Iron in PDB 7w2y: Active State Ci From Dq-Nadh Dataset, Subclass 3

All present enzymatic activity of Active State Ci From Dq-Nadh Dataset, Subclass 3:
7.1.1.2;

The structure of Active State Ci From Dq-Nadh Dataset, Subclass 3 also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
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 Active State Ci From Dq-Nadh Dataset, Subclass 3 (pdb code 7w2y). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 28 binding sites of Iron where determined in the Active State Ci From Dq-Nadh Dataset, Subclass 3, PDB code: 7w2y:
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 Active State Ci From Dq-Nadh Dataset, Subclass 3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Active State Ci From Dq-Nadh Dataset, Subclass 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:44.8 occ:1.00 FE1 A:SF4501 0.0 44.8 1.0 SG A:CYS382 2.3 29.9 1.0 S4 A:SF4501 2.3 24.5 1.0 S2 A:SF4501 2.3 10.3 1.0 S3 A:SF4501 2.3 13.6 1.0 FE3 A:SF4501 2.7 44.0 1.0 FE4 A:SF4501 2.7 43.1 1.0 FE2 A:SF4501 2.7 38.8 1.0 CB A:CYS382 3.3 14.8 1.0 N A:CYS382 3.6 8.2 1.0 CB A:CYS385 3.7 11.7 1.0 S1 A:SF4501 3.9 14.0 1.0 CA A:CYS382 4.0 6.3 1.0 N A:ILE424 4.2 16.3 1.0 CB A:ILE424 4.3 14.1 1.0 O A:CYS382 4.5 25.1 1.0 SG A:CYS385 4.5 28.1 1.0 CB A:THR423 4.6 13.6 1.0 C A:CYS382 4.6 15.1 1.0 N A:CYS425 4.6 14.8 1.0 N A:GLN381 4.7 22.4 1.0 CG1 A:ILE424 4.7 19.2 1.0 C A:GLN381 4.7 16.6 1.0 CB A:GLN381 4.7 18.7 1.0 CD1 A:ILE424 4.8 14.5 1.0 CA A:ILE424 4.8 8.0 1.0 SG A:CYS425 4.8 27.2 1.0 SG A:CYS379 4.9 16.1 1.0 CA A:CYS385 5.0 8.1 1.0 CG2 A:THR423 5.0 12.4 1.0 CA A:GLN381 5.0 9.6 1.0 N A:CYS385 5.0 15.1 1.0

Iron binding site 2 out of 28 in the Active State Ci From Dq-Nadh Dataset, Subclass 3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Active State Ci From Dq-Nadh Dataset, Subclass 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:38.8 occ:1.00 FE2 A:SF4501 0.0 38.8 1.0 SG A:CYS425 2.3 27.2 1.0 S4 A:SF4501 2.3 24.5 1.0 S1 A:SF4501 2.3 14.0 1.0 S3 A:SF4501 2.3 13.6 1.0 FE4 A:SF4501 2.7 43.1 1.0 FE3 A:SF4501 2.7 44.0 1.0 FE1 A:SF4501 2.7 44.8 1.0 CB A:CYS425 3.5 6.3 1.0 N A:CYS425 3.9 14.8 1.0 S2 A:SF4501 3.9 10.3 1.0 CA A:CYS425 4.1 12.0 1.0 CB A:LEU427 4.1 22.6 1.0 CG A:PRO223 4.3 19.7 1.0 CD1 A:ILE205 4.3 26.4 1.0 C A:CYS425 4.4 28.5 1.0 O A:CYS425 4.6 25.6 1.0 CD A:PRO223 4.6 20.1 1.0 N A:LEU427 4.6 13.6 1.0 SG A:CYS379 4.7 16.1 1.0 SG A:CYS385 4.7 28.1 1.0 SG A:CYS382 4.8 29.9 1.0 CB A:CYS385 4.9 11.7 1.0 CA A:LEU427 4.9 22.8 1.0 C A:ILE424 5.0 21.2 1.0 CB A:ILE424 5.0 14.1 1.0

