Iron in PDB 7q5y: Structure of Nadh:Ubichinon Oxidoreductase (Complex I) of the Hyperthermophilic Eubacterium Aquifex Aeolicus

The structure of Structure of Nadh:Ubichinon Oxidoreductase (Complex I) of the Hyperthermophilic Eubacterium Aquifex Aeolicus, PDB code: 7q5y was solved by E.Warkentin, U.Ermler, G.Peng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.95 / 2.70
Space group	P 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	132.88, 240.24, 230.92, 90, 95.57, 90
R / Rfree (%)	16.9 / 20.9

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 - 130; Page 14, Binding sites: 131 - 140; Page 15, Binding sites: 141 - 144;

Binding sites:

The binding sites of Iron atom in the Structure of Nadh:Ubichinon Oxidoreductase (Complex I) of the Hyperthermophilic Eubacterium Aquifex Aeolicus (pdb code 7q5y). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 144 binding sites of Iron where determined in the Structure of Nadh:Ubichinon Oxidoreductase (Complex I) of the Hyperthermophilic Eubacterium Aquifex Aeolicus, PDB code: 7q5y:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 144 in the Structure of Nadh:Ubichinon Oxidoreductase (Complex I) of the Hyperthermophilic Eubacterium Aquifex Aeolicus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Nadh:Ubichinon Oxidoreductase (Complex I) of the Hyperthermophilic Eubacterium Aquifex Aeolicus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe701 b:49.4 occ:1.00 FE1 A:SF4701 0.0 49.4 1.0 S4 A:SF4701 2.2 53.1 1.0 S2 A:SF4701 2.3 45.1 1.0 S3 A:SF4701 2.3 51.7 1.0 SG A:CYS106 2.3 52.4 1.0 FE3 A:SF4701 2.7 52.8 1.0 FE2 A:SF4701 2.7 53.2 1.0 FE4 A:SF4701 2.7 50.0 1.0 CB A:CYS106 3.2 53.2 1.0 S1 A:SF4701 3.8 47.8 1.0 CD A:ARG153 4.0 57.3 1.0 NE A:ARG153 4.4 58.5 1.0 NE2 A:HIS99 4.5 55.4 1.0 CB A:LYS108 4.5 42.6 1.0 N A:GLY209 4.6 48.9 1.0 CA A:CYS106 4.7 51.1 1.0 SG A:CYS112 4.7 58.0 1.0 SG A:CYS103 4.7 55.1 1.0 CA A:GLY209 4.8 46.8 1.0 CA A:CYS103 4.8 49.8 1.0 N A:CYS103 4.8 49.6 1.0 N A:ALA109 5.0 38.4 1.0 C A:ASP102 5.0 62.3 1.0

Iron binding site 2 out of 144 in the Structure of Nadh:Ubichinon Oxidoreductase (Complex I) of the Hyperthermophilic Eubacterium Aquifex Aeolicus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Nadh:Ubichinon Oxidoreductase (Complex I) of the Hyperthermophilic Eubacterium Aquifex Aeolicus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe701 b:53.2 occ:1.00 FE2 A:SF4701 0.0 53.2 1.0 SG A:CYS103 2.2 55.1 1.0 S1 A:SF4701 2.3 47.8 1.0 S3 A:SF4701 2.3 51.7 1.0 S4 A:SF4701 2.3 53.1 1.0 FE4 A:SF4701 2.7 50.0 1.0 FE3 A:SF4701 2.7 52.8 1.0 FE1 A:SF4701 2.7 49.4 1.0 CB A:CYS103 3.5 52.5 1.0 CA A:CYS103 3.7 49.8 1.0 NE2 A:GLN115 3.8 59.6 1.0 S2 A:SF4701 3.8 45.1 1.0 N A:CYS103 3.9 49.6 1.0 CB A:GLN115 4.6 58.1 1.0 CD A:GLN115 4.6 55.6 1.0 SG A:CYS106 4.7 52.4 1.0 CD1 B:LEU498 4.7 57.7 1.0 C A:ASP102 4.8 62.3 1.0 CG A:GLN115 4.8 47.8 1.0 CB A:CYS106 4.8 53.2 1.0 SG A:CYS112 4.8 58.0 1.0 NE2 A:HIS99 4.8 55.4 1.0

