ca3

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Iron binding site 1 out of 28 in the Cryo-Em Structure NDUFS4 Knockout Complex I From Mus Musculus Heart (Class 2).


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 NDUFS4 Knockout Complex I From Mus Musculus Heart (Class 2). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:40.6
occ:1.00
 FE1 B:SF4201 0.0 40.6 1.0
SG B:CYS129 2.2 28.8 1.0
S2 B:SF4201 2.3 25.0 1.0
S3 B:SF4201 2.3 51.2 1.0
S4 B:SF4201 2.3 31.7 1.0
FE4 B:SF4201 2.7 50.0 1.0
FE3 B:SF4201 2.7 41.1 1.0
FE2 B:SF4201 2.8 48.5 1.0
CB B:CYS129 3.3 22.2 1.0
N B:CYS129 3.9 23.2 1.0
S1 B:SF4201 3.9 42.7 1.0
OG1 B:THR101 4.1 25.8 1.0
CA B:CYS129 4.2 19.9 1.0
SG B:CYS159 4.6 33.6 1.0
CQ1 D:2MR85 4.7 29.8 1.0
N B:THR101 4.7 20.5 1.0
CA B:GLY100 4.8 21.3 1.0
SG B:CYS64 4.8 37.5 1.0
SG B:CYS65 4.9 38.2 1.0
N B:SER128 5.0 23.7 1.0

Iron binding site 2 out of 28 in 8ca3

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Iron binding site 2 out of 28 in the Cryo-Em Structure NDUFS4 Knockout Complex I From Mus Musculus Heart (Class 2).


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 NDUFS4 Knockout Complex I From Mus Musculus Heart (Class 2). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:48.5
occ:1.00
 FE2 B:SF4201 0.0 48.5 1.0
S3 B:SF4201 2.3 51.2 1.0
S1 B:SF4201 2.3 42.7 1.0
S4 B:SF4201 2.3 31.7 1.0
SG B:CYS65 2.4 38.2 1.0
FE4 B:SF4201 2.7 50.0 1.0
FE1 B:SF4201 2.8 40.6 1.0
FE3 B:SF4201 2.8 41.1 1.0
CB B:CYS65 3.3 25.3 1.0
N B:CYS65 3.8 28.0 1.0
S2 B:SF4201 3.9 25.0 1.0
CA B:CYS65 4.0 28.6 1.0
CA B:PRO160 4.1 29.6 1.0
CB B:PRO160 4.1 29.4 1.0
CB B:CYS64 4.2 32.4 1.0
CA B:GLY127 4.3 21.9 1.0
N B:PRO160 4.5 26.5 1.0
SG B:CYS64 4.6 37.5 1.0
CA B:CYS159 4.7 20.5 1.0
C B:CYS64 4.8 24.5 1.0
N B:SER128 4.8 23.7 1.0
SG B:CYS129 4.8 28.8 1.0
C B:CYS159 4.9 25.5 1.0
SG B:CYS159 4.9 33.6 1.0
CA B:GLY100 4.9 21.3 1.0
CA B:CYS64 4.9 26.0 1.0
N B:CYS64 5.0 27.4 1.0

Iron binding site 3 out of 28 in 8ca3

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Iron binding site 3 out of 28 in the Cryo-Em Structure NDUFS4 Knockout Complex I From Mus Musculus Heart (Class 2).


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 NDUFS4 Knockout Complex I From Mus Musculus Heart (Class 2). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:41.1
occ:1.00
 FE3 B:SF4201 0.0 41.1 1.0
S2 B:SF4201 2.3 25.0 1.0
S1 B:SF4201 2.3 42.7 1.0
S4 B:SF4201 2.3 31.7 1.0
SG B:CYS64 2.3 37.5 1.0
FE1 B:SF4201 2.7 40.6 1.0
FE4 B:SF4201 2.7 50.0 1.0
FE2 B:SF4201 2.8 48.5 1.0
CB B:CYS64 2.9 32.4 1.0
NE2 D:HIS190 3.7 35.7 1.0
S3 B:SF4201 3.9 51.2 1.0
CA B:CYS64 4.0 26.0 1.0
N B:CYS64 4.1 27.4 1.0
CG D:ARG105 4.1 32.7 1.0
CQ1 D:2MR85 4.3 29.8 1.0
CD2 D:HIS190 4.3 38.3 1.0
N B:CYS65 4.4 28.0 1.0
C B:CYS64 4.7 24.5 1.0
SG B:CYS129 4.7 28.8 1.0
CD D:ARG105 4.8 23.4 1.0
SG B:CYS159 4.8 33.6 1.0
CE1 D:HIS190 4.9 34.7 1.0
SG B:CYS65 4.9 38.2 1.0
NH1 D:ARG105 5.0 25.6 1.0