Iron binding site 3 out of 28 in the Active State Ci From Dq-Nadh Dataset, Subclass 3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Active State Ci From Dq-Nadh Dataset, Subclass 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:44.0 occ:1.00 FE3 A:SF4501 0.0 44.0 1.0 SG A:CYS385 2.3 28.1 1.0 S4 A:SF4501 2.3 24.5 1.0 S1 A:SF4501 2.3 14.0 1.0 S2 A:SF4501 2.3 10.3 1.0 CB A:CYS385 2.7 11.7 1.0 FE1 A:SF4501 2.7 44.8 1.0 FE4 A:SF4501 2.7 43.1 1.0 FE2 A:SF4501 2.7 38.8 1.0 OG A:SER378 3.7 22.9 1.0 S3 A:SF4501 3.9 13.6 1.0 CA A:CYS385 4.2 8.1 1.0 CB A:SER378 4.3 13.1 1.0 CB A:LEU427 4.3 22.6 1.0 CD2 A:LEU427 4.4 16.5 1.0 SG A:CYS382 4.4 29.9 1.0 N A:CYS379 4.4 13.5 1.0 CA A:SER378 4.6 16.1 1.0 N A:GLY380 4.7 18.1 1.0 SG A:CYS379 4.7 16.1 1.0 SG A:CYS425 4.7 27.2 1.0 C A:CYS385 4.7 8.8 1.0 CG A:LEU427 4.8 18.9 1.0 N A:ARG386 4.9 14.8 1.0 N A:GLY428 4.9 17.8 1.0 N A:CYS385 5.0 15.1 1.0 CD1 A:LEU427 5.0 22.7 1.0

Iron binding site 4 out of 28 in the Active State Ci From Dq-Nadh Dataset, Subclass 3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Active State Ci From Dq-Nadh Dataset, Subclass 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:43.1 occ:1.00 FE4 A:SF4501 0.0 43.1 1.0 SG A:CYS379 2.3 16.1 1.0 S2 A:SF4501 2.3 10.3 1.0 S1 A:SF4501 2.3 14.0 1.0 S3 A:SF4501 2.3 13.6 1.0 FE2 A:SF4501 2.7 38.8 1.0 FE1 A:SF4501 2.7 44.8 1.0 FE3 A:SF4501 2.7 44.0 1.0 CB A:CYS379 3.6 12.5 1.0 N A:GLN381 3.7 22.4 1.0 S4 A:SF4501 3.9 24.5 1.0 N A:GLY380 3.9 18.1 1.0 CB A:GLN381 3.9 18.7 1.0 N A:CYS379 4.0 13.5 1.0 CA A:CYS379 4.2 15.7 1.0 C A:CYS379 4.3 19.8 1.0 CD A:PRO223 4.3 20.1 1.0 CA A:GLN381 4.4 9.6 1.0 N A:CYS382 4.5 8.2 1.0 C A:GLY380 4.7 18.1 1.0 OE1 A:GLN381 4.7 30.5 1.0 CA A:GLY380 4.8 9.8 1.0 SG A:CYS425 4.8 27.2 1.0 SG A:CYS382 4.8 29.9 1.0 CG A:PRO223 4.9 19.7 1.0 OG A:SER378 4.9 22.9 1.0 SG A:CYS385 4.9 28.1 1.0 C A:GLN381 5.0 16.6 1.0 CG1 A:ILE205 5.0 26.3 1.0

Iron binding site 5 out of 28 in the Active State Ci From Dq-Nadh Dataset, Subclass 3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Active State Ci From Dq-Nadh Dataset, Subclass 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:26.4 occ:1.00 FE1 B:SF4301 0.0 26.4 1.0 SG B:CYS113 2.3 25.9 1.0 S4 B:SF4301 2.3 5.4 1.0 S3 B:SF4301 2.3 5.8 1.0 S2 B:SF4301 2.3 6.0 1.0 FE2 B:SF4301 2.7 24.8 1.0 FE3 B:SF4301 2.7 27.9 1.0 FE4 B:SF4301 2.7 30.7 1.0 CB B:CYS113 3.4 16.1 1.0 CA B:CYS113 3.7 12.3 1.0 S1 B:SF4301 3.9 8.9 1.0 N B:ILE114 3.9 11.0 1.0 N B:ALA115 4.0 12.2 1.0 C B:CYS113 4.3 16.8 1.0 CB B:ALA166 4.3 14.6 1.0 CE2 B:TYR145 4.4 11.9 1.0 CA B:ALA115 4.5 0.6 1.0 N B:CYS116 4.7 11.7 1.0 SG B:CYS119 4.8 3.4 1.0 SG B:CYS162 4.8 7.2 1.0 SG B:CYS116 4.9 17.0 1.0 C B:ILE114 4.9 9.5 1.0 N B:CYS113 5.0 12.4 1.0