Iron binding site 3 out of 144 in the Structure of Nadh:Ubichinon Oxidoreductase (Complex I) of the Hyperthermophilic Eubacterium Aquifex Aeolicus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Nadh:Ubichinon Oxidoreductase (Complex I) of the Hyperthermophilic Eubacterium Aquifex Aeolicus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe701 b:52.8 occ:1.00 FE3 A:SF4701 0.0 52.8 1.0 NE2 A:HIS99 2.2 55.4 1.0 S4 A:SF4701 2.2 53.1 1.0 S1 A:SF4701 2.3 47.8 1.0 S2 A:SF4701 2.3 45.1 1.0 FE2 A:SF4701 2.7 53.2 1.0 FE1 A:SF4701 2.7 49.4 1.0 FE4 A:SF4701 2.7 50.0 1.0 CD2 A:HIS99 2.7 55.9 1.0 CE1 A:HIS99 3.3 54.9 1.0 S3 A:SF4701 3.9 51.7 1.0 CG A:HIS99 4.0 56.2 1.0 ND1 A:HIS99 4.2 57.9 1.0 CD A:ARG153 4.4 57.3 1.0 SG A:CYS103 4.5 55.1 1.0 CD2 A:LEU114 4.6 46.2 1.0 O A:PRO100 4.6 57.8 1.0 SG A:CYS112 4.8 58.0 1.0 CB A:ARG153 4.8 45.2 1.0 SG A:CYS106 4.9 52.4 1.0 CD1 B:LEU498 4.9 57.7 1.0

Iron binding site 4 out of 144 in the Structure of Nadh:Ubichinon Oxidoreductase (Complex I) of the Hyperthermophilic Eubacterium Aquifex Aeolicus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Nadh:Ubichinon Oxidoreductase (Complex I) of the Hyperthermophilic Eubacterium Aquifex Aeolicus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe701 b:50.0 occ:1.00 FE4 A:SF4701 0.0 50.0 1.0 S3 A:SF4701 2.2 51.7 1.0 S1 A:SF4701 2.3 47.8 1.0 S2 A:SF4701 2.3 45.1 1.0 SG A:CYS112 2.3 58.0 1.0 FE2 A:SF4701 2.7 53.2 1.0 FE1 A:SF4701 2.7 49.4 1.0 FE3 A:SF4701 2.7 52.8 1.0 CB A:CYS112 3.2 48.7 1.0 S4 A:SF4701 3.8 53.1 1.0 CB A:GLN115 4.1 58.1 1.0 N A:GLN115 4.3 55.9 1.0 NE2 A:HIS99 4.4 55.4 1.0 CA A:CYS112 4.6 44.4 1.0 SG A:CYS106 4.7 52.4 1.0 CB A:LEU114 4.7 45.0 1.0 CB A:LYS108 4.8 42.6 1.0 SG A:CYS103 4.8 55.1 1.0 CA A:GLN115 4.8 54.8 1.0 N A:GLY209 4.8 48.9 1.0 NE2 A:GLN115 4.8 59.6 1.0 CB A:VAL208 4.8 43.8 1.0

Iron binding site 5 out of 144 in the Structure of Nadh:Ubichinon Oxidoreductase (Complex I) of the Hyperthermophilic Eubacterium Aquifex Aeolicus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of Nadh:Ubichinon Oxidoreductase (Complex I) of the Hyperthermophilic Eubacterium Aquifex Aeolicus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe702 b:41.2 occ:1.00 FE1 A:SF4702 0.0 41.2 1.0 S4 A:SF4702 2.2 41.9 1.0 S2 A:SF4702 2.2 49.7 1.0 SG A:CYS206 2.3 57.6 1.0 S3 A:SF4702 2.3 39.2 1.0 FE3 A:SF4702 2.7 41.2 1.0 FE2 A:SF4702 2.7 44.1 1.0 FE4 A:SF4702 2.8 46.7 1.0 CB A:CYS206 3.3 44.7 1.0 CA A:CYS206 3.8 49.7 1.0 CB A:ALA210 3.8 58.8 1.0 S1 A:SF4702 3.9 42.5 1.0 CD A:PRO207 4.1 50.2 1.0 CG1 A:ILE211 4.4 35.4 1.0 CD1 A:ILE211 4.4 36.0 1.0 C A:CYS206 4.6 52.6 1.0 CG2 A:VAL208 4.7 35.2 1.0 SG A:CYS157 4.7 45.0 1.0 N A:PRO207 4.7 47.0 1.0 SG A:CYS160 4.7 47.6 1.0 N A:ILE211 4.8 42.8 1.0 SG A:CYS154 4.8 49.3 1.0 CA A:ALA210 4.9 52.4 1.0 N A:CYS206 4.9 46.1 1.0

