Iron in PDB 7dgz: Activity Optimized Complex I (Closed Form)

All present enzymatic activity of Activity Optimized Complex I (Closed Form):
7.1.1.2;

The structure of Activity Optimized Complex I (Closed Form) also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Iron atom in the Activity Optimized Complex I (Closed Form) (pdb code 7dgz). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 28 binding sites of Iron where determined in the Activity Optimized Complex I (Closed Form), PDB code: 7dgz:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 28 in the Activity Optimized Complex I (Closed Form)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Activity Optimized Complex I (Closed Form) within 5.0Å range: probe atom residue distance (Å) B Occ 8:Fe502 b:49.7 occ:1.00 FE1 8:SF4502 0.0 49.7 1.0 S4 8:SF4502 2.3 49.7 1.0 S2 8:SF4502 2.3 49.7 1.0 S3 8:SF4502 2.3 49.7 1.0 FE3 8:SF4502 2.7 49.7 1.0 FE4 8:SF4502 2.7 49.7 1.0 FE2 8:SF4502 2.7 49.7 1.0 CB 8:CYS385 3.0 22.2 1.0 SG 8:CYS385 3.7 22.2 1.0 CB 8:THR423 3.8 20.5 1.0 S1 8:SF4502 3.9 49.7 1.0 CG2 8:THR423 4.0 20.5 1.0 CB 8:CYS382 4.2 21.8 1.0 CA 8:CYS385 4.4 22.2 1.0 N 8:ILE424 4.6 23.8 1.0 N 8:CYS382 4.6 21.8 1.0 CA 8:THR423 4.7 20.5 1.0 N 8:CYS385 4.7 22.2 1.0 OG1 8:THR423 4.8 20.5 1.0 O 8:CYS382 4.8 21.8 1.0 SG 8:CYS382 4.9 21.8 1.0 CA 8:CYS382 4.9 21.8 1.0 N 8:CYS425 5.0 27.7 1.0

Iron binding site 2 out of 28 in the Activity Optimized Complex I (Closed Form)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Activity Optimized Complex I (Closed Form) within 5.0Å range: probe atom residue distance (Å) B Occ 8:Fe502 b:49.7 occ:1.00 FE2 8:SF4502 0.0 49.7 1.0 S3 8:SF4502 2.3 49.7 1.0 S4 8:SF4502 2.3 49.7 1.0 S1 8:SF4502 2.3 49.7 1.0 FE4 8:SF4502 2.7 49.7 1.0 FE1 8:SF4502 2.7 49.7 1.0 FE3 8:SF4502 2.7 49.7 1.0 OH 8:TYR204 2.8 35.1 1.0 CZ 8:TYR204 3.8 35.1 1.0 S2 8:SF4502 3.9 49.7 1.0 CB 8:LEU427 3.9 25.6 1.0 N 8:CYS379 4.1 23.9 1.0 SG 8:CYS385 4.1 22.2 1.0 CD2 8:LEU427 4.1 25.6 1.0 CB 8:CYS379 4.2 23.9 1.0 CE1 8:TYR204 4.3 35.1 1.0 CG 8:LEU427 4.6 25.6 1.0 CB 8:CYS425 4.6 27.7 1.0 CB 8:CYS385 4.6 22.2 1.0 CE2 8:TYR204 4.6 35.1 1.0 CA 8:CYS379 4.8 23.9 1.0 CA 8:LEU427 4.8 25.6 1.0 CA 8:SER378 4.9 22.9 1.0 CB 8:SER378 4.9 22.9 1.0 N 8:GLY428 4.9 27.3 1.0 C 8:LEU427 5.0 25.6 1.0 N 8:LEU427 5.0 25.6 1.0

Iron binding site 3 out of 28 in the Activity Optimized Complex I (Closed Form)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Activity Optimized Complex I (Closed Form) within 5.0Å range: probe atom residue distance (Å) B Occ 8:Fe502 b:49.7 occ:1.00 FE3 8:SF4502 0.0 49.7 1.0 S2 8:SF4502 2.3 49.7 1.0 S1 8:SF4502 2.3 49.7 1.0 S4 8:SF4502 2.3 49.7 1.0 FE4 8:SF4502 2.7 49.7 1.0 FE1 8:SF4502 2.7 49.7 1.0 FE2 8:SF4502 2.7 49.7 1.0 CB 8:CYS379 3.2 23.9 1.0 SG 8:CYS379 3.8 23.9 1.0 S3 8:SF4502 3.9 49.7 1.0 N 8:GLY380 4.3 16.9 1.0 N 8:GLN381 4.3 24.8 1.0 CB 8:GLN381 4.3 24.8 1.0 CA 8:CYS379 4.3 23.9 1.0 N 8:CYS379 4.5 23.9 1.0 CD 8:PRO223 4.5 30.8 1.0 CG 8:PRO223 4.5 30.8 1.0 OE1 8:GLN381 4.5 24.8 1.0 N 8:CYS382 4.5 21.8 1.0 OH 8:TYR204 4.7 35.1 1.0 CA 8:GLN381 4.8 24.8 1.0 C 8:CYS379 4.8 23.9 1.0