Iron binding site 6 out of 28 in the Active State Ci From Dq-Nadh Dataset, Subclass 3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Active State Ci From Dq-Nadh Dataset, Subclass 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:24.8 occ:1.00 FE2 B:SF4301 0.0 24.8 1.0 SG B:CYS116 2.3 17.0 1.0 S1 B:SF4301 2.3 8.9 1.0 S3 B:SF4301 2.3 5.8 1.0 S4 B:SF4301 2.3 5.4 1.0 FE4 B:SF4301 2.7 30.7 1.0 FE1 B:SF4301 2.7 26.4 1.0 FE3 B:SF4301 2.7 27.9 1.0 N B:CYS116 3.5 11.7 1.0 CB B:CYS116 3.5 6.1 1.0 N B:LYS117 3.6 3.1 1.0 S2 B:SF4301 3.9 6.0 1.0 CA B:CYS116 3.9 5.9 1.0 N B:LEU118 4.1 5.9 1.0 C B:CYS116 4.1 16.2 1.0 CD B:PRO163 4.5 7.0 1.0 N B:ALA115 4.5 12.2 1.0 C B:ALA115 4.5 16.4 1.0 CA B:LYS117 4.5 10.6 1.0 SG B:CYS119 4.7 3.4 1.0 SG B:CYS162 4.7 7.2 1.0 CG1 B:ILE114 4.7 4.8 1.0 SG B:CYS113 4.8 25.9 1.0 CB B:LEU118 4.8 14.9 1.0 CA B:ALA115 4.8 0.6 1.0 C B:LYS117 4.8 10.1 1.0 N B:CYS119 4.9 10.0 1.0 N B:ILE114 5.0 11.0 1.0 CA B:LEU118 5.0 11.3 1.0

Iron binding site 7 out of 28 in the Active State Ci From Dq-Nadh Dataset, Subclass 3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Active State Ci From Dq-Nadh Dataset, Subclass 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:27.9 occ:1.00 FE3 B:SF4301 0.0 27.9 1.0 SG B:CYS119 2.3 3.4 1.0 S4 B:SF4301 2.3 5.4 1.0 S1 B:SF4301 2.3 8.9 1.0 S2 B:SF4301 2.3 6.0 1.0 FE2 B:SF4301 2.7 24.8 1.0 FE1 B:SF4301 2.7 26.4 1.0 FE4 B:SF4301 2.7 30.7 1.0 CB B:CYS119 3.4 13.9 1.0 S3 B:SF4301 3.9 5.8 1.0 N B:CYS119 3.9 10.0 1.0 CE2 B:TYR145 4.1 11.9 1.0 OH B:TYR145 4.1 11.7 1.0 CA B:CYS119 4.3 6.5 1.0 CD1 B:ILE130 4.6 17.3 1.0 N B:LEU118 4.6 5.9 1.0 CG2 B:ILE167 4.6 4.8 1.0 CZ B:TYR145 4.7 10.0 1.0 SG B:CYS116 4.7 17.0 1.0 N B:LYS117 4.7 3.1 1.0 SG B:CYS113 4.7 25.9 1.0 SG B:CYS162 4.7 7.2 1.0 CA B:LYS117 4.9 10.6 1.0