Iron binding site 6 out of 144 in the Structure of Nadh:Ubichinon Oxidoreductase (Complex I) of the Hyperthermophilic Eubacterium Aquifex Aeolicus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of Nadh:Ubichinon Oxidoreductase (Complex I) of the Hyperthermophilic Eubacterium Aquifex Aeolicus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe702 b:44.1 occ:1.00 FE2 A:SF4702 0.0 44.1 1.0 S1 A:SF4702 2.3 42.5 1.0 S3 A:SF4702 2.3 39.2 1.0 SG A:CYS154 2.3 49.3 1.0 S4 A:SF4702 2.3 41.9 1.0 FE3 A:SF4702 2.7 41.2 1.0 FE4 A:SF4702 2.7 46.7 1.0 FE1 A:SF4702 2.7 41.2 1.0 CB A:CYS154 3.5 36.8 1.0 S2 A:SF4702 3.8 49.7 1.0 CA A:CYS154 3.9 43.9 1.0 N A:VAL155 4.2 43.1 1.0 CB A:ALA210 4.2 58.8 1.0 CA A:VAL156 4.2 56.3 1.0 N A:VAL156 4.3 63.3 1.0 CG1 A:ILE184 4.4 46.9 1.0 C A:CYS154 4.5 49.6 1.0 CE1 A:TYR149 4.5 44.7 1.0 N A:CYS157 4.6 43.2 1.0 OH A:TYR149 4.7 52.4 1.0 SG A:CYS206 4.8 57.6 1.0 SG A:CYS160 4.9 47.6 1.0 C A:VAL155 4.9 60.9 1.0 SG A:CYS157 5.0 45.0 1.0

Iron binding site 7 out of 144 in the Structure of Nadh:Ubichinon Oxidoreductase (Complex I) of the Hyperthermophilic Eubacterium Aquifex Aeolicus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of Nadh:Ubichinon Oxidoreductase (Complex I) of the Hyperthermophilic Eubacterium Aquifex Aeolicus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe702 b:41.2 occ:1.00 FE3 A:SF4702 0.0 41.2 1.0 S2 A:SF4702 2.2 49.7 1.0 S4 A:SF4702 2.3 41.9 1.0 S1 A:SF4702 2.3 42.5 1.0 SG A:CYS160 2.3 47.6 1.0 FE1 A:SF4702 2.7 41.2 1.0 FE2 A:SF4702 2.7 44.1 1.0 FE4 A:SF4702 2.7 46.7 1.0 CB A:CYS160 3.5 45.6 1.0 S3 A:SF4702 3.8 39.2 1.0 N A:CYS160 4.0 47.4 1.0 CG1 A:ILE184 4.1 46.9 1.0 CD1 A:ILE211 4.2 36.0 1.0 CA A:CYS160 4.4 47.1 1.0 CD1 A:ILE184 4.7 31.8 1.0 SG A:CYS157 4.7 45.0 1.0 SG A:CYS154 4.7 49.3 1.0 N A:ARG159 4.7 44.7 1.0 SG A:CYS206 4.8 57.6 1.0 N A:TYR158 4.8 42.0 1.0 CG1 A:ILE211 4.8 35.4 1.0

Iron binding site 8 out of 144 in the Structure of Nadh:Ubichinon Oxidoreductase (Complex I) of the Hyperthermophilic Eubacterium Aquifex Aeolicus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of Nadh:Ubichinon Oxidoreductase (Complex I) of the Hyperthermophilic Eubacterium Aquifex Aeolicus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe702 b:46.7 occ:1.00 FE4 A:SF4702 0.0 46.7 1.0 S1 A:SF4702 2.3 42.5 1.0 S3 A:SF4702 2.3 39.2 1.0 S2 A:SF4702 2.3 49.7 1.0 SG A:CYS157 2.3 45.0 1.0 FE2 A:SF4702 2.7 44.1 1.0 FE3 A:SF4702 2.7 41.2 1.0 FE1 A:SF4702 2.8 41.2 1.0 CB A:CYS157 3.4 35.8 1.0 N A:CYS157 3.5 43.2 1.0 N A:TYR158 3.8 42.0 1.0 S4 A:SF4702 3.9 41.9 1.0 CA A:CYS157 3.9 37.4 1.0 CD A:PRO207 4.0 50.2 1.0 C A:CYS157 4.1 48.8 1.0 N A:ARG159 4.2 44.7 1.0 C A:VAL156 4.6 54.5 1.0 CA A:VAL156 4.6 56.3 1.0 SG A:CYS160 4.6 47.6 1.0 SG A:CYS206 4.7 57.6 1.0 CG A:PRO207 4.7 43.3 1.0 SG A:CYS154 4.7 49.3 1.0 CB A:ARG159 4.8 35.9 1.0 CA A:TYR158 4.8 39.7 1.0 CG2 A:VAL155 4.8 37.6 1.0 N A:VAL156 4.9 63.3 1.0 N A:CYS160 4.9 47.4 1.0 C A:TYR158 4.9 43.8 1.0

