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Iron in PDB 6y11: Respiratory Complex I From Thermus Thermophilus

Protein crystallography data

The structure of Respiratory Complex I From Thermus Thermophilus, PDB code: 6y11 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) 58.67 / 3.11
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 96.280, 340.890, 263.300, 90.00, 100.57, 90.00
R / Rfree (%) 20.4 / 22.9

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 (pdb code 6y11). 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, PDB code: 6y11:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 64 in 6y11

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Iron binding site 1 out of 64 in the Respiratory Complex I From Thermus Thermophilus


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

b:75.0
occ:1.00
 FE1 1:SF4501 0.0 75.0 1.0
S4 1:SF4501 2.3 75.0 1.0
S2 1:SF4501 2.3 75.0 1.0
S3 1:SF4501 2.3 75.0 1.0
SG 1:CYS356 2.3 0.9 1.0
FE2 1:SF4501 2.6 75.0 1.0
FE3 1:SF4501 2.7 75.0 1.0
FE4 1:SF4501 2.8 75.0 1.0
CB 1:CYS356 3.1 47.8 1.0
N 1:CYS356 3.4 61.2 1.0
CA 1:CYS356 3.9 52.7 1.0
S1 1:SF4501 3.9 75.0 1.0
SG 1:CYS400 4.2 84.2 1.0
CB 1:PHE399 4.3 87.1 1.0
CB 1:CYS359 4.3 0.9 1.0
N 1:PHE399 4.4 85.3 1.0
N 1:CYS400 4.4 93.8 1.0
C 1:LYS355 4.5 63.7 1.0
SG 1:CYS359 4.5 100.0 1.0
CB 1:LYS355 4.5 77.4 1.0
N 1:LYS355 4.6 53.8 1.0
CA 1:LYS355 4.8 66.3 1.0
CA 1:PHE399 4.8 92.2 1.0
SG 1:CYS353 4.8 72.4 1.0
CB 1:SER398 4.9 73.1 1.0
O 1:CYS356 4.9 52.0 1.0
C 1:CYS356 4.9 59.5 1.0

Iron binding site 2 out of 64 in 6y11

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Iron binding site 2 out of 64 in the Respiratory Complex I From Thermus Thermophilus


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

b:75.0
occ:1.00
 FE2 1:SF4501 0.0 75.0 1.0
S4 1:SF4501 2.3 75.0 1.0
S3 1:SF4501 2.3 75.0 1.0
S1 1:SF4501 2.3 75.0 1.0
SG 1:CYS359 2.3 100.0 1.0
FE1 1:SF4501 2.6 75.0 1.0
FE3 1:SF4501 2.7 75.0 1.0
FE4 1:SF4501 2.7 75.0 1.0
CB 1:CYS359 3.1 0.9 1.0
OG 1:SER352 3.2 59.4 1.0
S2 1:SF4501 3.8 75.0 1.0
CB 1:SER352 4.3 58.2 1.0
SG 1:CYS400 4.4 84.2 1.0
N 1:CYS353 4.4 64.5 1.0
CD2 1:LEU402 4.6 0.1 1.0
CA 1:CYS359 4.6 0.0 1.0
CB 1:LEU402 4.6 0.8 1.0
N 1:GLY354 4.6 84.0 1.0
SG 1:CYS356 4.7 0.9 1.0
CB 1:CYS356 4.7 47.8 1.0
N 1:ARG360 4.7 0.6 1.0
CA 1:SER352 4.8 72.6 1.0
SG 1:CYS353 4.9 72.4 1.0
C 1:CYS359 4.9 0.9 1.0
N 1:CYS356 4.9 61.2 1.0
CG 1:LEU402 5.0 97.1 1.0

Iron binding site 3 out of 64 in 6y11

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Iron binding site 3 out of 64 in the Respiratory Complex I From Thermus Thermophilus


