Iron in PDB 6q8x: Respiratory Complex I From Thermus Thermophilus with Bound Pyridaben.

Enzymatic activity of Respiratory Complex I From Thermus Thermophilus with Bound Pyridaben.

All present enzymatic activity of Respiratory Complex I From Thermus Thermophilus with Bound Pyridaben.:
1.6.5.11;

Protein crystallography data

The structure of Respiratory Complex I From Thermus Thermophilus with Bound Pyridaben., PDB code: 6q8x 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) 58.41 / 3.51
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 95.190, 338.640, 263.230, 90.00, 100.41, 90.00
R / Rfree (%) 21.5 / 23.2

Other elements in 6q8x:

The structure of Respiratory Complex I From Thermus Thermophilus with Bound Pyridaben. also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

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 Pyridaben. (pdb code 6q8x). 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 Pyridaben., PDB code: 6q8x:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 64 in 6q8x

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Iron binding site 1 out of 64 in the Respiratory Complex I From Thermus Thermophilus with Bound Pyridaben.


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 Pyridaben. within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Fe501

b:66.5
occ:1.00
FE1 1:SF4501 0.0 66.5 1.0
S2 1:SF4501 2.3 66.5 1.0
S4 1:SF4501 2.3 66.5 1.0
S3 1:SF4501 2.3 66.5 1.0
SG 1:CYS356 2.3 62.1 1.0
FE2 1:SF4501 2.7 66.5 1.0
FE3 1:SF4501 2.7 66.5 1.0
FE4 1:SF4501 2.7 66.5 1.0
CB 1:CYS356 3.0 57.7 1.0
N 1:CYS356 3.6 66.6 1.0
CA 1:CYS356 3.9 59.1 1.0
S1 1:SF4501 3.9 66.5 1.0
N 1:PHE399 4.1 92.2 1.0
N 1:CYS400 4.1 95.1 1.0
CB 1:PHE399 4.1 0.0 1.0
CB 1:CYS359 4.3 94.5 1.0
CA 1:PHE399 4.5 97.7 1.0
SG 1:CYS359 4.6 99.8 1.0
O 1:CYS400 4.6 78.0 1.0
C 1:LYS355 4.7 73.3 1.0
C 1:PHE399 4.8 0.3 1.0
CB 1:SER398 4.8 75.7 1.0
SG 1:CYS353 4.8 43.4 1.0
CB 1:LYS355 4.8 78.5 1.0
SG 1:CYS400 4.8 90.9 1.0
O 1:CYS356 4.9 52.8 1.0
C 1:CYS356 4.9 58.4 1.0
N 1:LYS355 4.9 83.9 1.0
C 1:SER398 5.0 88.5 1.0

Iron binding site 2 out of 64 in 6q8x

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Iron binding site 2 out of 64 in the Respiratory Complex I From Thermus Thermophilus with Bound Pyridaben.


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 Pyridaben. within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Fe501

b:66.5
occ:1.00
FE2 1:SF4501 0.0 66.5 1.0
S3 1:SF4501 2.3 66.5 1.0
S4 1:SF4501 2.3 66.5 1.0
S1 1:SF4501 2.3 66.5 1.0
SG 1:CYS359 2.3 99.8 1.0
FE1 1:SF4501 2.7 66.5 1.0
FE3 1:SF4501 2.7 66.5 1.0
FE4 1:SF4501 2.7 66.5 1.0
CB 1:CYS359 3.0 94.5 1.0
OG 1:SER352 3.3 62.0 1.0
S2 1:SF4501 3.9 66.5 1.0
CB 1:SER352 4.4 66.6 1.0
N 1:CYS353 4.4 64.0 1.0
CA 1:CYS359 4.5 81.0 1.0
CB 1:CYS356 4.7 57.7 1.0
CA 1:SER352 4.7 71.1 1.0
SG 1:CYS356 4.7 62.1 1.0
N 1:ARG360 4.8 58.3 1.0
SG 1:CYS400 4.8 90.9 1.0
CD2 1:LEU402 4.8 59.8 1.0
SG 1:CYS353 4.9 43.4 1.0
CB 1:LEU402 4.9 59.4 1.0
C 1:CYS359 4.9 73.6 1.0
N 1:GLY354 4.9 82.8 1.0

Iron binding site 3 out of 64 in 6q8x

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Iron binding site 3 out of 64 in the Respiratory Complex I From Thermus Thermophilus with Bound Pyridaben.


