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Iron in PDB 7w4f: Active State Ci From Q1-Nadh Dataset, Subclass 4

Enzymatic activity of Active State Ci From Q1-Nadh Dataset, Subclass 4

All present enzymatic activity of Active State Ci From Q1-Nadh Dataset, Subclass 4:
7.1.1.2;

Other elements in 7w4f:

The structure of Active State Ci From Q1-Nadh Dataset, Subclass 4 also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Zinc (Zn) 1 atom

Iron Binding Sites:

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 Q1-Nadh Dataset, Subclass 4 (pdb code 7w4f). 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 Q1-Nadh Dataset, Subclass 4, PDB code: 7w4f:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 28 in 7w4f

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Iron binding site 1 out of 28 in the Active State Ci From Q1-Nadh Dataset, Subclass 4


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 Q1-Nadh Dataset, Subclass 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:36.8
occ:1.00
 FE1 A:SF4501 0.0 36.8 1.0
SG A:CYS382 2.3 24.8 1.0
S2 A:SF4501 2.3 19.9 1.0
S4 A:SF4501 2.3 29.7 1.0
S3 A:SF4501 2.3 24.2 1.0
FE3 A:SF4501 2.7 52.4 1.0
FE4 A:SF4501 2.7 41.0 1.0
FE2 A:SF4501 2.7 41.0 1.0
CB A:CYS382 3.6 17.3 1.0
CB A:CYS385 3.7 10.9 1.0
N A:CYS382 3.8 17.7 1.0
S1 A:SF4501 3.9 18.6 1.0
CA A:CYS382 4.2 14.3 1.0
N A:ILE424 4.3 22.5 1.0
CB A:ILE424 4.4 20.6 1.0
O A:CYS382 4.4 15.0 1.0
SG A:CYS385 4.5 37.7 1.0
CB A:THR423 4.5 18.4 1.0
N A:CYS425 4.6 25.4 1.0
C A:CYS382 4.7 14.9 1.0
SG A:CYS425 4.8 23.5 1.0
SG A:CYS379 4.8 20.0 1.0
CA A:ILE424 4.9 19.1 1.0
CB A:GLN381 4.9 13.8 1.0
N A:GLN381 4.9 17.6 1.0
C A:GLN381 4.9 16.7 1.0
CG1 A:ILE424 5.0 20.6 1.0
CA A:CYS385 5.0 16.1 1.0
CD1 A:ILE424 5.0 16.3 1.0

Iron binding site 2 out of 28 in 7w4f

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Iron binding site 2 out of 28 in the Active State Ci From Q1-Nadh Dataset, Subclass 4


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 Q1-Nadh Dataset, Subclass 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:41.0
occ:1.00
 FE2 A:SF4501 0.0 41.0 1.0
SG A:CYS425 2.3 23.5 1.0
S4 A:SF4501 2.3 29.7 1.0
S3 A:SF4501 2.3 24.2 1.0
S1 A:SF4501 2.3 18.6 1.0
FE4 A:SF4501 2.7 41.0 1.0
FE1 A:SF4501 2.7 36.8 1.0
FE3 A:SF4501 2.7 52.4 1.0
CB A:CYS425 3.5 19.9 1.0
S2 A:SF4501 3.9 19.9 1.0
N A:CYS425 4.0 25.4 1.0
CB A:LEU427 4.1 23.7 1.0
CA A:CYS425 4.2 23.7 1.0
CG A:PRO223 4.3 23.5 1.0
CD1 A:ILE205 4.3 30.6 1.0
C A:CYS425 4.4 23.1 1.0
O A:CYS425 4.5 26.8 1.0
CD A:PRO223 4.6 27.8 1.0
SG A:CYS379 4.7 20.0 1.0
N A:LEU427 4.7 22.7 1.0
SG A:CYS385 4.8 37.7 1.0
SG A:CYS382 4.9 24.8 1.0
CB A:CYS385 5.0 10.9 1.0
CA A:LEU427 5.0 23.9 1.0

Iron binding site 3 out of 28 in 7w4f

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Iron binding site 3 out of 28 in the Active State Ci From Q1-Nadh Dataset, Subclass 4


