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Iron in PDB 6i0d: Respiratory Complex I From Thermus Thermophilus with Bound Decyl- Ubiquinone

Enzymatic activity of Respiratory Complex I From Thermus Thermophilus with Bound Decyl- Ubiquinone

All present enzymatic activity of Respiratory Complex I From Thermus Thermophilus with Bound Decyl- Ubiquinone:
1.6.5.11;

Protein crystallography data

The structure of Respiratory Complex I From Thermus Thermophilus with Bound Decyl- Ubiquinone, PDB code: 6i0d was solved by J.Gutierrez-Fernandez, G.S.Minhas, L.A.Sazanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.87 / 3.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 94.700, 328.000, 260.900, 90.00, 100.40, 90.00
R / Rfree (%) 21.4 / 22.5

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 64;

Binding sites:

The binding sites of Iron atom in the Respiratory Complex I From Thermus Thermophilus with Bound Decyl- Ubiquinone (pdb code 6i0d). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 64 binding sites of Iron where determined in the Respiratory Complex I From Thermus Thermophilus with Bound Decyl- Ubiquinone, PDB code: 6i0d:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 64 in 6i0d

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Iron binding site 1 out of 64 in the Respiratory Complex I From Thermus Thermophilus with Bound Decyl- Ubiquinone


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Respiratory Complex I From Thermus Thermophilus with Bound Decyl- Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Fe501

b:69.0
occ:1.00
 FE1 1:SF4501 0.0 69.0 1.0
S3 1:SF4501 2.3 60.5 1.0
S4 1:SF4501 2.3 63.7 1.0
S2 1:SF4501 2.3 66.1 1.0
SG 1:CYS356 2.3 79.8 1.0
FE2 1:SF4501 2.7 64.2 1.0
FE3 1:SF4501 2.7 64.8 1.0
FE4 1:SF4501 2.7 60.7 1.0
CB 1:CYS356 3.2 71.3 1.0
N 1:CYS356 3.6 59.3 1.0
S1 1:SF4501 3.9 60.2 1.0
CA 1:CYS356 4.0 64.0 1.0
CB 1:PHE399 4.1 26.1 1.0
CB 1:CYS359 4.1 37.5 1.0
N 1:CYS400 4.3 52.0 1.0
N 1:PHE399 4.4 50.2 1.0
SG 1:CYS359 4.5 29.2 1.0
CB 1:LYS355 4.6 63.5 1.0
CA 1:PHE399 4.7 49.0 1.0
C 1:LYS355 4.7 59.8 1.0
SG 1:CYS353 4.8 32.1 1.0
SG 1:CYS400 4.8 64.6 1.0
N 1:LYS355 4.9 64.6 1.0
CA 1:LYS355 5.0 63.0 1.0
C 1:PHE399 5.0 50.4 1.0

Iron binding site 2 out of 64 in 6i0d

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Iron binding site 2 out of 64 in the Respiratory Complex I From Thermus Thermophilus with Bound Decyl- Ubiquinone


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Respiratory Complex I From Thermus Thermophilus with Bound Decyl- Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Fe501

b:64.2
occ:1.00
 FE2 1:SF4501 0.0 64.2 1.0
S4 1:SF4501 2.3 63.7 1.0
SG 1:CYS359 2.3 29.2 1.0
S3 1:SF4501 2.3 60.5 1.0
S1 1:SF4501 2.3 60.2 1.0
FE1 1:SF4501 2.7 69.0 1.0
FE3 1:SF4501 2.7 64.8 1.0
FE4 1:SF4501 2.7 60.7 1.0
CB 1:CYS359 3.0 37.5 1.0
OG 1:SER352 3.4 28.7 1.0
S2 1:SF4501 3.9 66.1 1.0
CA 1:CYS359 4.4 46.8 1.0
CB 1:SER352 4.4 28.5 1.0
N 1:CYS353 4.4 40.0 1.0
SG 1:CYS356 4.7 79.8 1.0
N 1:ARG360 4.7 50.1 1.0
CB 1:CYS356 4.7 71.3 1.0
CA 1:SER352 4.8 28.4 1.0
N 1:GLY354 4.8 46.1 1.0
SG 1:CYS400 4.8 64.6 1.0
SG 1:CYS353 4.8 32.1 1.0
C 1:CYS359 4.8 52.9 1.0
CD2 1:LEU402 4.9 33.8 1.0
CB 1:LEU402 5.0 30.1 1.0

