Iron in PDB 6q8o: Respiratory Complex I From Thermus Thermophilus with Bound Piericidin A

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

The structure of Respiratory Complex I From Thermus Thermophilus with Bound Piericidin A, PDB code: 6q8o 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)	49.16 / 3.61
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	95.140, 336.590, 262.790, 90.00, 100.41, 90.00
R / Rfree (%)	21.8 / 23.5

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 Piericidin A (pdb code 6q8o). 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 Piericidin A, PDB code: 6q8o:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

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


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 Piericidin A within 5.0Å range: probe atom residue distance (Å) B Occ 1:Fe501 b:76.9 occ:1.00 FE1 1:SF4501 0.0 76.9 1.0 S4 1:SF4501 2.3 76.9 1.0 S2 1:SF4501 2.3 76.9 1.0 S3 1:SF4501 2.3 76.9 1.0 SG 1:CYS356 2.3 99.2 1.0 FE2 1:SF4501 2.7 76.9 1.0 FE3 1:SF4501 2.7 76.9 1.0 FE4 1:SF4501 2.7 76.9 1.0 CB 1:CYS356 3.1 86.6 1.0 N 1:CYS356 3.5 80.9 1.0 S1 1:SF4501 3.9 76.9 1.0 CA 1:CYS356 3.9 76.3 1.0 CB 1:PHE399 4.2 0.4 1.0 CB 1:CYS359 4.3 81.1 1.0 N 1:CYS400 4.4 0.3 1.0 N 1:PHE399 4.4 0.1 1.0 CB 1:LYS355 4.5 0.4 1.0 C 1:LYS355 4.5 90.8 1.0 SG 1:CYS359 4.6 84.2 1.0 N 1:LYS355 4.7 0.2 1.0 CA 1:PHE399 4.8 0.3 1.0 SG 1:CYS400 4.8 0.8 1.0 SG 1:CYS353 4.8 38.3 1.0 CA 1:LYS355 4.8 0.8 1.0 C 1:CYS356 5.0 67.5 1.0

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


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 Piericidin A within 5.0Å range: probe atom residue distance (Å) B Occ 1:Fe501 b:76.9 occ:1.00 FE2 1:SF4501 0.0 76.9 1.0 S3 1:SF4501 2.3 76.9 1.0 S4 1:SF4501 2.3 76.9 1.0 S1 1:SF4501 2.3 76.9 1.0 SG 1:CYS359 2.3 84.2 1.0 FE1 1:SF4501 2.7 76.9 1.0 FE3 1:SF4501 2.7 76.9 1.0 FE4 1:SF4501 2.7 76.9 1.0 CB 1:CYS359 3.1 81.1 1.0 OG 1:SER352 3.5 39.2 1.0 S2 1:SF4501 3.9 76.9 1.0 N 1:CYS353 4.4 55.0 1.0 CB 1:SER352 4.5 42.0 1.0 CA 1:CYS359 4.6 74.0 1.0 CB 1:CYS356 4.6 86.6 1.0 SG 1:CYS356 4.7 99.2 1.0 N 1:GLY354 4.7 65.0 1.0 CA 1:SER352 4.7 52.6 1.0 SG 1:CYS400 4.8 0.8 1.0 N 1:CYS356 4.8 80.9 1.0 SG 1:CYS353 4.9 38.3 1.0 N 1:ARG360 5.0 66.8 1.0

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


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 Piericidin A within 5.0Å range: probe atom residue distance (Å) B Occ 1:Fe501 b:76.9 occ:1.00 FE3 1:SF4501 0.0 76.9 1.0 S4 1:SF4501 2.3 76.9 1.0 S2 1:SF4501 2.3 76.9 1.0 S1 1:SF4501 2.3 76.9 1.0 SG 1:CYS400 2.3 0.8 1.0 FE4 1:SF4501 2.7 76.9 1.0 FE2 1:SF4501 2.7 76.9 1.0 FE1 1:SF4501 2.7 76.9 1.0 CB 1:CYS400 3.3 0.4 1.0 S3 1:SF4501 3.9 76.9 1.0 O 1:CYS400 4.0 0.1 1.0 N 1:CYS400 4.0 0.3 1.0 CA 1:CYS400 4.0 1.0 1.0 CB 1:LEU402 4.3 0.1 1.0 C 1:CYS400 4.3 0.2 1.0 CD1 1:ILE181 4.6 0.6 1.0 SG 1:CYS353 4.7 38.3 1.0 SG 1:CYS359 4.8 84.2 1.0 SG 1:CYS356 4.9 99.2 1.0 CG 1:PRO199 4.9 96.6 1.0 N 1:LEU402 4.9 0.0 1.0

