Iron in PDB 3ias: Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution

All present enzymatic activity of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution:
1.6.99.5;

The structure of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution, PDB code: 3ias was solved by L.A.Sazanov, J.M.Berrisford, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.98 / 3.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	135.080, 266.112, 201.731, 90.00, 104.71, 90.00
R / Rfree (%)	23.7 / 27

The structure of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution also contains other interesting chemical elements:

Calcium

(Ca)

16 atoms

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 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 100; Page 11, Binding sites: 101 - 110; Page 12, Binding sites: 111 - 120; Page 13, Binding sites: 121 - 128;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution (pdb code 3ias). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 128 binding sites of Iron where determined in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution, PDB code: 3ias:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 128 in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ 6:Fe182 b:24.7 occ:1.00 FE1 6:SF4182 0.0 24.7 1.0 SG 6:CYS111 2.2 45.4 1.0 S4 6:SF4182 2.3 51.4 1.0 S3 6:SF4182 2.3 69.0 1.0 S2 6:SF4182 2.3 69.1 1.0 FE4 6:SF4182 2.7 37.1 1.0 FE3 6:SF4182 2.7 30.3 1.0 FE2 6:SF4182 2.8 32.4 1.0 CB 6:CYS111 3.2 55.6 1.0 CD 6:ARG83 3.7 55.1 1.0 S1 6:SF4182 4.0 47.5 1.0 N 6:CYS111 4.0 58.2 1.0 NE 6:ARG83 4.1 53.6 1.0 CA 6:CYS111 4.2 57.1 1.0 CE2 6:PHE118 4.4 53.4 1.0 N 6:ARG83 4.5 54.3 1.0 CG 6:ARG83 4.7 55.2 1.0 SG 6:CYS140 4.7 54.0 1.0 SG 6:CYS46 4.8 55.7 1.0 SG 6:CYS45 4.8 54.4 1.0 CA 6:GLY82 4.9 56.2 1.0 C 6:GLY82 4.9 54.6 1.0 CB 6:ARG83 5.0 55.7 1.0

Iron binding site 2 out of 128 in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ 6:Fe182 b:32.4 occ:1.00 FE2 6:SF4182 0.0 32.4 1.0 S1 6:SF4182 2.3 47.5 1.0 SG 6:CYS46 2.3 55.7 1.0 S3 6:SF4182 2.3 69.0 1.0 S4 6:SF4182 2.3 51.4 1.0 FE4 6:SF4182 2.6 37.1 1.0 FE3 6:SF4182 2.7 30.3 1.0 FE1 6:SF4182 2.8 24.7 1.0 CB 6:CYS46 3.4 61.7 1.0 N 6:CYS46 3.7 64.4 1.0 S2 6:SF4182 3.9 69.1 1.0 CA 6:CYS46 4.0 64.6 1.0 CB 6:PRO141 4.2 58.4 1.0 CA 6:PRO141 4.3 57.2 1.0 SG 6:CYS45 4.6 54.4 1.0 CA 6:GLY82 4.6 56.2 1.0 C 6:CYS45 4.7 64.0 1.0 CB 6:CYS45 4.7 56.5 1.0 SG 6:CYS140 4.7 54.0 1.0 N 6:PRO141 4.8 58.9 1.0 SG 6:CYS111 4.8 45.4 1.0 CA 6:CYS140 4.8 53.6 1.0

Iron binding site 3 out of 128 in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ 6:Fe182 b:30.3 occ:1.00 FE3 6:SF4182 0.0 30.3 1.0 SG 6:CYS45 2.3 54.4 1.0 S4 6:SF4182 2.3 51.4 1.0 S2 6:SF4182 2.3 69.1 1.0 S1 6:SF4182 2.3 47.5 1.0 FE2 6:SF4182 2.7 32.4 1.0 FE4 6:SF4182 2.7 37.1 1.0 FE1 6:SF4182 2.7 24.7 1.0 CB 6:CYS45 3.2 56.5 1.0 NE2 4:HIS169 3.8 59.2 1.0 NE 6:ARG83 3.9 53.6 1.0 S3 6:SF4182 3.9 69.0 1.0 N 6:CYS45 4.0 64.9 1.0 CA 6:CYS45 4.1 63.1 1.0 N 6:CYS46 4.2 64.4 1.0 CG 4:ARG84 4.3 54.7 1.0 CD 6:ARG83 4.4 55.1 1.0 CB 6:ALA44 4.6 60.4 1.0 C 6:CYS45 4.6 64.0 1.0 CE1 4:HIS169 4.6 60.5 1.0 CD2 4:HIS169 4.7 57.9 1.0 SG 6:CYS46 4.8 55.7 1.0 SG 6:CYS140 4.8 54.0 1.0 SG 6:CYS111 4.8 45.4 1.0 CZ 6:ARG83 4.9 56.5 1.0 NH2 6:ARG83 5.0 55.8 1.0