Iron binding site 3 out of 64 in 6i0d

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Iron binding site 3 out of 64 in the Respiratory Complex I From Thermus Thermophilus with Bound Decyl- Ubiquinone


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Respiratory Complex I From Thermus Thermophilus with Bound Decyl- Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Fe501

b:64.8
occ:1.00
 FE3 1:SF4501 0.0 64.8 1.0
S4 1:SF4501 2.3 63.7 1.0
S2 1:SF4501 2.3 66.1 1.0
S1 1:SF4501 2.3 60.2 1.0
SG 1:CYS400 2.3 64.6 1.0
FE2 1:SF4501 2.7 64.2 1.0
FE4 1:SF4501 2.7 60.7 1.0
FE1 1:SF4501 2.7 69.0 1.0
CB 1:CYS400 3.3 54.7 1.0
O 1:CYS400 3.8 54.5 1.0
N 1:CYS400 3.9 52.0 1.0
S3 1:SF4501 3.9 60.5 1.0
CA 1:CYS400 4.0 54.6 1.0
CD1 1:ILE181 4.2 95.6 1.0
C 1:CYS400 4.3 55.3 1.0
CB 1:LEU402 4.4 30.1 1.0
CG 1:PRO199 4.4 31.3 1.0
CD 1:PRO199 4.8 31.1 1.0
SG 1:CYS359 4.8 29.2 1.0
SG 1:CYS353 4.8 32.1 1.0
SG 1:CYS356 4.9 79.8 1.0

Iron binding site 4 out of 64 in 6i0d

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Iron binding site 4 out of 64 in the Respiratory Complex I From Thermus Thermophilus with Bound Decyl- Ubiquinone


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Respiratory Complex I From Thermus Thermophilus with Bound Decyl- Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Fe501

b:60.7
occ:1.00
 FE4 1:SF4501 0.0 60.7 1.0
S3 1:SF4501 2.3 60.5 1.0
S2 1:SF4501 2.3 66.1 1.0
S1 1:SF4501 2.3 60.2 1.0
SG 1:CYS353 2.3 32.1 1.0
FE3 1:SF4501 2.7 64.8 1.0
FE2 1:SF4501 2.7 64.2 1.0
FE1 1:SF4501 2.7 69.0 1.0
CB 1:CYS353 3.4 34.5 1.0
N 1:CYS353 3.8 40.0 1.0
N 1:GLY354 3.8 46.1 1.0
S4 1:SF4501 3.9 63.7 1.0
N 1:LYS355 3.9 64.6 1.0
CA 1:CYS353 4.0 40.2 1.0
C 1:CYS353 4.2 39.0 1.0
CB 1:LYS355 4.2 63.5 1.0
N 1:CYS356 4.6 59.3 1.0
CA 1:LYS355 4.6 63.0 1.0
OG 1:SER352 4.6 28.7 1.0
CD 1:PRO199 4.7 31.1 1.0
C 1:GLY354 4.8 63.9 1.0
SG 1:CYS400 4.8 64.6 1.0
CA 1:GLY354 4.8 54.6 1.0
SG 1:CYS356 4.8 79.8 1.0
SG 1:CYS359 4.9 29.2 1.0
C 1:SER352 5.0 34.5 1.0
CD1 1:ILE181 5.0 95.6 1.0

Iron binding site 5 out of 64 in 6i0d

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Iron binding site 5 out of 64 in the Respiratory Complex I From Thermus Thermophilus with Bound Decyl- Ubiquinone


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Respiratory Complex I From Thermus Thermophilus with Bound Decyl- Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Fe201

b:50.6
occ:1.00
 FE1 2:FES201 0.0 50.6 1.0
S1 2:FES201 2.2 47.4 1.0
S2 2:FES201 2.2 44.9 1.0
SG 2:CYS83 2.3 71.5 1.0
SG 2:CYS88 2.3 73.2 1.0
FE2 2:FES201 3.1 55.0 1.0
CB 2:CYS83 3.3 68.8 1.0
CB 2:CYS88 3.3 68.6 1.0
N 2:CYS88 4.2 53.4 1.0
CA 2:CYS124 4.3 0.8 1.0
CA 2:CYS88 4.3 62.7 1.0
OG1 2:THR85 4.4 46.3 1.0
N 2:LEU125 4.5 99.0 1.0
CB 2:THR85 4.5 46.3 1.0
CA 2:CYS83 4.6 66.7 1.0
CG2 2:VAL133 4.6 65.7 1.0
SG 2:CYS124 4.6 0.3 1.0
N 2:THR85 4.7 56.5 1.0
C 2:CYS83 4.7 76.7 1.0
CB 2:CYS124 4.7 0.3 1.0
O 2:SER127 4.8 77.1 1.0
SG 2:CYS128 4.9 75.1 1.0
C 2:CYS124 5.0 0.9 1.0
O 2:CYS83 5.0 85.5 1.0