Iron binding site 8 out of 28 in the Active State Ci From Dq-Nadh Dataset, Subclass 3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Active State Ci From Dq-Nadh Dataset, Subclass 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:30.7 occ:1.00 FE4 B:SF4301 0.0 30.7 1.0 SG B:CYS162 2.3 7.2 1.0 S2 B:SF4301 2.3 6.0 1.0 S3 B:SF4301 2.3 5.8 1.0 S1 B:SF4301 2.3 8.9 1.0 FE2 B:SF4301 2.7 24.8 1.0 FE1 B:SF4301 2.7 26.4 1.0 FE3 B:SF4301 2.7 27.9 1.0 CB B:CYS162 3.4 16.4 1.0 CB B:ALA166 3.8 14.6 1.0 S4 B:SF4301 3.9 5.4 1.0 CA B:CYS162 3.9 2.4 1.0 CD B:PRO163 4.2 7.0 1.0 CG2 B:VAL164 4.3 7.3 1.0 CG2 B:ILE167 4.4 4.8 1.0 N B:ILE167 4.5 8.4 1.0 SG B:CYS116 4.6 17.0 1.0 N B:ALA166 4.6 12.3 1.0 CA B:ALA166 4.7 1.2 1.0 SG B:CYS119 4.8 3.4 1.0 C B:CYS162 4.8 18.1 1.0 N B:PRO163 4.8 19.4 1.0 SG B:CYS113 4.8 25.9 1.0

Iron binding site 9 out of 28 in the Active State Ci From Dq-Nadh Dataset, Subclass 3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Active State Ci From Dq-Nadh Dataset, Subclass 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:26.5 occ:1.00 FE1 B:SF4302 0.0 26.5 1.0 SG B:CYS123 2.3 3.3 1.0 S2 B:SF4302 2.3 5.8 1.0 S3 B:SF4302 2.3 5.2 1.0 S4 B:SF4302 2.3 1.6 1.0 FE2 B:SF4302 2.7 23.7 1.0 FE4 B:SF4302 2.7 25.4 1.0 FE3 B:SF4302 2.7 38.6 1.0 CB B:CYS123 3.3 15.1 1.0 CA B:CYS123 3.8 20.8 1.0 S1 B:SF4302 3.9 7.7 1.0 CD B:PRO124 4.2 20.2 1.0 CD1 B:ILE128 4.3 3.9 1.0 CB B:ALA127 4.4 0.0 1.0 CG1 B:ILE128 4.5 0.0 1.0 C B:CYS123 4.5 27.6 1.0 N B:PRO124 4.6 26.0 1.0 SG B:CYS155 4.7 6.2 1.0 SG B:CYS152 4.8 7.9 1.0 SG B:CYS158 4.9 10.5 1.0 N B:ALA127 4.9 21.2 1.0 CB B:CYS158 5.0 19.8 1.0

Iron binding site 10 out of 28 in the Active State Ci From Dq-Nadh Dataset, Subclass 3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Active State Ci From Dq-Nadh Dataset, Subclass 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:23.7 occ:1.00 FE2 B:SF4302 0.0 23.7 1.0 SG B:CYS152 2.3 7.9 1.0 S1 B:SF4302 2.3 7.7 1.0 S3 B:SF4302 2.3 5.2 1.0 S4 B:SF4302 2.3 1.6 1.0 FE1 B:SF4302 2.7 26.5 1.0 FE4 B:SF4302 2.7 25.4 1.0 FE3 B:SF4302 2.7 38.6 1.0 CB B:CYS152 3.5 16.1 1.0 NE2 B:HIS101 3.6 18.8 1.0 N B:TYR154 3.8 26.1 1.0 S2 B:SF4302 3.9 5.8 1.0 CA B:CYS152 3.9 14.2 1.0 N B:ILE153 4.1 30.3 1.0 CE1 B:HIS101 4.1 17.4 1.0 CA B:TYR154 4.3 18.6 1.0 C B:CYS152 4.5 27.8 1.0 N B:CYS155 4.6 25.0 1.0 SG B:CYS123 4.7 3.3 1.0 CD2 B:HIS101 4.7 18.5 1.0 SG B:CYS158 4.8 10.5 1.0 C B:ILE153 4.8 21.5 1.0 SG B:CYS155 4.8 6.2 1.0 CB B:ALA127 4.9 0.0 1.0 C B:TYR154 5.0 20.5 1.0

J.Gu, T.Liu, R.Guo, L.Zhang, M.Yang. The Coupling Mechanism of Mammalian Mitochondrial Complex I. Nat.Struct.Mol.Biol. V. 29 172 2022.
ISSN: ESSN 1545-9985
PubMed: 35145322
DOI: 10.1038/S41594-022-00722-W