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 Pyridaben. within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Fe501

b:66.5
occ:1.00
FE3 1:SF4501 0.0 66.5 1.0
S2 1:SF4501 2.3 66.5 1.0
S4 1:SF4501 2.3 66.5 1.0
S1 1:SF4501 2.3 66.5 1.0
SG 1:CYS400 2.3 90.9 1.0
FE4 1:SF4501 2.7 66.5 1.0
FE2 1:SF4501 2.7 66.5 1.0
FE1 1:SF4501 2.7 66.5 1.0
CB 1:CYS400 3.3 88.4 1.0
O 1:CYS400 3.5 78.0 1.0
N 1:CYS400 3.7 95.1 1.0
CA 1:CYS400 3.9 88.0 1.0
S3 1:SF4501 3.9 66.5 1.0
C 1:CYS400 4.0 80.2 1.0
CB 1:LEU402 4.1 59.4 1.0
CD1 1:ILE181 4.6 54.3 1.0
CG 1:PRO199 4.7 57.5 1.0
SG 1:CYS353 4.7 43.4 1.0
N 1:LEU402 4.7 70.0 1.0
SG 1:CYS359 4.8 99.8 1.0
SG 1:CYS356 4.9 62.1 1.0
C 1:PHE399 4.9 0.3 1.0
CD1 1:LEU402 5.0 54.1 1.0

Iron binding site 4 out of 64 in 6q8x

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Iron binding site 4 out of 64 in the Respiratory Complex I From Thermus Thermophilus with Bound Pyridaben.


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 Pyridaben. within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Fe501

b:66.5
occ:1.00
FE4 1:SF4501 0.0 66.5 1.0
S2 1:SF4501 2.3 66.5 1.0
S3 1:SF4501 2.3 66.5 1.0
S1 1:SF4501 2.3 66.5 1.0
SG 1:CYS353 2.3 43.4 1.0
FE3 1:SF4501 2.7 66.5 1.0
FE1 1:SF4501 2.7 66.5 1.0
FE2 1:SF4501 2.7 66.5 1.0
CB 1:CYS353 3.3 55.0 1.0
N 1:CYS353 3.7 64.0 1.0
N 1:GLY354 3.7 82.8 1.0
N 1:LYS355 3.8 83.9 1.0
CA 1:CYS353 3.9 67.0 1.0
S4 1:SF4501 3.9 66.5 1.0
C 1:CYS353 4.2 76.7 1.0
CB 1:LYS355 4.2 78.5 1.0
N 1:CYS356 4.3 66.6 1.0
OG 1:SER352 4.5 62.0 1.0
CA 1:LYS355 4.5 80.6 1.0
CD 1:PRO199 4.7 54.0 1.0
C 1:GLY354 4.7 85.3 1.0
SG 1:CYS400 4.7 90.9 1.0
CA 1:GLY354 4.7 84.5 1.0
CG 1:PRO199 4.7 57.5 1.0
SG 1:CYS356 4.8 62.1 1.0
C 1:SER352 4.9 62.4 1.0
SG 1:CYS359 4.9 99.8 1.0
C 1:LYS355 5.0 73.3 1.0

Iron binding site 5 out of 64 in 6q8x

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Iron binding site 5 out of 64 in the Respiratory Complex I From Thermus Thermophilus with Bound Pyridaben.


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 Pyridaben. within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Fe201

b:67.0
occ:1.00
FE1 2:FES201 0.0 67.0 1.0
S2 2:FES201 2.2 67.0 1.0
S1 2:FES201 2.2 67.0 1.0
SG 2:CYS88 2.3 98.0 1.0
SG 2:CYS83 2.3 0.5 1.0
FE2 2:FES201 3.1 67.0 1.0
CB 2:CYS88 3.1 0.0 1.0
CB 2:CYS83 3.5 0.4 1.0
N 2:CYS88 3.9 0.8 1.0
CA 2:CYS88 4.1 0.4 1.0
N 2:LEU125 4.1 0.6 1.0
OG1 2:THR85 4.2 80.1 1.0
CB 2:THR85 4.2 82.2 1.0
CA 2:CYS124 4.4 0.9 1.0
CG2 2:VAL133 4.5 87.3 1.0
SG 2:CYS124 4.5 0.8 1.0
CB 2:VAL133 4.8 89.5 1.0
N 2:THR85 4.8 91.3 1.0
C 2:CYS124 4.8 0.6 1.0
CA 2:CYS83 4.9 0.3 1.0
SG 2:CYS128 4.9 0.7 1.0
O 2:SER127 4.9 0.3 1.0
CB 2:CYS124 4.9 0.6 1.0
CA 2:THR85 5.0 90.7 1.0