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 Q1-Nadh Dataset, Subclass 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:52.4
occ:1.00
 FE3 A:SF4501 0.0 52.4 1.0
SG A:CYS385 2.3 37.7 1.0
S1 A:SF4501 2.3 18.6 1.0
S2 A:SF4501 2.3 19.9 1.0
S4 A:SF4501 2.3 29.7 1.0
CB A:CYS385 2.7 10.9 1.0
FE1 A:SF4501 2.7 36.8 1.0
FE4 A:SF4501 2.7 41.0 1.0
FE2 A:SF4501 2.7 41.0 1.0
OG A:SER378 3.8 25.8 1.0
S3 A:SF4501 3.9 24.2 1.0
CA A:CYS385 4.2 16.1 1.0
CB A:LEU427 4.3 23.7 1.0
CB A:SER378 4.4 23.9 1.0
CD2 A:LEU427 4.4 28.0 1.0
N A:CYS379 4.5 19.5 1.0
SG A:CYS382 4.5 24.8 1.0
CA A:SER378 4.7 21.7 1.0
SG A:CYS425 4.7 23.5 1.0
C A:CYS385 4.8 18.5 1.0
SG A:CYS379 4.8 20.0 1.0
CG A:LEU427 4.8 23.2 1.0
N A:GLY428 4.9 27.0 1.0
N A:GLY380 4.9 21.6 1.0
N A:ARG386 4.9 18.4 1.0

Iron binding site 4 out of 28 in 7w4f

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Iron binding site 4 out of 28 in the Active State Ci From Q1-Nadh Dataset, Subclass 4


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 Q1-Nadh Dataset, Subclass 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:41.0
occ:1.00
 FE4 A:SF4501 0.0 41.0 1.0
SG A:CYS379 2.3 20.0 1.0
S2 A:SF4501 2.3 19.9 1.0
S1 A:SF4501 2.3 18.6 1.0
S3 A:SF4501 2.3 24.2 1.0
FE2 A:SF4501 2.7 41.0 1.0
FE1 A:SF4501 2.7 36.8 1.0
FE3 A:SF4501 2.7 52.4 1.0
CB A:CYS379 3.5 16.4 1.0
N A:CYS379 3.8 19.5 1.0
N A:GLN381 3.8 17.6 1.0
N A:GLY380 3.9 21.6 1.0
S4 A:SF4501 3.9 29.7 1.0
CA A:CYS379 4.0 19.8 1.0
CB A:GLN381 4.1 13.8 1.0
C A:CYS379 4.2 22.8 1.0
CD A:PRO223 4.5 27.8 1.0
CA A:GLN381 4.5 9.9 1.0
N A:CYS382 4.6 17.7 1.0
C A:GLY380 4.7 20.7 1.0
OG A:SER378 4.7 25.8 1.0
CA A:GLY380 4.8 15.4 1.0
SG A:CYS382 4.8 24.8 1.0
SG A:CYS425 4.8 23.5 1.0
OE1 A:GLN381 4.8 22.3 1.0
SG A:CYS385 4.8 37.7 1.0
CB A:CYS385 4.9 10.9 1.0
CG1 A:ILE205 5.0 33.0 1.0
C A:SER378 5.0 26.3 1.0

Iron binding site 5 out of 28 in 7w4f

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Iron binding site 5 out of 28 in the Active State Ci From Q1-Nadh Dataset, Subclass 4


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 Q1-Nadh Dataset, Subclass 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:20.4
occ:1.00
 FE1 B:SF4301 0.0 20.4 1.0
SG B:CYS113 2.3 19.8 1.0
S4 B:SF4301 2.3 9.6 1.0
S3 B:SF4301 2.3 3.1 1.0
S2 B:SF4301 2.3 10.1 1.0
FE2 B:SF4301 2.7 30.9 1.0
FE4 B:SF4301 2.7 35.3 1.0
FE3 B:SF4301 2.7 33.6 1.0
CB B:CYS113 3.3 15.9 1.0
CA B:CYS113 3.7 11.8 1.0
S1 B:SF4301 3.9 11.2 1.0
N B:ILE114 3.9 11.8 1.0
N B:ALA115 4.0 22.6 1.0
C B:CYS113 4.2 18.2 1.0
CB B:ALA166 4.4 19.1 1.0
CE2 B:TYR145 4.4 16.3 1.0
CA B:ALA115 4.5 20.5 1.0
N B:CYS116 4.6 18.2 1.0
SG B:CYS119 4.9 3.1 1.0
SG B:CYS162 4.9 10.5 1.0
C B:ILE114 4.9 18.0 1.0
SG B:CYS116 4.9 9.2 1.0
N B:CYS113 4.9 14.3 1.0
CA B:ILE114 5.0 12.1 1.0

