Iron in PDB 7vbn: Matrix Arm of Deactive State Ci From Dq-Nadh Dataset

All present enzymatic activity of Matrix Arm of Deactive State Ci From Dq-Nadh Dataset:
7.1.1.2;

The structure of Matrix Arm of Deactive State Ci From Dq-Nadh Dataset 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 Matrix Arm of Deactive State Ci From Dq-Nadh Dataset (pdb code 7vbn). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 28 binding sites of Iron where determined in the Matrix Arm of Deactive State Ci From Dq-Nadh Dataset, PDB code: 7vbn:
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 Matrix Arm of Deactive State Ci From Dq-Nadh Dataset


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Matrix Arm of Deactive State Ci From Dq-Nadh Dataset within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:21.7 occ:1.00 FE1 A:SF4501 0.0 21.7 1.0 SG A:CYS382 2.3 15.2 1.0 S4 A:SF4501 2.3 21.7 1.0 S3 A:SF4501 2.3 21.7 1.0 S2 A:SF4501 2.3 21.7 1.0 FE3 A:SF4501 2.7 21.7 1.0 FE4 A:SF4501 2.7 21.7 1.0 FE2 A:SF4501 2.7 21.7 1.0 CB A:CYS382 3.5 15.2 1.0 CB A:CYS385 3.7 16.2 1.0 N A:CYS382 3.7 15.2 1.0 S1 A:SF4501 3.9 21.7 1.0 CA A:CYS382 4.1 15.2 1.0 N A:ILE424 4.2 16.2 1.0 CB A:ILE424 4.2 16.2 1.0 O A:CYS382 4.3 15.2 1.0 SG A:CYS385 4.4 16.2 1.0 CB A:THR423 4.5 16.6 1.0 CG1 A:ILE424 4.6 16.2 1.0 N A:CYS425 4.6 19.9 1.0 C A:CYS382 4.7 15.2 1.0 CA A:ILE424 4.8 16.2 1.0 SG A:CYS379 4.8 18.5 1.0 CB A:GLN381 4.8 16.4 1.0 SG A:CYS425 4.8 19.9 1.0 N A:GLN381 4.8 16.4 1.0 C A:GLN381 4.8 16.4 1.0 CD1 A:ILE424 4.9 16.2 1.0 CG2 A:THR423 4.9 16.6 1.0 CA A:CYS385 5.0 16.2 1.0

Iron binding site 2 out of 28 in the Matrix Arm of Deactive State Ci From Dq-Nadh Dataset


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Matrix Arm of Deactive State Ci From Dq-Nadh Dataset within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:21.7 occ:1.00 FE2 A:SF4501 0.0 21.7 1.0 SG A:CYS425 2.3 19.9 1.0 S4 A:SF4501 2.3 21.7 1.0 S3 A:SF4501 2.3 21.7 1.0 S1 A:SF4501 2.3 21.7 1.0 FE4 A:SF4501 2.7 21.7 1.0 FE3 A:SF4501 2.7 21.7 1.0 FE1 A:SF4501 2.7 21.7 1.0 CB A:CYS425 3.5 19.9 1.0 N A:CYS425 3.9 19.9 1.0 S2 A:SF4501 3.9 21.7 1.0 CB A:LEU427 4.0 22.8 1.0 CA A:CYS425 4.1 19.9 1.0 CG A:PRO223 4.3 20.6 1.0 CD1 A:ILE205 4.4 25.4 1.0 C A:CYS425 4.4 19.9 1.0 O A:CYS425 4.5 19.9 1.0 N A:LEU427 4.6 22.8 1.0 CD A:PRO223 4.6 20.6 1.0 SG A:CYS379 4.7 18.5 1.0 SG A:CYS385 4.8 16.2 1.0 SG A:CYS382 4.8 15.2 1.0 CA A:LEU427 4.9 22.8 1.0 CB A:CYS385 4.9 16.2 1.0 C A:ILE424 5.0 16.2 1.0 CB A:ILE424 5.0 16.2 1.0

Iron binding site 3 out of 28 in the Matrix Arm of Deactive State Ci From Dq-Nadh Dataset