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

b:75.0
occ:1.00
 FE3 1:SF4501 0.0 75.0 1.0
SG 1:CYS400 1.8 84.2 1.0
S4 1:SF4501 2.3 75.0 1.0
S1 1:SF4501 2.3 75.0 1.0
S2 1:SF4501 2.3 75.0 1.0
FE2 1:SF4501 2.7 75.0 1.0
FE1 1:SF4501 2.7 75.0 1.0
FE4 1:SF4501 2.7 75.0 1.0
CB 1:CYS400 3.4 84.5 1.0
S3 1:SF4501 3.9 75.0 1.0
O 1:CYS400 3.9 79.0 1.0
CB 1:LEU402 4.0 0.8 1.0
N 1:CYS400 4.0 93.8 1.0
CA 1:CYS400 4.1 90.1 1.0
CD1 1:ILE181 4.2 96.2 1.0
C 1:CYS400 4.3 86.7 1.0
CG 1:PRO199 4.6 84.2 1.0
N 1:LEU402 4.7 0.9 1.0
SG 1:CYS359 4.8 100.0 1.0
SG 1:CYS356 4.8 0.9 1.0
SG 1:CYS353 4.8 72.4 1.0
CD1 1:LEU402 4.9 86.1 1.0
CG 1:LEU402 4.9 97.1 1.0
CA 1:LEU402 4.9 1.0 1.0

Iron binding site 4 out of 64 in 6y11

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Iron binding site 4 out of 64 in the Respiratory Complex I From Thermus Thermophilus


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

b:75.0
occ:1.00
 FE4 1:SF4501 0.0 75.0 1.0
S2 1:SF4501 2.3 75.0 1.0
S3 1:SF4501 2.3 75.0 1.0
S1 1:SF4501 2.3 75.0 1.0
SG 1:CYS353 2.3 72.4 1.0
FE2 1:SF4501 2.7 75.0 1.0
FE3 1:SF4501 2.7 75.0 1.0
FE1 1:SF4501 2.8 75.0 1.0
CB 1:CYS353 3.3 61.1 1.0
N 1:GLY354 3.5 84.0 1.0
N 1:LYS355 3.6 53.8 1.0
N 1:CYS353 3.7 64.5 1.0
CA 1:CYS353 3.9 57.0 1.0
S4 1:SF4501 4.0 75.0 1.0
C 1:CYS353 4.1 86.1 1.0
CB 1:LYS355 4.1 77.4 1.0
SG 1:CYS400 4.3 84.2 1.0
OG 1:SER352 4.3 59.4 1.0
N 1:CYS356 4.4 61.2 1.0
CA 1:LYS355 4.4 66.3 1.0
C 1:GLY354 4.5 55.0 1.0
CA 1:GLY354 4.5 71.8 1.0
CD 1:PRO199 4.8 85.1 1.0
CD1 1:ILE181 4.8 96.2 1.0
SG 1:CYS356 4.9 0.9 1.0
SG 1:CYS359 4.9 100.0 1.0
C 1:SER352 4.9 67.1 1.0
C 1:LYS355 5.0 63.7 1.0

Iron binding site 5 out of 64 in 6y11

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Iron binding site 5 out of 64 in the Respiratory Complex I From Thermus Thermophilus


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

b:75.5
occ:1.00
 FE1 2:FES201 0.0 75.5 1.0
S1 2:FES201 2.2 75.5 1.0
S2 2:FES201 2.2 75.5 1.0
SG 2:CYS88 2.3 83.5 1.0
SG 2:CYS83 2.3 0.8 1.0
FE2 2:FES201 3.0 75.5 1.0
CB 2:CYS88 3.4 77.1 1.0
CB 2:CYS83 3.5 0.5 1.0
CG2 2:VAL133 4.2 0.1 1.0
N 2:CYS88 4.2 76.3 1.0
CA 2:CYS124 4.2 0.1 1.0
N 2:LEU125 4.3 97.5 1.0
OG1 2:THR85 4.3 85.8 1.0
CB 2:THR85 4.4 90.7 1.0
CA 2:CYS88 4.4 75.0 1.0
SG 2:CYS124 4.5 0.4 1.0
N 2:THR85 4.7 84.9 1.0
CB 2:VAL133 4.7 0.4 1.0
CB 2:CYS124 4.8 0.8 1.0
CA 2:CYS83 4.8 95.0 1.0
O 2:SER127 4.8 0.2 1.0
C 2:CYS83 4.8 94.1 1.0
C 2:CYS124 4.8 1.0 1.0
O 2:THR85 4.9 0.1 1.0
O 2:CYS83 4.9 92.4 1.0
CA 2:THR85 5.0 91.8 1.0
SG 2:CYS128 5.0 0.8 1.0