Iron binding site 4 out of 28 in 8ca3

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Iron binding site 4 out of 28 in the Cryo-Em Structure NDUFS4 Knockout Complex I From Mus Musculus Heart (Class 2).


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 NDUFS4 Knockout Complex I From Mus Musculus Heart (Class 2). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:50.0
occ:1.00
 FE4 B:SF4201 0.0 50.0 1.0
S1 B:SF4201 2.3 42.7 1.0
S2 B:SF4201 2.3 25.0 1.0
S3 B:SF4201 2.3 51.2 1.0
SG B:CYS159 2.3 33.6 1.0
FE1 B:SF4201 2.7 40.6 1.0
FE3 B:SF4201 2.7 41.1 1.0
FE2 B:SF4201 2.7 48.5 1.0
CA B:CYS159 3.3 20.5 1.0
CB B:CYS159 3.4 29.1 1.0
C B:CYS159 3.6 25.5 1.0
S4 B:SF4201 3.9 31.7 1.0
N B:PRO160 4.1 26.5 1.0
O B:CYS159 4.1 33.8 1.0
NH1 D:ARG105 4.2 25.6 1.0
CA B:PRO160 4.5 29.6 1.0
O B:GLY158 4.6 33.4 1.0
N B:CYS159 4.6 27.1 1.0
SG B:CYS129 4.6 28.8 1.0
CD2 D:HIS190 4.7 38.3 1.0
SG B:CYS65 4.8 38.2 1.0
N B:SER128 4.8 23.7 1.0
CD B:PRO160 4.9 26.4 1.0
SG B:CYS64 4.9 37.5 1.0
NE2 D:HIS190 5.0 35.7 1.0

Iron binding site 5 out of 28 in 8ca3

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Iron binding site 5 out of 28 in the Cryo-Em Structure NDUFS4 Knockout Complex I From Mus Musculus Heart (Class 2).


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 NDUFS4 Knockout Complex I From Mus Musculus Heart (Class 2). within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe301

b:74.8
occ:1.00
 FE1 E:FES301 0.0 74.8 1.0
S2 E:FES301 2.2 52.1 1.0
S1 E:FES301 2.2 68.2 1.0
SG E:CYS103 2.3 65.7 1.0
SG E:CYS108 2.3 53.2 1.0
FE2 E:FES301 2.7 64.9 1.0
CB E:CYS108 3.3 48.0 1.0
CB E:CYS103 3.3 48.7 1.0
N E:CYS108 4.2 50.2 1.0
CA E:CYS108 4.3 47.2 1.0
CA E:CYS144 4.4 44.5 1.0
SG E:CYS144 4.6 42.4 1.0
CA E:CYS103 4.6 44.5 1.0
N E:LEU145 4.6 47.7 1.0
C E:CYS103 4.7 45.0 1.0
SG E:CYS148 4.8 71.9 1.0
CB E:THR105 4.8 41.6 1.0
N E:THR105 4.8 46.2 1.0
CB E:CYS144 4.8 35.2 1.0
OG1 E:THR105 4.9 44.0 1.0
CA E:CYS148 4.9 52.1 1.0
O E:CYS103 4.9 58.4 1.0
O E:THR105 5.0 54.0 1.0
CB E:MET153 5.0 51.8 1.0
O E:GLU143 5.0 54.8 1.0

Iron binding site 6 out of 28 in 8ca3

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Iron binding site 6 out of 28 in the Cryo-Em Structure NDUFS4 Knockout Complex I From Mus Musculus Heart (Class 2).