Iron binding site 6 out of 64 in 6i0d

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Iron binding site 6 out of 64 in the Respiratory Complex I From Thermus Thermophilus with Bound Decyl- Ubiquinone


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Respiratory Complex I From Thermus Thermophilus with Bound Decyl- Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Fe201

b:55.0
occ:1.00
 FE2 2:FES201 0.0 55.0 1.0
S2 2:FES201 2.2 44.9 1.0
S1 2:FES201 2.2 47.4 1.0
SG 2:CYS128 2.3 75.1 1.0
SG 2:CYS124 2.3 0.3 1.0
FE1 2:FES201 3.1 50.6 1.0
CB 2:CYS124 3.5 0.3 1.0
CB 2:CYS128 3.6 77.0 1.0
CA 2:CYS124 4.0 0.8 1.0
CA 2:CYS128 4.0 80.3 1.0
N 2:GLY126 4.1 76.8 1.0
N 2:CYS128 4.2 76.0 1.0
N 2:LEU125 4.3 99.0 1.0
N 1:GLY99 4.4 0.9 1.0
N 2:SER127 4.4 80.2 1.0
C 2:SER127 4.5 77.2 1.0
C 2:CYS124 4.5 0.9 1.0
CA 2:GLY126 4.6 75.3 1.0
SG 2:CYS83 4.6 71.5 1.0
O 2:SER127 4.7 77.1 1.0
CA 1:PRO98 4.9 0.5 1.0
SG 2:CYS88 4.9 73.2 1.0
C 2:GLY126 4.9 74.0 1.0
CB 2:SER87 5.0 46.5 1.0

Iron binding site 7 out of 64 in 6i0d

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Iron binding site 7 out of 64 in the Respiratory Complex I From Thermus Thermophilus with Bound Decyl- Ubiquinone


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Respiratory Complex I From Thermus Thermophilus with Bound Decyl- Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Fe801

b:33.4
occ:1.00
 FE1 3:SF4801 0.0 33.4 1.0
S2 3:SF4801 2.3 33.4 1.0
S4 3:SF4801 2.3 33.4 1.0
S3 3:SF4801 2.3 33.4 1.0
SG 3:CYS128 2.3 79.2 1.0
FE3 3:SF4801 2.7 33.4 1.0
FE2 3:SF4801 2.7 33.4 1.0
FE4 3:SF4801 2.7 33.4 1.0
CB 3:CYS128 3.4 60.5 1.0
CG 3:GLN131 3.9 34.6 1.0
S1 3:SF4801 3.9 33.4 1.0
N 3:GLN131 4.4 34.8 1.0
CD 3:GLN131 4.5 45.0 1.0
CB 3:GLN131 4.6 34.4 1.0
NE2 3:GLN131 4.6 44.1 1.0
CB 3:LEU130 4.7 64.3 1.0
NE2 3:HIS115 4.7 49.2 1.0
O 3:PRO231 4.7 42.0 1.0
CA 3:CYS128 4.8 40.7 1.0
SG 3:CYS122 4.8 43.0 1.0
SG 3:CYS119 4.8 64.3 1.0
CA 3:GLN131 5.0 34.8 1.0

Iron binding site 8 out of 64 in 6i0d

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Iron binding site 8 out of 64 in the Respiratory Complex I From Thermus Thermophilus with Bound Decyl- Ubiquinone