Iron binding site 9 out of 144 in the Structure of Nadh:Ubichinon Oxidoreductase (Complex I) of the Hyperthermophilic Eubacterium Aquifex Aeolicus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Structure of Nadh:Ubichinon Oxidoreductase (Complex I) of the Hyperthermophilic Eubacterium Aquifex Aeolicus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe703 b:46.0 occ:1.00 FE1 A:SF4703 0.0 46.0 1.0 S2 A:SF4703 2.2 42.8 1.0 S3 A:SF4703 2.3 42.4 1.0 SG A:CYS235 2.3 46.0 1.0 S4 A:SF4703 2.3 47.3 1.0 FE4 A:SF4703 2.6 45.2 1.0 FE3 A:SF4703 2.7 38.2 1.0 FE2 A:SF4703 2.8 37.1 1.0 CB A:CYS235 3.3 43.2 1.0 S1 A:SF4703 3.9 41.1 1.0 O A:HOH821 3.9 44.0 1.0 N A:CYS235 3.9 30.8 1.0 CA A:CYS235 4.0 34.4 1.0 CB A:VAL237 4.0 48.1 1.0 C A:CYS235 4.2 38.9 1.0 CG2 A:VAL237 4.2 47.2 1.0 O A:CYS235 4.3 40.9 1.0 N A:VAL237 4.4 43.7 1.0 C A:LEU234 4.6 40.2 1.0 SG A:CYS268 4.6 43.3 1.0 SG A:CYS232 4.7 47.2 1.0 SG A:CYS239 4.8 47.0 1.0 CA A:VAL237 4.8 47.0 1.0 N A:PRO236 5.0 41.9 1.0

Iron binding site 10 out of 144 in the Structure of Nadh:Ubichinon Oxidoreductase (Complex I) of the Hyperthermophilic Eubacterium Aquifex Aeolicus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Structure of Nadh:Ubichinon Oxidoreductase (Complex I) of the Hyperthermophilic Eubacterium Aquifex Aeolicus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe703 b:37.1 occ:1.00 FE2 A:SF4703 0.0 37.1 1.0 S1 A:SF4703 2.2 41.1 1.0 SG A:CYS268 2.3 43.3 1.0 S4 A:SF4703 2.3 47.3 1.0 S3 A:SF4703 2.3 42.4 1.0 FE3 A:SF4703 2.7 38.2 1.0 FE4 A:SF4703 2.7 45.2 1.0 FE1 A:SF4703 2.8 46.0 1.0 CB A:CYS268 3.2 30.7 1.0 N A:CYS268 3.7 44.7 1.0 S2 A:SF4703 3.9 42.8 1.0 CA A:CYS268 4.0 36.6 1.0 N A:GLY271 4.3 43.9 1.0 O A:HOH821 4.4 44.0 1.0 CG2 A:VAL385 4.6 36.0 1.0 C A:CYS268 4.6 42.0 1.0 C A:ILE267 4.6 49.5 1.0 SG A:CYS235 4.6 46.0 1.0 CB A:LYS270 4.7 29.9 1.0 O A:CYS268 4.7 46.4 1.0 CA A:GLY271 4.7 38.9 1.0 SG A:CYS239 4.8 47.0 1.0 SG A:CYS232 4.8 47.2 1.0 CA A:ILE267 4.9 41.7 1.0 NZ A:LYS270 5.0 55.2 1.0

E.Warkentin, U.Ermler, G.Peng. Structure of Nadh:Ubichinon Oxidoreductase (Complex I) of the Hyperthermophilic Eubacterium Aquifex Aeolicus To Be Published.