Iron binding site 4 out of 28 in the Activity Optimized Complex I (Closed Form)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Activity Optimized Complex I (Closed Form) within 5.0Å range: probe atom residue distance (Å) B Occ 8:Fe502 b:49.7 occ:1.00 FE4 8:SF4502 0.0 49.7 1.0 S1 8:SF4502 2.3 49.7 1.0 S2 8:SF4502 2.3 49.7 1.0 S3 8:SF4502 2.3 49.7 1.0 FE3 8:SF4502 2.7 49.7 1.0 FE2 8:SF4502 2.7 49.7 1.0 FE1 8:SF4502 2.7 49.7 1.0 N 8:CYS425 2.8 27.7 1.0 CB 8:CYS425 3.1 27.7 1.0 CA 8:CYS425 3.5 27.7 1.0 SG 8:CYS425 3.6 27.7 1.0 S4 8:SF4502 3.9 49.7 1.0 N 8:ILE424 3.9 23.8 1.0 C 8:ILE424 3.9 23.8 1.0 CB 8:ILE424 3.9 23.8 1.0 CA 8:ILE424 4.1 23.8 1.0 OH 8:TYR204 4.1 35.1 1.0 C 8:CYS425 4.1 27.7 1.0 O 8:CYS425 4.3 27.7 1.0 CB 8:THR423 4.5 20.5 1.0 CG 8:PRO223 4.8 30.8 1.0 CG1 8:ILE424 4.8 23.8 1.0 C 8:THR423 4.9 20.5 1.0 CG2 8:ILE424 4.9 23.8 1.0 OG1 8:THR423 5.0 20.5 1.0

Iron binding site 5 out of 28 in the Activity Optimized Complex I (Closed Form)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Activity Optimized Complex I (Closed Form) within 5.0Å range: probe atom residue distance (Å) B Occ 9:Fe301 b:93.3 occ:1.00 FE1 9:FES301 0.0 93.3 1.0 S1 9:FES301 2.2 93.3 1.0 S2 9:FES301 2.2 93.3 1.0 OG1 9:THR137 2.8 73.1 1.0 FE2 9:FES301 3.1 93.3 1.0 SG 9:CYS140 3.1 69.7 1.0 O 9:CYS135 3.2 73.1 1.0 CB 9:CYS135 3.2 73.1 1.0 C 9:CYS135 3.7 73.1 1.0 CA 9:CYS135 4.0 73.1 1.0 CB 9:THR137 4.0 73.1 1.0 SG 9:CYS180 4.2 75.6 1.0 N 9:CYS176 4.4 76.2 1.0 CB 9:CYS140 4.4 69.7 1.0 N 9:THR136 4.5 59.3 1.0 N 9:THR137 4.5 73.1 1.0 C 9:THR136 4.6 59.3 1.0 SG 9:CYS135 4.6 73.1 1.0 N 9:LEU177 4.8 70.8 1.0 O 9:THR136 4.9 59.3 1.0 CA 9:GLU175 4.9 55.3 1.0 O 9:VAL174 4.9 54.7 1.0 CA 9:THR137 4.9 73.1 1.0 CG2 9:THR137 4.9 73.1 1.0 C 9:GLU175 4.9 55.3 1.0 CA 9:THR136 5.0 59.3 1.0

Iron binding site 6 out of 28 in the Activity Optimized Complex I (Closed Form)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Activity Optimized Complex I (Closed Form) within 5.0Å range: probe atom residue distance (Å) B Occ 9:Fe301 b:93.3 occ:1.00 FE2 9:FES301 0.0 93.3 1.0 S1 9:FES301 2.2 93.3 1.0 S2 9:FES301 2.2 93.3 1.0 FE1 9:FES301 3.1 93.3 1.0 SG 9:CYS180 3.1 75.6 1.0 O 9:GLY178 3.4 76.5 1.0 O 9:LEU177 3.5 70.8 1.0 O 9:ALA179 3.5 77.7 1.0 C 9:ALA179 3.6 77.7 1.0 N 9:CYS180 3.6 75.6 1.0 C 9:GLY178 3.8 76.5 1.0 C 9:LEU177 3.8 70.8 1.0 N 9:LEU177 3.8 70.8 1.0 N 9:GLY178 4.1 76.5 1.0 N 9:ALA179 4.2 77.7 1.0 CA 9:CYS180 4.2 75.6 1.0 CB 9:CYS180 4.2 75.6 1.0 N 8:GLY123 4.3 72.6 1.0 CA 9:LEU177 4.5 70.8 1.0 CA 9:ALA179 4.5 77.7 1.0 CA 9:GLY178 4.5 76.5 1.0 CA 9:CYS176 4.6 76.2 1.0 CA 8:GLY123 4.6 72.6 1.0 C 9:CYS176 4.7 76.2 1.0 SG 9:CYS140 4.7 69.7 1.0 N 9:CYS176 4.8 76.2 1.0 OG1 9:THR137 4.8 73.1 1.0