Iron binding site 4 out of 128 in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ 6:Fe182 b:37.1 occ:1.00 FE4 6:SF4182 0.0 37.1 1.0 S1 6:SF4182 2.3 47.5 1.0 SG 6:CYS140 2.3 54.0 1.0 S3 6:SF4182 2.3 69.0 1.0 S2 6:SF4182 2.3 69.1 1.0 FE2 6:SF4182 2.6 32.4 1.0 FE3 6:SF4182 2.7 30.3 1.0 FE1 6:SF4182 2.7 24.7 1.0 CB 6:CYS140 3.4 53.8 1.0 CA 6:CYS140 3.7 53.6 1.0 S4 6:SF4182 3.8 51.4 1.0 C 6:CYS140 3.9 58.8 1.0 N 6:PRO141 4.2 58.9 1.0 O 6:CYS140 4.4 60.2 1.0 CA 6:PRO141 4.4 57.2 1.0 NE 4:ARG84 4.4 50.6 1.0 NE2 4:HIS169 4.5 59.2 1.0 CD2 4:HIS169 4.5 57.9 1.0 SG 6:CYS46 4.6 55.7 1.0 SG 6:CYS111 4.6 45.4 1.0 SG 6:CYS45 4.7 54.4 1.0 NH2 4:ARG84 4.9 57.2 1.0 CB 6:PRO141 5.0 58.4 1.0 CG 4:ARG84 5.0 54.7 1.0 CD 6:PRO141 5.0 58.4 1.0

Iron binding site 5 out of 128 in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ 9:Fe183 b:19.8 occ:1.00 FE1 9:SF4183 0.0 19.8 1.0 S2 9:SF4183 2.3 45.7 1.0 S3 9:SF4183 2.3 48.2 1.0 SG 9:CYS101 2.3 54.0 1.0 S4 9:SF4183 2.3 38.4 1.0 FE3 9:SF4183 2.7 12.9 1.0 FE2 9:SF4183 2.7 18.8 1.0 FE4 9:SF4183 2.7 19.7 1.0 N 9:CYS101 3.4 44.3 1.0 CB 9:CYS101 3.5 47.6 1.0 S1 9:SF4183 3.9 41.2 1.0 N 9:GLY102 3.9 43.6 1.0 CA 9:CYS101 4.0 44.8 1.0 CD 9:PRO64 4.1 41.0 1.0 N 9:PHE100 4.2 46.0 1.0 CG 9:PRO64 4.3 41.9 1.0 C 9:PHE100 4.4 45.8 1.0 N 9:LEU103 4.4 43.9 1.0 CA 9:PHE100 4.4 45.2 1.0 C 9:CYS101 4.5 46.8 1.0 CG2 9:ILE99 4.5 43.0 1.0 SG 9:CYS63 4.6 43.1 1.0 N 9:ILE99 4.7 42.1 1.0 SG 9:CYS98 4.7 46.2 1.0 SG 9:CYS104 4.7 41.1 1.0 CB 9:LEU103 4.8 44.3 1.0 C 9:ILE99 4.9 43.7 1.0 CA 9:GLY102 4.9 47.7 1.0 N 9:CYS104 5.0 42.8 1.0

Iron binding site 6 out of 128 in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ 9:Fe183 b:18.8 occ:1.00 FE2 9:SF4183 0.0 18.8 1.0 S4 9:SF4183 2.3 38.4 1.0 SG 9:CYS98 2.3 46.2 1.0 S3 9:SF4183 2.3 48.2 1.0 S1 9:SF4183 2.3 41.2 1.0 FE3 9:SF4183 2.6 12.9 1.0 FE1 9:SF4183 2.7 19.8 1.0 FE4 9:SF4183 2.8 19.7 1.0 CB 9:CYS98 3.4 44.6 1.0 NE2 9:HIS41 3.6 43.8 1.0 N 9:PHE100 3.8 46.0 1.0 CA 9:CYS98 3.8 40.9 1.0 S2 9:SF4183 3.8 45.7 1.0 N 9:ILE99 3.9 42.1 1.0 CE1 9:HIS41 4.1 48.4 1.0 C 9:CYS98 4.2 41.3 1.0 CA 9:PHE100 4.2 45.2 1.0 N 9:CYS101 4.6 44.3 1.0 SG 9:CYS104 4.7 41.1 1.0 SG 9:CYS101 4.7 54.0 1.0 SG 9:CYS63 4.8 43.1 1.0 CD2 9:HIS41 4.8 43.3 1.0 C 9:ILE99 4.8 43.7 1.0 CA 9:ILE99 4.9 44.4 1.0

Iron binding site 7 out of 128 in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ 9:Fe183 b:12.9 occ:1.00 FE3 9:SF4183 0.0 12.9 1.0 SG 9:CYS104 2.3 41.1 1.0 S4 9:SF4183 2.3 38.4 1.0 S2 9:SF4183 2.3 45.7 1.0 S1 9:SF4183 2.3 41.2 1.0 FE2 9:SF4183 2.6 18.8 1.0 FE1 9:SF4183 2.7 19.8 1.0 FE4 9:SF4183 2.7 19.7 1.0 CB 9:CYS104 3.3 40.0 1.0 NE2 9:HIS41 3.8 43.8 1.0 S3 9:SF4183 3.8 48.2 1.0 N 9:CYS104 3.9 42.8 1.0 CA 9:CYS104 4.2 40.8 1.0 N 9:GLY102 4.4 43.6 1.0 CD2 9:HIS41 4.4 43.3 1.0 N 9:LEU103 4.5 43.9 1.0 SG 9:CYS98 4.7 46.2 1.0 CA 9:GLY102 4.7 47.7 1.0 CD1 9:ILE68 4.7 42.0 1.0 SG 9:CYS101 4.8 54.0 1.0 SG 9:CYS63 4.9 43.1 1.0 CE1 9:HIS41 4.9 48.4 1.0