Iron binding site 6 out of 64 in 6q8x

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Iron binding site 6 out of 64 in the Respiratory Complex I From Thermus Thermophilus with Bound Pyridaben.


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 Pyridaben. within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Fe201

b:67.0
occ:1.00
FE2 2:FES201 0.0 67.0 1.0
S2 2:FES201 2.2 67.0 1.0
S1 2:FES201 2.2 67.0 1.0
SG 2:CYS124 2.3 0.8 1.0
SG 2:CYS128 2.3 0.7 1.0
FE1 2:FES201 3.1 67.0 1.0
N 2:GLY126 3.7 0.8 1.0
CB 2:CYS124 3.7 0.6 1.0
CB 2:CYS128 3.8 0.4 1.0
CA 2:GLY126 4.1 0.7 1.0
CA 2:CYS124 4.1 0.9 1.0
N 2:SER127 4.1 1.0 1.0
CA 2:CYS128 4.2 0.8 1.0
N 2:LEU125 4.2 0.6 1.0
N 2:CYS128 4.2 0.7 1.0
N 1:GLY99 4.4 0.5 1.0
CB 2:SER87 4.4 0.5 1.0
C 2:SER127 4.5 0.5 1.0
C 2:GLY126 4.5 0.5 1.0
C 2:CYS124 4.5 0.6 1.0
CA 1:PRO98 4.5 0.7 1.0
C 2:LEU125 4.7 0.9 1.0
CB 1:PRO98 4.7 0.5 1.0
SG 2:CYS83 4.7 0.5 1.0
O 2:SER127 4.8 0.3 1.0
OG 2:SER87 4.9 0.2 1.0
CB 2:THR85 4.9 82.2 1.0
SG 2:CYS88 4.9 98.0 1.0

Iron binding site 7 out of 64 in 6q8x

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Iron binding site 7 out of 64 in the Respiratory Complex I From Thermus Thermophilus with Bound Pyridaben.


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 Pyridaben. within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Fe801

b:43.8
occ:1.00
FE1 3:SF4801 0.0 43.8 1.0
S4 3:SF4801 2.3 43.8 1.0
S2 3:SF4801 2.3 43.8 1.0
S3 3:SF4801 2.3 43.8 1.0
SG 3:CYS128 2.3 44.7 1.0
FE3 3:SF4801 2.7 43.8 1.0
FE4 3:SF4801 2.7 43.8 1.0
FE2 3:SF4801 2.7 43.8 1.0
CB 3:CYS128 3.3 58.3 1.0
NE2 3:HIS115 3.7 61.5 1.0
S1 3:SF4801 3.9 43.8 1.0
CD2 3:HIS115 4.4 62.1 1.0
CG 3:GLN131 4.5 51.8 1.0
CA 3:VAL232 4.6 36.7 1.0
CE1 3:HIS115 4.6 60.3 1.0
CA 3:CYS128 4.7 62.7 1.0
CG1 3:VAL232 4.7 32.6 1.0
N 3:GLY233 4.8 39.5 1.0
SG 3:CYS122 4.8 73.9 1.0
SG 3:CYS119 4.8 84.8 1.0
O 3:PRO231 4.8 56.5 1.0
CD 3:GLN131 4.9 53.1 1.0
CB 3:VAL232 4.9 36.2 1.0
NE2 3:GLN131 4.9 50.9 1.0
CB 3:LEU130 4.9 58.8 1.0

Iron binding site 8 out of 64 in 6q8x

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Iron binding site 8 out of 64 in the Respiratory Complex I From Thermus Thermophilus with Bound Pyridaben.