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 NDUFS4 Knockout Complex I From Mus Musculus Heart (Class 2). within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe301

b:64.9
occ:1.00
 FE2 E:FES301 0.0 64.9 1.0
S2 E:FES301 2.2 52.1 1.0
S1 E:FES301 2.2 68.2 1.0
SG E:CYS148 2.3 71.9 1.0
SG E:CYS144 2.3 42.4 1.0
FE1 E:FES301 2.7 74.8 1.0
CB E:CYS148 3.3 66.4 1.0
CB E:CYS144 3.3 35.2 1.0
CA E:CYS148 3.7 52.1 1.0
CA E:CYS144 3.7 44.5 1.0
N E:LEU145 4.1 47.7 1.0
O E:GLY146 4.1 60.8 1.0
N E:CYS148 4.1 54.2 1.0
SG E:CYS103 4.2 65.7 1.0
N E:GLY146 4.3 64.2 1.0
N F:GLY103 4.3 64.1 1.0
C E:CYS144 4.3 46.1 1.0
C E:GLY146 4.5 57.3 1.0
SG E:CYS108 4.6 53.2 1.0
CA E:GLY146 4.7 61.4 1.0
C E:ALA147 4.8 63.2 1.0
CG E:PRO107 4.8 43.4 1.0
CB E:PRO107 4.9 35.3 1.0
N E:CYS144 4.9 47.3 1.0
CA F:PRO102 5.0 55.1 1.0

Iron binding site 7 out of 28 in 8ca3

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Iron binding site 7 out of 28 in the Cryo-Em Structure NDUFS4 Knockout Complex I From Mus Musculus Heart (Class 2).


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 NDUFS4 Knockout Complex I From Mus Musculus Heart (Class 2). within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:49.7
occ:1.00
 FE1 F:SF4501 0.0 49.7 1.0
S3 F:SF4501 2.3 57.7 1.0
S4 F:SF4501 2.3 36.2 1.0
S2 F:SF4501 2.3 34.4 1.0
SG F:CYS362 2.3 43.5 1.0
FE2 F:SF4501 2.7 54.0 1.0
FE4 F:SF4501 2.7 45.5 1.0
FE3 F:SF4501 2.7 42.0 1.0
CB F:CYS362 3.4 24.1 1.0
N F:CYS362 3.6 19.1 1.0
S1 F:SF4501 3.9 48.9 1.0
CA F:CYS362 4.0 11.3 1.0
O F:CYS362 4.0 31.7 1.0
CB F:CYS365 4.1 27.9 1.0
N F:ILE404 4.3 24.2 1.0
C F:CYS362 4.4 12.6 1.0
CB F:ILE404 4.5 26.8 1.0
CB F:THR403 4.5 32.9 1.0
SG F:CYS365 4.5 24.7 1.0
N F:CYS405 4.6 33.4 1.0
CG2 F:THR403 4.7 31.0 1.0
CB F:GLN361 4.7 18.5 1.0
N F:GLN361 4.7 21.1 1.0
C F:GLN361 4.7 24.7 1.0
SG F:CYS359 4.8 23.7 1.0
SG F:CYS405 4.8 42.7 1.0
CA F:ILE404 4.9 21.7 1.0
CA F:GLN361 5.0 25.5 1.0

Iron binding site 8 out of 28 in 8ca3

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Iron binding site 8 out of 28 in the Cryo-Em Structure NDUFS4 Knockout Complex I From Mus Musculus Heart (Class 2).


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 NDUFS4 Knockout Complex I From Mus Musculus Heart (Class 2). within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:54.0
occ:1.00
 FE2 F:SF4501 0.0 54.0 1.0
SG F:CYS365 2.2 24.7 1.0
S4 F:SF4501 2.3 36.2 1.0
S3 F:SF4501 2.3 57.7 1.0
S1 F:SF4501 2.3 48.9 1.0
FE1 F:SF4501 2.7 49.7 1.0
FE4 F:SF4501 2.7 45.5 1.0
FE3 F:SF4501 2.7 42.0 1.0
CB F:CYS365 2.9 27.9 1.0
S2 F:SF4501 3.9 34.4 1.0
CD2 F:LEU407 4.1 43.3 1.0
CB F:SER358 4.2 28.8 1.0
CA F:CYS365 4.3 25.5 1.0
N F:CYS359 4.3 21.7 1.0
N F:GLY360 4.5 25.4 1.0
CA F:SER358 4.6 23.6 1.0
N F:ARG366 4.6 22.5 1.0
SG F:CYS362 4.6 43.5 1.0
C F:CYS365 4.7 28.2 1.0
CB F:LEU407 4.7 35.2 1.0
SG F:CYS405 4.7 42.7 1.0
SG F:CYS359 4.8 23.7 1.0
C F:SER358 4.9 21.4 1.0
O F:CYS362 4.9 31.7 1.0
N F:GLY408 5.0 37.9 1.0
CG F:LEU407 5.0 37.5 1.0