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Matrix Arm of Deactive State Ci From Dq-Nadh Dataset within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:21.7 occ:1.00 FE3 A:SF4501 0.0 21.7 1.0 SG A:CYS385 2.3 16.2 1.0 S4 A:SF4501 2.3 21.7 1.0 S2 A:SF4501 2.3 21.7 1.0 S1 A:SF4501 2.3 21.7 1.0 FE1 A:SF4501 2.7 21.7 1.0 FE4 A:SF4501 2.7 21.7 1.0 FE2 A:SF4501 2.7 21.7 1.0 CB A:CYS385 2.8 16.2 1.0 S3 A:SF4501 3.9 21.7 1.0 CB A:SER378 4.1 20.8 1.0 CD2 A:LEU427 4.1 22.8 1.0 CA A:CYS385 4.3 16.2 1.0 CB A:LEU427 4.3 22.8 1.0 N A:CYS379 4.4 18.5 1.0 SG A:CYS382 4.4 15.2 1.0 CA A:SER378 4.5 20.8 1.0 CG A:LEU427 4.6 22.8 1.0 SG A:CYS425 4.7 19.9 1.0 C A:CYS385 4.8 16.2 1.0 N A:GLY380 4.8 17.1 1.0 SG A:CYS379 4.8 18.5 1.0 N A:GLY428 4.8 23.3 1.0 N A:ARG386 4.9 17.2 1.0 CD1 A:LEU427 4.9 22.8 1.0 C A:SER378 4.9 20.8 1.0 OG A:SER378 5.0 20.8 1.0

Iron binding site 4 out of 28 in the Matrix Arm of Deactive State Ci From Dq-Nadh Dataset


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Matrix Arm of Deactive State Ci From Dq-Nadh Dataset within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:21.7 occ:1.00 FE4 A:SF4501 0.0 21.7 1.0 SG A:CYS379 2.3 18.5 1.0 S2 A:SF4501 2.3 21.7 1.0 S1 A:SF4501 2.3 21.7 1.0 S3 A:SF4501 2.3 21.7 1.0 FE2 A:SF4501 2.7 21.7 1.0 FE1 A:SF4501 2.7 21.7 1.0 FE3 A:SF4501 2.7 21.7 1.0 CB A:CYS379 3.5 18.5 1.0 N A:CYS379 3.8 18.5 1.0 N A:GLN381 3.8 16.4 1.0 N A:GLY380 3.8 17.1 1.0 S4 A:SF4501 3.9 21.7 1.0 CA A:CYS379 4.0 18.5 1.0 CB A:GLN381 4.1 16.4 1.0 C A:CYS379 4.2 18.5 1.0 CD A:PRO223 4.3 20.6 1.0 CA A:GLN381 4.5 16.4 1.0 N A:CYS382 4.6 15.2 1.0 C A:GLY380 4.7 17.1 1.0 CA A:GLY380 4.7 17.1 1.0 SG A:CYS425 4.8 19.9 1.0 NE2 A:GLN381 4.8 16.4 1.0 SG A:CYS382 4.8 15.2 1.0 CG A:PRO223 4.8 20.6 1.0 SG A:CYS385 4.9 16.2 1.0 C A:SER378 4.9 20.8 1.0 CG1 A:ILE205 5.0 25.4 1.0

Iron binding site 5 out of 28 in the Matrix Arm of Deactive State Ci From Dq-Nadh Dataset


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Matrix Arm of Deactive State Ci From Dq-Nadh Dataset within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:14.2 occ:1.00 FE1 B:SF4301 0.0 14.2 1.0 SG B:CYS113 2.3 12.3 1.0 S2 B:SF4301 2.3 14.2 1.0 S3 B:SF4301 2.3 14.2 1.0 S4 B:SF4301 2.3 14.2 1.0 FE3 B:SF4301 2.7 14.2 1.0 FE4 B:SF4301 2.7 14.2 1.0 FE2 B:SF4301 2.7 14.2 1.0 CB B:CYS113 3.4 12.3 1.0 CA B:CYS113 3.8 12.3 1.0 N B:ALA115 3.9 12.4 1.0 S1 B:SF4301 3.9 14.2 1.0 N B:ILE114 4.1 11.7 1.0 C B:CYS113 4.3 12.3 1.0 CA B:ALA115 4.4 12.4 1.0 CB B:ALA166 4.4 11.8 1.0 CE2 B:TYR145 4.5 11.1 1.0 N B:CYS116 4.5 11.4 1.0 SG B:CYS119 4.8 12.1 1.0 SG B:CYS162 4.9 11.2 1.0 C B:ILE114 4.9 11.7 1.0 SG B:CYS116 4.9 11.4 1.0 O B:HOH425 5.0 11.9 1.0 C B:ALA115 5.0 12.4 1.0