Iron binding site 6 out of 28 in 7w4f

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Iron binding site 6 out of 28 in the Active State Ci From Q1-Nadh Dataset, Subclass 4


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 Q1-Nadh Dataset, Subclass 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:30.9
occ:1.00
 FE2 B:SF4301 0.0 30.9 1.0
SG B:CYS116 2.3 9.2 1.0
S3 B:SF4301 2.3 3.1 1.0
S1 B:SF4301 2.3 11.2 1.0
S4 B:SF4301 2.3 9.6 1.0
FE4 B:SF4301 2.7 35.3 1.0
FE1 B:SF4301 2.7 20.4 1.0
FE3 B:SF4301 2.7 33.6 1.0
CB B:CYS116 3.5 13.5 1.0
N B:CYS116 3.5 18.2 1.0
N B:LYS117 3.6 22.7 1.0
CA B:CYS116 3.9 15.3 1.0
S2 B:SF4301 3.9 10.1 1.0
C B:CYS116 4.1 19.7 1.0
N B:LEU118 4.1 21.5 1.0
CD B:PRO163 4.4 11.9 1.0
CA B:LYS117 4.5 18.7 1.0
C B:ALA115 4.6 21.7 1.0
N B:ALA115 4.6 22.6 1.0
SG B:CYS162 4.7 10.5 1.0
SG B:CYS119 4.7 3.1 1.0
SG B:CYS113 4.8 19.8 1.0
C B:LYS117 4.8 16.2 1.0
CB B:LEU118 4.8 27.3 1.0
CG1 B:ILE114 4.8 15.1 1.0
CA B:ALA115 4.9 20.5 1.0
N B:CYS119 4.9 19.9 1.0
N B:ILE114 5.0 11.8 1.0

Iron binding site 7 out of 28 in 7w4f

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Iron binding site 7 out of 28 in the Active State Ci From Q1-Nadh Dataset, Subclass 4


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 Q1-Nadh Dataset, Subclass 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:33.6
occ:1.00
 FE3 B:SF4301 0.0 33.6 1.0
SG B:CYS119 2.3 3.1 1.0
S1 B:SF4301 2.3 11.2 1.0
S2 B:SF4301 2.3 10.1 1.0
S4 B:SF4301 2.3 9.6 1.0
FE1 B:SF4301 2.7 20.4 1.0
FE2 B:SF4301 2.7 30.9 1.0
FE4 B:SF4301 2.7 35.3 1.0
CB B:CYS119 3.5 23.0 1.0
OH B:TYR145 3.9 16.0 1.0
S3 B:SF4301 3.9 3.1 1.0
N B:CYS119 4.0 19.9 1.0
CE2 B:TYR145 4.1 16.3 1.0
CA B:CYS119 4.4 25.1 1.0
CD1 B:ILE130 4.4 18.9 1.0
CZ B:TYR145 4.5 12.9 1.0
CG2 B:ILE167 4.5 15.8 1.0
N B:LEU118 4.6 21.5 1.0
N B:LYS117 4.6 22.7 1.0
SG B:CYS116 4.7 9.2 1.0
SG B:CYS162 4.7 10.5 1.0
SG B:CYS113 4.7 19.8 1.0
CA B:LYS117 4.8 18.7 1.0
C B:LYS117 5.0 16.2 1.0

Iron binding site 8 out of 28 in 7w4f

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Iron binding site 8 out of 28 in the Active State Ci From Q1-Nadh Dataset, Subclass 4