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


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 Piericidin A within 5.0Å range: probe atom residue distance (Å) B Occ 1:Fe501 b:76.9 occ:1.00 FE4 1:SF4501 0.0 76.9 1.0 S3 1:SF4501 2.3 76.9 1.0 S2 1:SF4501 2.3 76.9 1.0 S1 1:SF4501 2.3 76.9 1.0 SG 1:CYS353 2.3 38.3 1.0 FE3 1:SF4501 2.7 76.9 1.0 FE2 1:SF4501 2.7 76.9 1.0 FE1 1:SF4501 2.7 76.9 1.0 CB 1:CYS353 3.3 44.0 1.0 N 1:CYS353 3.7 55.0 1.0 N 1:GLY354 3.8 65.0 1.0 N 1:LYS355 3.8 0.2 1.0 CA 1:CYS353 3.9 51.1 1.0 S4 1:SF4501 3.9 76.9 1.0 C 1:CYS353 4.1 53.8 1.0 CB 1:LYS355 4.1 0.4 1.0 N 1:CYS356 4.5 80.9 1.0 CA 1:LYS355 4.5 0.8 1.0 C 1:GLY354 4.7 0.6 1.0 CG 1:PRO199 4.7 96.6 1.0 OG 1:SER352 4.7 39.2 1.0 SG 1:CYS400 4.7 0.8 1.0 CD 1:PRO199 4.7 96.6 1.0 CA 1:GLY354 4.7 83.3 1.0 SG 1:CYS356 4.8 99.2 1.0 SG 1:CYS359 4.9 84.2 1.0 C 1:SER352 4.9 53.7 1.0 O 1:CYS353 5.0 51.6 1.0

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


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 Piericidin A within 5.0Å range: probe atom residue distance (Å) B Occ 2:Fe201 b:77.5 occ:1.00 FE1 2:FES201 0.0 77.5 1.0 S1 2:FES201 2.2 77.5 1.0 S2 2:FES201 2.2 77.5 1.0 SG 2:CYS83 2.3 0.0 1.0 SG 2:CYS88 2.3 0.3 1.0 FE2 2:FES201 3.1 77.5 1.0 CB 2:CYS88 3.1 0.1 1.0 CB 2:CYS83 3.4 0.0 1.0 N 2:CYS88 4.0 0.9 1.0 CA 2:CYS88 4.1 0.9 1.0 CG2 2:VAL133 4.3 84.3 1.0 CB 2:THR85 4.3 93.9 1.0 N 2:LEU125 4.3 1.0 1.0 OG1 2:THR85 4.3 91.0 1.0 CA 2:CYS124 4.5 0.2 1.0 O 2:SER127 4.6 0.5 1.0 SG 2:CYS124 4.7 0.6 1.0 CA 2:CYS83 4.8 1.0 1.0 N 2:THR85 4.9 92.4 1.0 CB 2:VAL133 4.9 85.3 1.0 SG 2:CYS128 4.9 92.7 1.0 C 2:CYS124 5.0 0.5 1.0

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


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 Piericidin A within 5.0Å range: probe atom residue distance (Å) B Occ 2:Fe201 b:77.5 occ:1.00 FE2 2:FES201 0.0 77.5 1.0 S2 2:FES201 2.2 77.5 1.0 S1 2:FES201 2.2 77.5 1.0 SG 2:CYS128 2.3 92.7 1.0 SG 2:CYS124 2.3 0.6 1.0 FE1 2:FES201 3.1 77.5 1.0 CB 2:CYS128 3.6 0.9 1.0 CB 2:CYS124 3.7 0.5 1.0 CA 2:CYS128 4.0 0.6 1.0 CA 2:CYS124 4.0 0.2 1.0 N 2:CYS128 4.1 0.0 1.0 N 2:GLY126 4.2 0.0 1.0 N 2:LEU125 4.2 1.0 1.0 N 2:SER127 4.4 0.9 1.0 C 2:SER127 4.4 0.1 1.0 C 2:CYS124 4.5 0.5 1.0 O 2:SER127 4.6 0.5 1.0 CA 2:GLY126 4.7 0.7 1.0 SG 2:CYS83 4.7 0.0 1.0 CB 2:SER87 4.7 0.1 1.0 N 1:GLY99 4.8 0.9 1.0 CA 1:PRO98 4.9 0.8 1.0 CB 1:PRO98 4.9 0.3 1.0 C 2:GLY126 4.9 0.9 1.0 SG 2:CYS88 4.9 0.3 1.0 CB 2:THR85 4.9 93.9 1.0

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


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 Piericidin A within 5.0Å range: probe atom residue distance (Å) B Occ 3:Fe801 b:54.2 occ:1.00 FE1 3:SF4801 0.0 54.2 1.0 S4 3:SF4801 2.3 54.2 1.0 S2 3:SF4801 2.3 54.2 1.0 S3 3:SF4801 2.3 54.2 1.0 SG 3:CYS128 2.3 65.9 1.0 FE3 3:SF4801 2.7 54.2 1.0 FE2 3:SF4801 2.7 54.2 1.0 FE4 3:SF4801 2.7 54.2 1.0 CB 3:CYS128 3.2 73.0 1.0 NE2 3:HIS115 3.6 0.4 1.0 S1 3:SF4801 3.9 54.2 1.0 CE1 3:HIS115 4.1 0.2 1.0 CG 3:GLN131 4.4 73.1 1.0 CA 3:CYS128 4.6 82.5 1.0 CD2 3:HIS115 4.7 0.4 1.0 CB 3:LEU130 4.7 63.6 1.0 N 3:GLN131 4.8 54.1 1.0 SG 3:CYS119 4.8 89.3 1.0 N 3:GLY233 4.8 46.6 1.0 CA 3:VAL232 4.8 57.5 1.0 SG 3:CYS122 4.8 69.3 1.0 CD 3:GLN131 4.9 77.5 1.0 CB 3:GLN131 5.0 64.5 1.0