Iron binding site 6 out of 28 in the Matrix Arm of Deactive State Ci From Dq-Nadh Dataset


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Matrix Arm of Deactive State Ci From Dq-Nadh Dataset within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:14.2 occ:1.00 FE2 B:SF4301 0.0 14.2 1.0 SG B:CYS116 2.3 11.4 1.0 S1 B:SF4301 2.3 14.2 1.0 S3 B:SF4301 2.3 14.2 1.0 S4 B:SF4301 2.3 14.2 1.0 FE4 B:SF4301 2.7 14.2 1.0 FE3 B:SF4301 2.7 14.2 1.0 FE1 B:SF4301 2.7 14.2 1.0 N B:CYS116 3.5 11.4 1.0 CB B:CYS116 3.5 11.4 1.0 N B:LYS117 3.6 12.6 1.0 CA B:CYS116 3.8 11.4 1.0 S2 B:SF4301 3.9 14.2 1.0 N B:LEU118 4.0 11.8 1.0 C B:CYS116 4.1 11.4 1.0 CD B:PRO163 4.3 10.4 1.0 C B:ALA115 4.5 12.4 1.0 CA B:LYS117 4.5 12.6 1.0 N B:ALA115 4.6 12.4 1.0 CD1 B:ILE114 4.6 11.7 1.0 SG B:CYS162 4.7 11.2 1.0 CB B:LEU118 4.7 11.8 1.0 SG B:CYS119 4.8 12.1 1.0 C B:LYS117 4.8 12.6 1.0 CA B:ALA115 4.8 12.4 1.0 N B:CYS119 4.8 12.1 1.0 SG B:CYS113 4.8 12.3 1.0 CG B:PRO163 4.9 10.4 1.0 CA B:LEU118 4.9 11.8 1.0

Iron binding site 7 out of 28 in the Matrix Arm of Deactive State Ci From Dq-Nadh Dataset


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Matrix Arm of Deactive State Ci From Dq-Nadh Dataset within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:14.2 occ:1.00 FE3 B:SF4301 0.0 14.2 1.0 SG B:CYS119 2.3 12.1 1.0 S1 B:SF4301 2.3 14.2 1.0 S2 B:SF4301 2.3 14.2 1.0 S4 B:SF4301 2.3 14.2 1.0 FE1 B:SF4301 2.7 14.2 1.0 FE2 B:SF4301 2.7 14.2 1.0 FE4 B:SF4301 2.7 14.2 1.0 CB B:CYS119 3.3 12.1 1.0 N B:CYS119 3.8 12.1 1.0 S3 B:SF4301 3.9 14.2 1.0 OH B:TYR145 4.0 11.1 1.0 CE2 B:TYR145 4.0 11.1 1.0 CA B:CYS119 4.2 12.1 1.0 CD1 B:ILE130 4.3 12.2 1.0 CG2 B:ILE167 4.4 11.1 1.0 CZ B:TYR145 4.5 11.1 1.0 N B:LEU118 4.6 11.8 1.0 N B:LYS117 4.6 12.6 1.0 SG B:CYS116 4.7 11.4 1.0 SG B:CYS113 4.7 12.3 1.0 SG B:CYS162 4.7 11.2 1.0 CA B:LYS117 4.8 12.6 1.0 N B:GLU120 4.9 13.6 1.0 C B:LYS117 5.0 12.6 1.0

Iron binding site 8 out of 28 in the Matrix Arm of Deactive State Ci From Dq-Nadh Dataset