Iron binding site 7 out of 28 in the Activity Optimized Complex I (Closed Form)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Activity Optimized Complex I (Closed Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:49.7 occ:1.00 FE1 A:SF4801 0.0 49.7 1.0 S4 A:SF4801 2.3 49.7 1.0 S3 A:SF4801 2.3 49.7 1.0 S2 A:SF4801 2.3 49.7 1.0 FE3 A:SF4801 2.7 49.7 1.0 FE2 A:SF4801 2.7 49.7 1.0 FE4 A:SF4801 2.7 49.7 1.0 SG A:CYS137 3.1 22.1 1.0 CB A:LEU139 3.7 19.1 1.0 CD1 A:LEU139 3.8 19.1 1.0 S1 A:SF4801 3.9 49.7 1.0 CB A:CYS137 4.0 22.1 1.0 CG A:LEU139 4.1 19.1 1.0 NE2 A:HIS124 4.2 22.1 1.0 CE1 A:HIS124 4.5 22.1 1.0 CG1 A:VAL228 4.6 22.2 1.0 N A:LEU139 4.6 19.1 1.0 CA A:LEU139 4.6 19.1 1.0 CB A:VAL228 4.7 22.2 1.0 C A:LEU139 5.0 19.1 1.0

Iron binding site 8 out of 28 in the Activity Optimized Complex I (Closed Form)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Activity Optimized Complex I (Closed Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:49.7 occ:1.00 FE2 A:SF4801 0.0 49.7 1.0 S3 A:SF4801 2.2 49.7 1.0 S4 A:SF4801 2.3 49.7 1.0 S1 A:SF4801 2.3 49.7 1.0 FE4 A:SF4801 2.7 49.7 1.0 FE1 A:SF4801 2.7 49.7 1.0 FE3 A:SF4801 2.7 49.7 1.0 SG A:CYS128 3.0 20.2 1.0 O A:ASP127 3.9 22.8 1.0 S2 A:SF4801 3.9 49.7 1.0 C A:ASP127 4.3 22.8 1.0 CE B:MET375 4.3 16.4 1.0 CB A:CYS128 4.3 20.2 1.0 N A:CYS128 4.4 20.2 1.0 NE2 A:HIS124 4.6 22.1 1.0 OE1 A:GLN140 4.7 22.4 1.0 CA A:CYS128 4.8 20.2 1.0

Iron binding site 9 out of 28 in the Activity Optimized Complex I (Closed Form)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Activity Optimized Complex I (Closed Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:49.7 occ:1.00 FE3 A:SF4801 0.0 49.7 1.0 S2 A:SF4801 2.3 49.7 1.0 S1 A:SF4801 2.3 49.7 1.0 S4 A:SF4801 2.3 49.7 1.0 FE1 A:SF4801 2.7 49.7 1.0 FE4 A:SF4801 2.7 49.7 1.0 FE2 A:SF4801 2.7 49.7 1.0 SG A:CYS131 3.5 20.7 1.0 S3 A:SF4801 3.8 49.7 1.0 SG A:CYS128 4.1 20.2 1.0 CB A:CYS137 4.1 22.1 1.0 SG A:CYS137 4.1 22.1 1.0 CB A:CYS131 4.2 20.7 1.0 O A:GLN133 4.5 23.0 1.0 N A:GLY229 4.7 49.7 1.0 C A:GLN133 4.7 23.0 1.0 OE1 A:GLN140 5.0 22.4 1.0 CA A:GLY229 5.0 49.7 1.0

Iron binding site 10 out of 28 in the Activity Optimized Complex I (Closed Form)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Activity Optimized Complex I (Closed Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:49.7 occ:1.00 FE4 A:SF4801 0.0 49.7 1.0 S1 A:SF4801 2.3 49.7 1.0 S2 A:SF4801 2.3 49.7 1.0 S3 A:SF4801 2.3 49.7 1.0 FE2 A:SF4801 2.7 49.7 1.0 FE3 A:SF4801 2.7 49.7 1.0 FE1 A:SF4801 2.7 49.7 1.0 NE2 A:HIS124 2.8 22.1 1.0 CD A:ARG175 3.7 17.4 1.0 CE1 A:HIS124 3.7 22.1 1.0 CD2 A:HIS124 3.8 22.1 1.0 S4 A:SF4801 3.8 49.7 1.0 CG A:ARG175 4.4 17.4 1.0 SG A:CYS131 4.5 20.7 1.0 CB A:ARG175 4.8 17.4 1.0 CB A:ASP127 4.9 22.8 1.0 NE A:ARG175 4.9 17.4 1.0 ND1 A:HIS124 4.9 22.1 1.0 CB A:CYS131 4.9 20.7 1.0 CG A:HIS124 4.9 22.1 1.0 O A:PRO125 5.0 21.1 1.0

T.J.Jeon, S.G.Lee, S.H.Yoo, M.Kim, D.Song, J.Ryu, H.Park, D.S.Kim, J.Hyun, H.M.Kim, S.E.Ryu. A Dynamic Substrate Pool Revealed By Cryo-Em of A Lipid-Preserved Respiratory Supercomplex. Antioxid.Redox Signal. 2022.
ISSN: ESSN 1557-7716
PubMed: 34913730
DOI: 10.1089/ARS.2021.0114