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


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 Piericidin A within 5.0Å range: probe atom residue distance (Å) B Occ 3:Fe801 b:54.2 occ:1.00 FE2 3:SF4801 0.0 54.2 1.0 S1 3:SF4801 2.3 54.2 1.0 S3 3:SF4801 2.3 54.2 1.0 S4 3:SF4801 2.3 54.2 1.0 SG 3:CYS119 2.3 89.3 1.0 FE4 3:SF4801 2.7 54.2 1.0 FE1 3:SF4801 2.7 54.2 1.0 FE3 3:SF4801 2.7 54.2 1.0 NE2 3:HIS115 3.1 0.4 1.0 CB 3:CYS119 3.4 86.0 1.0 CA 3:CYS119 3.5 83.7 1.0 CD2 3:HIS115 3.6 0.4 1.0 N 3:CYS119 3.7 76.6 1.0 S2 3:SF4801 3.9 54.2 1.0 CE1 3:HIS115 4.3 0.2 1.0 C 3:ASP118 4.7 65.7 1.0 CB 3:CYS122 4.7 70.2 1.0 SG 3:CYS122 4.7 69.3 1.0 NE2 3:GLN131 4.8 75.9 1.0 SG 3:CYS128 4.8 65.9 1.0 SD 4:MET321 4.8 89.9 1.0 CE 4:MET321 4.8 89.7 1.0 C 3:CYS119 4.9 85.9 1.0 CG 3:HIS115 4.9 0.7 1.0 CG 3:GLN131 4.9 73.1 1.0

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


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 Piericidin A within 5.0Å range: probe atom residue distance (Å) B Occ 3:Fe801 b:54.2 occ:1.00 FE3 3:SF4801 0.0 54.2 1.0 NE2 3:HIS115 1.7 0.4 1.0 S2 3:SF4801 2.3 54.2 1.0 S1 3:SF4801 2.3 54.2 1.0 S4 3:SF4801 2.3 54.2 1.0 CE1 3:HIS115 2.3 0.2 1.0 FE4 3:SF4801 2.7 54.2 1.0 FE1 3:SF4801 2.7 54.2 1.0 FE2 3:SF4801 2.7 54.2 1.0 CD2 3:HIS115 2.9 0.4 1.0 ND1 3:HIS115 3.5 0.7 1.0 CG 3:HIS115 3.8 0.7 1.0 S3 3:SF4801 3.9 54.2 1.0 CG 3:ARG180 4.2 54.2 1.0 CB 3:ARG180 4.4 68.0 1.0 CD 3:ARG180 4.4 51.7 1.0 N 3:GLY233 4.5 46.6 1.0 CB 3:VAL232 4.7 55.1 1.0 SG 3:CYS122 4.7 69.3 1.0 SG 3:CYS128 4.8 65.9 1.0 SG 3:CYS119 4.8 89.3 1.0 CG1 3:VAL232 4.8 40.6 1.0

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


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 Piericidin A within 5.0Å range: probe atom residue distance (Å) B Occ 3:Fe801 b:54.2 occ:1.00 FE4 3:SF4801 0.0 54.2 1.0 S2 3:SF4801 2.3 54.2 1.0 SG 3:CYS122 2.3 69.3 1.0 S1 3:SF4801 2.3 54.2 1.0 S3 3:SF4801 2.3 54.2 1.0 FE3 3:SF4801 2.7 54.2 1.0 FE2 3:SF4801 2.7 54.2 1.0 FE1 3:SF4801 2.7 54.2 1.0 CB 3:CYS122 3.1 70.2 1.0 S4 3:SF4801 3.9 54.2 1.0 NE2 3:HIS115 4.2 0.4 1.0 N 3:GLY233 4.2 46.6 1.0 CA 3:CYS119 4.4 83.7 1.0 CA 3:GLY233 4.4 46.0 1.0 CA 3:CYS122 4.5 74.8 1.0 N 3:CYS119 4.6 76.6 1.0 CD 3:ARG180 4.7 51.7 1.0 SG 3:CYS119 4.8 89.3 1.0 SG 3:CYS128 4.8 65.9 1.0 CB 3:LYS124 4.8 58.0 1.0 C 3:ASP118 4.9 65.7 1.0 CE1 3:HIS115 5.0 0.2 1.0

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