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Matrix Arm of Deactive State Ci From Dq-Nadh Dataset within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:14.2 occ:1.00 FE4 B:SF4301 0.0 14.2 1.0 SG B:CYS162 2.3 11.2 1.0 S1 B:SF4301 2.3 14.2 1.0 S2 B:SF4301 2.3 14.2 1.0 S3 B:SF4301 2.3 14.2 1.0 FE2 B:SF4301 2.7 14.2 1.0 FE3 B:SF4301 2.7 14.2 1.0 FE1 B:SF4301 2.7 14.2 1.0 CB B:CYS162 3.4 11.2 1.0 CB B:ALA166 3.8 11.8 1.0 S4 B:SF4301 3.9 14.2 1.0 CA B:CYS162 4.0 11.2 1.0 CG2 B:ILE167 4.2 11.1 1.0 CD B:PRO163 4.2 10.4 1.0 N B:ILE167 4.4 11.1 1.0 CG2 B:VAL164 4.5 12.3 1.0 N B:ALA166 4.6 11.8 1.0 SG B:CYS116 4.6 11.4 1.0 CA B:ALA166 4.7 11.8 1.0 SG B:CYS119 4.7 12.1 1.0 SG B:CYS113 4.8 12.3 1.0 N B:PRO163 4.8 10.4 1.0 C B:CYS162 4.8 11.2 1.0 CB B:ILE167 4.9 11.1 1.0 C B:ALA166 5.0 11.8 1.0

Iron binding site 9 out of 28 in the Matrix Arm of Deactive State Ci From Dq-Nadh Dataset


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Matrix Arm of Deactive State Ci From Dq-Nadh Dataset within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:21.8 occ:1.00 FE1 B:SF4302 0.0 21.8 1.0 SG B:CYS123 2.3 12.1 1.0 S2 B:SF4302 2.3 21.8 1.0 S3 B:SF4302 2.3 21.8 1.0 S4 B:SF4302 2.3 21.8 1.0 FE2 B:SF4302 2.7 21.8 1.0 FE4 B:SF4302 2.7 21.8 1.0 FE3 B:SF4302 2.7 21.8 1.0 CB B:CYS123 3.4 12.1 1.0 CA B:CYS123 3.8 12.1 1.0 S1 B:SF4302 3.9 21.8 1.0 CD B:PRO124 4.1 21.8 1.0 CD1 B:ILE128 4.2 11.5 1.0 CG1 B:ILE128 4.4 11.5 1.0 CB B:ALA127 4.4 11.7 1.0 C B:CYS123 4.5 12.1 1.0 N B:PRO124 4.5 21.8 1.0 SG B:CYS155 4.7 21.8 1.0 SG B:CYS152 4.8 11.1 1.0 SG B:CYS158 4.8 21.8 1.0 N B:ALA125 5.0 18.3 1.0 CB B:CYS158 5.0 21.8 1.0 N B:ALA127 5.0 11.7 1.0

Iron binding site 10 out of 28 in the Matrix Arm of Deactive State Ci From Dq-Nadh Dataset


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Matrix Arm of Deactive State Ci From Dq-Nadh Dataset within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:21.8 occ:1.00 FE2 B:SF4302 0.0 21.8 1.0 SG B:CYS152 2.3 11.1 1.0 S3 B:SF4302 2.3 21.8 1.0 S1 B:SF4302 2.3 21.8 1.0 S4 B:SF4302 2.3 21.8 1.0 FE1 B:SF4302 2.7 21.8 1.0 FE4 B:SF4302 2.7 21.8 1.0 FE3 B:SF4302 2.7 21.8 1.0 CB B:CYS152 3.4 11.1 1.0 NE2 B:HIS101 3.6 12.6 1.0 N B:TYR154 3.7 13.3 1.0 S2 B:SF4302 3.9 21.8 1.0 CA B:CYS152 3.9 11.1 1.0 CE1 B:HIS101 4.0 12.6 1.0 N B:ILE153 4.0 21.8 1.0 CA B:TYR154 4.2 13.3 1.0 C B:CYS152 4.4 11.1 1.0 N B:CYS155 4.5 21.8 1.0 C B:ILE153 4.7 21.8 1.0 SG B:CYS123 4.7 12.1 1.0 SG B:CYS158 4.8 21.8 1.0 CD2 B:HIS101 4.8 12.6 1.0 SG B:CYS155 4.8 21.8 1.0 C B:TYR154 4.9 13.3 1.0 CA B:ILE153 4.9 21.8 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