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 Q1-Nadh Dataset, Subclass 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:35.3
occ:1.00
 FE4 B:SF4301 0.0 35.3 1.0
SG B:CYS162 2.3 10.5 1.0
S1 B:SF4301 2.3 11.2 1.0
S2 B:SF4301 2.3 10.1 1.0
S3 B:SF4301 2.3 3.1 1.0
FE2 B:SF4301 2.7 30.9 1.0
FE1 B:SF4301 2.7 20.4 1.0
FE3 B:SF4301 2.7 33.6 1.0
CB B:CYS162 3.4 17.1 1.0
CB B:ALA166 3.8 19.1 1.0
S4 B:SF4301 3.9 9.6 1.0
CA B:CYS162 4.0 9.0 1.0
CD B:PRO163 4.2 11.9 1.0
CG2 B:ILE167 4.3 15.8 1.0
CG2 B:VAL164 4.4 18.4 1.0
N B:ILE167 4.6 7.7 1.0
SG B:CYS116 4.6 9.2 1.0
N B:ALA166 4.6 20.0 1.0
CA B:ALA166 4.7 8.2 1.0
SG B:CYS119 4.7 3.1 1.0
N B:PRO163 4.8 18.6 1.0
SG B:CYS113 4.8 19.8 1.0
C B:CYS162 4.8 16.9 1.0

Iron binding site 9 out of 28 in 7w4f

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Iron binding site 9 out of 28 in the Active State Ci From Q1-Nadh Dataset, Subclass 4


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 Q1-Nadh Dataset, Subclass 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:23.9
occ:1.00
 FE1 B:SF4302 0.0 23.9 1.0
SG B:CYS123 2.3 3.4 1.0
S2 B:SF4302 2.3 5.9 1.0
S4 B:SF4302 2.3 2.3 1.0
S3 B:SF4302 2.3 15.1 1.0
FE2 B:SF4302 2.7 31.9 1.0
FE4 B:SF4302 2.7 21.7 1.0
FE3 B:SF4302 2.7 26.1 1.0
CB B:CYS123 3.4 7.7 1.0
CA B:CYS123 3.9 12.3 1.0
S1 B:SF4302 3.9 5.4 1.0
CD B:PRO124 4.0 20.8 1.0
CD1 B:ILE128 4.3 15.2 1.0
CB B:ALA127 4.4 14.3 1.0
N B:PRO124 4.5 22.4 1.0
C B:CYS123 4.5 20.3 1.0
CG1 B:ILE128 4.5 7.9 1.0
SG B:CYS155 4.8 7.7 1.0
SG B:CYS152 4.8 7.2 1.0
SG B:CYS158 4.8 21.1 1.0
N B:ALA125 4.9 26.5 1.0
N B:ALA127 5.0 27.9 1.0

Iron binding site 10 out of 28 in 7w4f

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Iron binding site 10 out of 28 in the Active State Ci From Q1-Nadh Dataset, Subclass 4


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 Q1-Nadh Dataset, Subclass 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:31.9
occ:1.00
 FE2 B:SF4302 0.0 31.9 1.0
SG B:CYS152 2.3 7.2 1.0
S1 B:SF4302 2.3 5.4 1.0
S4 B:SF4302 2.3 2.3 1.0
S3 B:SF4302 2.3 15.1 1.0
FE1 B:SF4302 2.7 23.9 1.0
FE3 B:SF4302 2.7 26.1 1.0
FE4 B:SF4302 2.7 21.7 1.0
CB B:CYS152 3.4 16.7 1.0
NE2 B:HIS101 3.6 14.3 1.0
N B:TYR154 3.8 16.2 1.0
S2 B:SF4302 3.9 5.9 1.0
CA B:CYS152 3.9 19.1 1.0
N B:ILE153 4.0 20.2 1.0
CE1 B:HIS101 4.0 14.4 1.0
CA B:TYR154 4.3 6.5 1.0
C B:CYS152 4.4 21.9 1.0
N B:CYS155 4.6 22.1 1.0
SG B:CYS123 4.8 3.4 1.0
C B:ILE153 4.8 19.8 1.0
CD2 B:HIS101 4.8 9.8 1.0
SG B:CYS155 4.8 7.7 1.0
SG B:CYS158 4.8 21.1 1.0
CA B:ILE153 5.0 21.8 1.0
C B:TYR154 5.0 13.8 1.0

Reference:

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
DOI: 10.1038/S41594-022-00722-W
Page generated: Fri Aug 9 08:58:39 2024

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