Iron binding site 9 out of 28 in 8ca3

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Iron binding site 9 out of 28 in the Cryo-Em Structure NDUFS4 Knockout Complex I From Mus Musculus Heart (Class 2).


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 NDUFS4 Knockout Complex I From Mus Musculus Heart (Class 2). within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:42.0
occ:1.00
 FE3 F:SF4501 0.0 42.0 1.0
S4 F:SF4501 2.3 36.2 1.0
S1 F:SF4501 2.3 48.9 1.0
SG F:CYS405 2.3 42.7 1.0
S2 F:SF4501 2.3 34.4 1.0
FE4 F:SF4501 2.7 45.5 1.0
FE2 F:SF4501 2.7 54.0 1.0
FE1 F:SF4501 2.7 49.7 1.0
CB F:CYS405 3.3 30.8 1.0
S3 F:SF4501 3.9 57.7 1.0
N F:CYS405 4.0 33.4 1.0
CB F:LEU407 4.1 35.2 1.0
CA F:CYS405 4.1 29.7 1.0
CD1 F:ILE185 4.3 45.2 1.0
CG F:PRO203 4.3 36.9 1.0
C F:CYS405 4.4 36.3 1.0
N F:LEU407 4.6 32.7 1.0
O F:CYS405 4.6 43.7 1.0
SG F:CYS365 4.7 24.7 1.0
SG F:CYS359 4.8 23.7 1.0
CD F:PRO203 4.8 30.4 1.0
SG F:CYS362 4.8 43.5 1.0
N F:GLY408 4.9 37.9 1.0
CA F:LEU407 4.9 33.0 1.0

Iron binding site 10 out of 28 in 8ca3

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Iron binding site 10 out of 28 in the Cryo-Em Structure NDUFS4 Knockout Complex I From Mus Musculus Heart (Class 2).


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 NDUFS4 Knockout Complex I From Mus Musculus Heart (Class 2). within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:45.5
occ:1.00
 FE4 F:SF4501 0.0 45.5 1.0
SG F:CYS359 2.3 23.7 1.0
S3 F:SF4501 2.3 57.7 1.0
S2 F:SF4501 2.3 34.4 1.0
S1 F:SF4501 2.3 48.9 1.0
FE3 F:SF4501 2.7 42.0 1.0
FE2 F:SF4501 2.7 54.0 1.0
FE1 F:SF4501 2.7 49.7 1.0
CB F:CYS359 3.3 19.1 1.0
N F:GLN361 3.6 21.1 1.0
N F:GLY360 3.7 25.4 1.0
N F:CYS359 3.8 21.7 1.0
CB F:GLN361 3.8 18.5 1.0
S4 F:SF4501 3.9 36.2 1.0
CA F:CYS359 3.9 23.2 1.0
C F:CYS359 4.0 22.9 1.0
CA F:GLN361 4.3 25.5 1.0
CD F:PRO203 4.4 30.4 1.0
N F:CYS362 4.4 19.1 1.0
C F:GLY360 4.5 8.9 1.0
CA F:GLY360 4.6 19.9 1.0
OE1 F:GLN361 4.8 32.9 1.0
CG F:PRO203 4.8 36.9 1.0
SG F:CYS365 4.8 24.7 1.0
SG F:CYS405 4.8 42.7 1.0
C F:GLN361 4.9 24.7 1.0
SG F:CYS362 4.9 43.5 1.0
C F:SER358 4.9 21.4 1.0
O F:CYS359 5.0 32.0 1.0

Reference:

Z.Yin, A.N.A.Agip, H.Bridges, J.Hirst. Cryo-Em Structure NDUFS4 Knockout Complex I From Mus Musculus Heart (Class 2). To Be Published 2023.
DOI: 10.1038/S44318-023-00001-4
Page generated: Fri Aug 9 21:14:45 2024

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