Iron binding site 6 out of 64 in 6y11

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Iron binding site 6 out of 64 in the Respiratory Complex I From Thermus Thermophilus


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

b:75.5
occ:1.00
 FE2 2:FES201 0.0 75.5 1.0
S1 2:FES201 2.2 75.5 1.0
S2 2:FES201 2.2 75.5 1.0
SG 2:CYS124 2.3 0.4 1.0
SG 2:CYS128 2.3 0.8 1.0
FE1 2:FES201 3.0 75.5 1.0
CB 2:CYS124 3.6 0.8 1.0
CB 2:CYS128 3.6 0.1 1.0
CA 2:CYS128 3.9 0.3 1.0
N 2:CYS128 4.0 1.0 1.0
N 2:GLY126 4.0 0.0 1.0
CA 2:CYS124 4.1 0.1 1.0
N 2:SER127 4.2 0.6 1.0
C 2:SER127 4.3 0.4 1.0
N 1:GLY99 4.3 0.1 1.0
N 2:LEU125 4.4 97.5 1.0
CA 1:PRO98 4.4 0.9 1.0
CA 2:GLY126 4.4 0.9 1.0
C 2:CYS124 4.6 1.0 1.0
O 2:SER127 4.6 0.2 1.0
CB 1:PRO98 4.6 0.1 1.0
SG 2:CYS83 4.7 0.8 1.0
C 2:GLY126 4.7 1.0 1.0
CB 2:SER87 4.8 1.0 1.0
C 1:PRO98 4.9 0.0 1.0
CA 2:SER127 4.9 0.7 1.0
SG 2:CYS88 5.0 83.5 1.0

Iron binding site 7 out of 64 in 6y11

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Iron binding site 7 out of 64 in the Respiratory Complex I From Thermus Thermophilus


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

b:52.3
occ:1.00
 FE1 3:SF4801 0.0 52.3 1.0
S2 3:SF4801 2.3 52.3 1.0
S4 3:SF4801 2.3 52.3 1.0
S3 3:SF4801 2.3 52.3 1.0
SG 3:CYS128 2.3 73.9 1.0
FE4 3:SF4801 2.7 52.3 1.0
FE3 3:SF4801 2.7 52.3 1.0
FE2 3:SF4801 2.8 52.3 1.0
CB 3:CYS128 3.2 69.8 1.0
S1 3:SF4801 3.9 52.3 1.0
CG 3:GLN131 4.1 41.4 1.0
NE2 3:HIS115 4.2 80.3 1.0
CD 3:GLN131 4.5 32.7 1.0
N 3:GLN131 4.5 32.3 1.0
CB 3:LEU130 4.6 61.0 1.0
CB 3:GLN131 4.6 42.3 1.0
CA 3:CYS128 4.7 72.4 1.0
CB 3:LYS124 4.7 80.0 1.0
SG 3:CYS122 4.7 55.8 1.0
NE2 3:GLN131 4.8 43.1 1.0
SG 3:CYS119 4.8 57.7 1.0
CD2 3:HIS115 4.8 79.8 1.0
CG1 3:VAL232 4.9 74.3 1.0
OE1 3:GLN131 4.9 32.6 1.0
CD2 3:LEU130 5.0 73.7 1.0

Iron binding site 8 out of 64 in 6y11

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Iron binding site 8 out of 64 in the Respiratory Complex I From Thermus Thermophilus