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 Pyridaben. within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Fe801

b:43.8
occ:1.00
FE2 3:SF4801 0.0 43.8 1.0
S1 3:SF4801 2.3 43.8 1.0
S4 3:SF4801 2.3 43.8 1.0
S3 3:SF4801 2.3 43.8 1.0
SG 3:CYS119 2.3 84.8 1.0
FE3 3:SF4801 2.6 43.8 1.0
FE4 3:SF4801 2.7 43.8 1.0
FE1 3:SF4801 2.7 43.8 1.0
CB 3:CYS119 3.4 79.7 1.0
CA 3:CYS119 3.5 72.2 1.0
N 3:CYS119 3.8 76.7 1.0
NE2 3:GLN131 3.9 50.9 1.0
S2 3:SF4801 3.9 43.8 1.0
NE2 3:HIS115 4.0 61.5 1.0
CD2 3:HIS115 4.0 62.1 1.0
CD 3:GLN131 4.6 53.1 1.0
CG 3:GLN131 4.6 51.8 1.0
CE 4:MET321 4.8 53.1 1.0
SG 3:CYS122 4.8 73.9 1.0
CB 3:CYS122 4.8 74.5 1.0
C 3:ASP118 4.8 73.5 1.0
SD 4:MET321 4.8 61.0 1.0
SG 3:CYS128 4.8 44.7 1.0
C 3:CYS119 4.9 59.5 1.0

Iron binding site 9 out of 64 in 6q8x

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Iron binding site 9 out of 64 in the Respiratory Complex I From Thermus Thermophilus with Bound Pyridaben.


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 Pyridaben. within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Fe801

b:43.8
occ:1.00
FE3 3:SF4801 0.0 43.8 1.0
NE2 3:HIS115 1.5 61.5 1.0
CD2 3:HIS115 2.2 62.1 1.0
S2 3:SF4801 2.3 43.8 1.0
S1 3:SF4801 2.3 43.8 1.0
S4 3:SF4801 2.3 43.8 1.0
FE2 3:SF4801 2.6 43.8 1.0
FE1 3:SF4801 2.7 43.8 1.0
FE4 3:SF4801 2.7 43.8 1.0
CE1 3:HIS115 2.7 60.3 1.0
CG 3:HIS115 3.5 61.3 1.0
ND1 3:HIS115 3.7 59.1 1.0
S3 3:SF4801 3.9 43.8 1.0
CG 3:ARG180 4.4 61.5 1.0
CD 3:ARG180 4.5 56.5 1.0
SG 3:CYS119 4.7 84.8 1.0
CE 4:MET321 4.7 53.1 1.0
SG 3:CYS122 4.8 73.9 1.0
SG 3:CYS128 4.8 44.7 1.0
CB 3:ARG180 4.8 68.3 1.0
CB 3:HIS115 4.8 66.9 1.0
N 3:GLY233 4.9 39.5 1.0
CG1 3:VAL232 4.9 32.6 1.0
CB 3:VAL232 4.9 36.2 1.0
CD 3:PRO116 5.0 85.5 1.0

Iron binding site 10 out of 64 in 6q8x

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Iron binding site 10 out of 64 in the Respiratory Complex I From Thermus Thermophilus with Bound Pyridaben.


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 Pyridaben. within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Fe801

b:43.8
occ:1.00
FE4 3:SF4801 0.0 43.8 1.0
S2 3:SF4801 2.3 43.8 1.0
S1 3:SF4801 2.3 43.8 1.0
S3 3:SF4801 2.3 43.8 1.0
SG 3:CYS122 2.3 73.9 1.0
FE3 3:SF4801 2.7 43.8 1.0
FE2 3:SF4801 2.7 43.8 1.0
FE1 3:SF4801 2.7 43.8 1.0
CB 3:CYS122 3.1 74.5 1.0
S4 3:SF4801 3.9 43.8 1.0
NE2 3:HIS115 4.1 61.5 1.0
N 3:GLY233 4.3 39.5 1.0
CA 3:CYS119 4.4 72.2 1.0
CD 3:ARG180 4.6 56.5 1.0
CA 3:GLY233 4.6 40.2 1.0
CA 3:CYS122 4.6 68.1 1.0
N 3:CYS119 4.6 76.7 1.0
SG 3:CYS119 4.8 84.8 1.0
SG 3:CYS128 4.8 44.7 1.0
CB 3:LYS124 4.8 96.8 1.0
CD2 3:HIS115 4.9 62.1 1.0
NE 3:ARG180 5.0 53.7 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: Sun Dec 13 16:50:30 2020

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