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Respiratory Complex I From Thermus Thermophilus with Bound Decyl- Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Fe801

b:33.4
occ:1.00
 FE2 3:SF4801 0.0 33.4 1.0
S1 3:SF4801 2.3 33.4 1.0
S3 3:SF4801 2.3 33.4 1.0
S4 3:SF4801 2.3 33.4 1.0
SG 3:CYS119 2.3 64.3 1.0
FE3 3:SF4801 2.7 33.4 1.0
FE4 3:SF4801 2.7 33.4 1.0
FE1 3:SF4801 2.7 33.4 1.0
CB 3:CYS119 3.3 59.3 1.0
CA 3:CYS119 3.5 50.7 1.0
N 3:CYS119 3.8 46.5 1.0
S2 3:SF4801 3.9 33.4 1.0
NE2 3:GLN131 4.2 44.1 1.0
CG 3:GLN131 4.4 34.6 1.0
NE2 3:HIS115 4.5 49.2 1.0
CG1 4:ILE325 4.5 26.8 1.0
CD2 3:HIS115 4.6 49.5 1.0
CD1 4:ILE325 4.6 26.2 1.0
SG 3:CYS122 4.8 43.0 1.0
CD 3:GLN131 4.8 45.0 1.0
CB 3:CYS122 4.8 37.6 1.0
C 3:ASP118 4.8 42.6 1.0
C 3:CYS119 4.8 48.0 1.0
SD 4:MET321 4.9 40.8 1.0
SG 3:CYS128 4.9 79.2 1.0

Iron binding site 9 out of 64 in 6i0d

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Iron binding site 9 out of 64 in the Respiratory Complex I From Thermus Thermophilus with Bound Decyl- Ubiquinone


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Respiratory Complex I From Thermus Thermophilus with Bound Decyl- Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Fe801

b:33.4
occ:1.00
 FE3 3:SF4801 0.0 33.4 1.0
NE2 3:HIS115 2.2 49.2 1.0
S2 3:SF4801 2.3 33.4 1.0
S1 3:SF4801 2.3 33.4 1.0
S4 3:SF4801 2.3 33.4 1.0
FE2 3:SF4801 2.7 33.4 1.0
FE1 3:SF4801 2.7 33.4 1.0
FE4 3:SF4801 2.7 33.4 1.0
CD2 3:HIS115 3.0 49.5 1.0
CE1 3:HIS115 3.3 43.5 1.0
S3 3:SF4801 3.9 33.4 1.0
CG 3:HIS115 4.2 46.3 1.0
ND1 3:HIS115 4.3 46.1 1.0
CG1 3:VAL232 4.5 61.8 1.0
SG 3:CYS119 4.7 64.3 1.0
CD2 3:LEU130 4.7 73.1 1.0
SG 3:CYS128 4.7 79.2 1.0
SG 3:CYS122 4.8 43.0 1.0
CB 3:VAL232 4.9 56.5 1.0

Iron binding site 10 out of 64 in 6i0d

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Iron binding site 10 out of 64 in the Respiratory Complex I From Thermus Thermophilus with Bound Decyl- Ubiquinone


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Respiratory Complex I From Thermus Thermophilus with Bound Decyl- Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Fe801

b:33.4
occ:1.00
 FE4 3:SF4801 0.0 33.4 1.0
S2 3:SF4801 2.3 33.4 1.0
S1 3:SF4801 2.3 33.4 1.0
S3 3:SF4801 2.3 33.4 1.0
SG 3:CYS122 2.3 43.0 1.0
FE2 3:SF4801 2.7 33.4 1.0
FE3 3:SF4801 2.7 33.4 1.0
FE1 3:SF4801 2.7 33.4 1.0
CB 3:CYS122 3.1 37.6 1.0
S4 3:SF4801 3.9 33.4 1.0
CA 3:CYS119 4.3 50.7 1.0
N 3:GLY233 4.3 47.2 1.0
N 3:CYS119 4.5 46.5 1.0
CA 3:CYS122 4.6 34.1 1.0
CA 3:GLY233 4.7 49.9 1.0
SG 3:CYS119 4.7 64.3 1.0
NE2 3:HIS115 4.8 49.2 1.0
SG 3:CYS128 4.8 79.2 1.0
C 3:ASP118 4.8 42.6 1.0
CB 3:LYS124 4.9 55.4 1.0
CD 3:ARG180 5.0 56.6 1.0

Reference:

J.Gutierrez-Fernandez, K.Kaszuba, G.S.Minhas, R.Baradaran, M.Tambalo, D.T.Gallagher, L.A.Sazanov. Key Role of Quinone in the Mechanism of Respiratory Complex I. Nat Commun V. 11 4135 2020.
ISSN: ESSN 2041-1723
PubMed: 32811817
DOI: 10.1038/S41467-020-17957-0
Page generated: Tue Aug 6 21:53:33 2024

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