Iron binding site 8 out of 128 in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ 9:Fe183 b:19.7 occ:1.00 FE4 9:SF4183 0.0 19.7 1.0 SG 9:CYS63 2.3 43.1 1.0 S1 9:SF4183 2.3 41.2 1.0 S3 9:SF4183 2.3 48.2 1.0 S2 9:SF4183 2.3 45.7 1.0 FE1 9:SF4183 2.7 19.8 1.0 FE3 9:SF4183 2.7 12.9 1.0 FE2 9:SF4183 2.8 18.8 1.0 CB 9:CYS63 3.3 42.2 1.0 CA 9:CYS63 3.8 41.0 1.0 S4 9:SF4183 4.0 38.4 1.0 CD 9:PRO64 4.1 41.0 1.0 CB 9:ALA67 4.3 43.1 1.0 C 9:CYS63 4.6 42.1 1.0 N 9:PRO64 4.6 39.4 1.0 SG 9:CYS101 4.7 54.0 1.0 CG1 9:ILE68 4.7 42.2 1.0 CD1 9:ILE68 4.7 42.0 1.0 SG 9:CYS104 4.8 41.1 1.0 CG 9:PRO64 4.8 41.9 1.0 SG 9:CYS98 4.8 46.2 1.0 N 9:CYS63 4.9 43.8 1.0

Iron binding site 9 out of 128 in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ 9:Fe184 b:13.7 occ:1.00 FE1 9:SF4184 0.0 13.7 1.0 SG 9:CYS108 2.3 40.5 1.0 S2 9:SF4184 2.3 43.7 1.0 S3 9:SF4184 2.3 44.5 1.0 S4 9:SF4184 2.3 48.5 1.0 FE2 9:SF4184 2.6 7.9 1.0 FE4 9:SF4184 2.6 27.5 1.0 FE3 9:SF4184 2.7 14.3 1.0 CB 9:CYS108 3.3 44.4 1.0 OG1 9:THR110 3.6 45.0 1.0 S1 9:SF4184 3.9 43.6 1.0 CB 9:ALA112 3.9 43.6 1.0 CA 9:CYS108 3.9 39.4 1.0 CD 9:PRO109 4.0 40.8 1.0 N 9:ILE113 4.5 46.4 1.0 CG2 9:ILE113 4.5 42.0 1.0 N 9:ALA112 4.6 44.6 1.0 SG 9:CYS56 4.6 41.2 1.0 SG 9:CYS59 4.7 44.2 1.0 N 9:PRO109 4.7 41.9 1.0 SG 9:CYS53 4.7 38.0 1.0 C 9:CYS108 4.7 43.2 1.0 CA 9:ALA112 4.8 46.8 1.0

Iron binding site 10 out of 128 in the Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of the Hydrophilic Domain of Respiratory Complex I From Thermus Thermophilus, Oxidized, 4 Mol/Asu, Re-Refined to 3.15 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ 9:Fe184 b:7.9 occ:1.00 FE2 9:SF4184 0.0 7.9 1.0 S3 9:SF4184 2.3 44.5 1.0 S4 9:SF4184 2.3 48.5 1.0 S1 9:SF4184 2.3 43.6 1.0 SG 9:CYS59 2.3 44.2 1.0 FE4 9:SF4184 2.6 27.5 1.0 FE1 9:SF4184 2.6 13.7 1.0 FE3 9:SF4184 2.7 14.3 1.0 CB 9:CYS59 3.4 35.1 1.0 S2 9:SF4184 3.8 43.7 1.0 N 9:CYS59 3.9 35.1 1.0 CE1 9:TYR91 3.9 41.6 1.0 CA 9:CYS59 4.2 33.9 1.0 OH 9:TYR91 4.2 39.7 1.0 CZ 9:TYR91 4.5 41.7 1.0 N 9:SER57 4.5 38.9 1.0 SG 9:CYS56 4.6 41.2 1.0 SG 9:CYS108 4.7 40.5 1.0 N 9:LEU58 4.7 39.2 1.0 CG2 9:ILE113 4.7 42.0 1.0 SG 9:CYS53 4.8 38.0 1.0 CA 9:SER57 4.9 43.3 1.0 CD1 9:TYR91 4.9 44.7 1.0 CB 9:CYS108 5.0 44.4 1.0

J.M.Berrisford, L.A.Sazanov. Structural Basis For the Mechanism of Respiratory Complex I J.Biol.Chem. V. 284 29773 2009.
ISSN: ISSN 0021-9258
PubMed: 19635800
DOI: 10.1074/JBC.M109.032144