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

b:52.3
occ:1.00
 FE2 3:SF4801 0.0 52.3 1.0
S4 3:SF4801 2.3 52.3 1.0
S1 3:SF4801 2.3 52.3 1.0
S3 3:SF4801 2.3 52.3 1.0
SG 3:CYS119 2.3 57.7 1.0
FE3 3:SF4801 2.7 52.3 1.0
FE4 3:SF4801 2.7 52.3 1.0
FE1 3:SF4801 2.8 52.3 1.0
CA 3:CYS119 3.1 48.3 1.0
CB 3:CYS119 3.2 49.2 1.0
N 3:CYS119 3.5 57.7 1.0
NE2 3:GLN131 3.7 43.1 1.0
S2 3:SF4801 3.9 52.3 1.0
CG 3:GLN131 4.2 41.4 1.0
CD 3:GLN131 4.2 32.7 1.0
C 3:ASP118 4.4 66.1 1.0
CG1 4:ILE325 4.5 56.0 1.0
C 3:CYS119 4.5 59.2 1.0
CB 3:CYS122 4.6 60.3 1.0
SD 4:MET321 4.6 79.9 1.0
CD2 3:HIS115 4.7 79.8 1.0
SG 3:CYS122 4.8 55.8 1.0
NE2 3:HIS115 4.8 80.3 1.0
SG 3:CYS128 4.9 73.9 1.0
O 3:CYS119 4.9 57.8 1.0

Iron binding site 9 out of 64 in 6y11

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Iron binding site 9 out of 64 in the Respiratory Complex I From Thermus Thermophilus


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

b:52.3
occ:1.00
 FE3 3:SF4801 0.0 52.3 1.0
NE2 3:HIS115 2.1 80.3 1.0
S1 3:SF4801 2.3 52.3 1.0
S2 3:SF4801 2.3 52.3 1.0
S4 3:SF4801 2.3 52.3 1.0
CD2 3:HIS115 2.4 79.8 1.0
FE2 3:SF4801 2.7 52.3 1.0
FE4 3:SF4801 2.7 52.3 1.0
FE1 3:SF4801 2.7 52.3 1.0
CE1 3:HIS115 3.4 80.2 1.0
CG 3:HIS115 3.7 87.5 1.0
S3 3:SF4801 3.9 52.3 1.0
ND1 3:HIS115 4.1 79.3 1.0
CE 4:MET321 4.4 48.7 1.0
SD 4:MET321 4.6 79.9 1.0
CD2 3:LEU130 4.6 73.7 1.0
SG 3:CYS119 4.7 57.7 1.0
CG 3:ARG180 4.7 77.2 1.0
SG 3:CYS122 4.7 55.8 1.0
SG 3:CYS128 4.8 73.9 1.0
CB 3:HIS115 4.9 91.1 1.0
CD 3:ARG180 5.0 76.5 1.0
N 3:CYS119 5.0 57.7 1.0

Iron binding site 10 out of 64 in 6y11

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Iron binding site 10 out of 64 in the Respiratory Complex I From Thermus Thermophilus


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

b:52.3
occ:1.00
 FE4 3:SF4801 0.0 52.3 1.0
S2 3:SF4801 2.3 52.3 1.0
S1 3:SF4801 2.3 52.3 1.0
SG 3:CYS122 2.3 55.8 1.0
S3 3:SF4801 2.3 52.3 1.0
FE1 3:SF4801 2.7 52.3 1.0
FE2 3:SF4801 2.7 52.3 1.0
FE3 3:SF4801 2.7 52.3 1.0
CB 3:CYS122 3.0 60.3 1.0
S4 3:SF4801 3.8 52.3 1.0
CB 3:LYS124 4.1 80.0 1.0
CA 3:CYS119 4.3 48.3 1.0
N 3:CYS119 4.4 57.7 1.0
NE2 3:HIS115 4.4 80.3 1.0
CD 3:ARG180 4.5 76.5 1.0
CA 3:CYS122 4.5 56.1 1.0
NE 3:ARG180 4.6 69.8 1.0
C 3:ASP118 4.6 66.1 1.0
SG 3:CYS128 4.7 73.9 1.0
N 3:GLY233 4.7 56.8 1.0
SG 3:CYS119 4.9 57.7 1.0
O 3:ASP118 4.9 76.8 1.0
CD2 3:HIS115 4.9 79.8 1.0
CB 3:ASP118 5.0 75.5 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: Wed Aug 7 15:48:53 2024

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