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Iron in PDB 7w35: Deactive State Ci From Dq-Nadh Dataset, Subclass 3

Enzymatic activity of Deactive State Ci From Dq-Nadh Dataset, Subclass 3

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

Other elements in 7w35:

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

Zinc (Zn) 1 atom
Magnesium (Mg) 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 Deactive State Ci From Dq-Nadh Dataset, Subclass 3 (pdb code 7w35). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 28 binding sites of Iron where determined in the Deactive State Ci From Dq-Nadh Dataset, Subclass 3, PDB code: 7w35:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 28 in 7w35

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Iron binding site 1 out of 28 in the Deactive 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 Deactive State Ci From Dq-Nadh Dataset, Subclass 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:31.9
occ:1.00
 FE1 A:SF4501 0.0 31.9 1.0
SG A:CYS382 2.3 23.1 1.0
S2 A:SF4501 2.3 6.6 1.0
S4 A:SF4501 2.3 28.1 1.0
S3 A:SF4501 2.3 18.2 1.0
FE3 A:SF4501 2.7 31.1 1.0
FE4 A:SF4501 2.7 36.0 1.0
FE2 A:SF4501 2.7 22.4 1.0
CB A:CYS382 3.6 7.0 1.0
CB A:CYS385 3.7 1.3 1.0
N A:CYS382 3.8 12.6 1.0
S1 A:SF4501 3.9 17.6 1.0
N A:ILE424 4.2 7.0 1.0
CA A:CYS382 4.2 1.2 1.0
CB A:ILE424 4.3 11.6 1.0
SG A:CYS385 4.5 27.5 1.0
O A:CYS382 4.5 11.9 1.0
CG1 A:ILE424 4.5 14.2 1.0
CB A:THR423 4.6 15.0 1.0
N A:CYS425 4.6 16.5 1.0
N A:GLN381 4.7 8.5 1.0
C A:CYS382 4.8 2.7 1.0
CA A:ILE424 4.8 5.9 1.0
SG A:CYS425 4.8 20.4 1.0
CB A:GLN381 4.8 4.6 1.0
SG A:CYS379 4.8 21.2 1.0
CD1 A:ILE424 4.9 9.4 1.0
C A:GLN381 4.9 9.6 1.0

Iron binding site 2 out of 28 in 7w35

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Iron binding site 2 out of 28 in the Deactive 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 Deactive State Ci From Dq-Nadh Dataset, Subclass 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:22.4
occ:1.00
 FE2 A:SF4501 0.0 22.4 1.0
SG A:CYS425 2.3 20.4 1.0
S4 A:SF4501 2.3 28.1 1.0
S1 A:SF4501 2.3 17.6 1.0
S3 A:SF4501 2.3 18.2 1.0
FE4 A:SF4501 2.7 36.0 1.0
FE3 A:SF4501 2.7 31.1 1.0
FE1 A:SF4501 2.7 31.9 1.0
CB A:CYS425 3.5 5.8 1.0
S2 A:SF4501 3.9 6.6 1.0
N A:CYS425 3.9 16.5 1.0
CB A:LEU427 4.1 18.4 1.0
CA A:CYS425 4.1 0.0 1.0
CD1 A:ILE205 4.3 25.9 1.0
CG A:PRO223 4.4 15.4 1.0
C A:CYS425 4.5 20.9 1.0
O A:CYS425 4.6 28.4 1.0
N A:LEU427 4.6 17.7 1.0
SG A:CYS385 4.7 27.5 1.0
SG A:CYS379 4.7 21.2 1.0
CD A:PRO223 4.7 14.6 1.0
CB A:CYS385 4.8 1.3 1.0
SG A:CYS382 4.9 23.1 1.0
CA A:LEU427 4.9 16.9 1.0

Iron binding site 3 out of 28 in 7w35

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Iron binding site 3 out of 28 in the Deactive 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 Deactive State Ci From Dq-Nadh Dataset, Subclass 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:31.1
occ:1.00
 FE3 A:SF4501 0.0 31.1 1.0
SG A:CYS385 2.3 27.5 1.0
S4 A:SF4501 2.3 28.1 1.0
S1 A:SF4501 2.3 17.6 1.0
S2 A:SF4501 2.3 6.6 1.0
CB A:CYS385 2.7 1.3 1.0
FE1 A:SF4501 2.7 31.9 1.0
FE4 A:SF4501 2.7 36.0 1.0
FE2 A:SF4501 2.7 22.4 1.0
S3 A:SF4501 3.9 18.2 1.0
CB A:SER378 4.2 11.3 1.0
CA A:CYS385 4.2 0.0 1.0
CD2 A:LEU427 4.3 24.4 1.0
SG A:CYS382 4.4 23.1 1.0
CB A:LEU427 4.4 18.4 1.0
N A:CYS379 4.5 14.3 1.0
N A:GLY380 4.6 13.4 1.0
C A:CYS385 4.7 1.6 1.0
SG A:CYS425 4.7 20.4 1.0
CA A:SER378 4.7 16.5 1.0
SG A:CYS379 4.8 21.2 1.0
N A:ARG386 4.8 7.8 1.0
CG A:LEU427 4.8 20.1 1.0
OG A:SER378 5.0 21.2 1.0

Iron binding site 4 out of 28 in 7w35

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Iron binding site 4 out of 28 in the Deactive 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 Deactive State Ci From Dq-Nadh Dataset, Subclass 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:36.0
occ:1.00
 FE4 A:SF4501 0.0 36.0 1.0
SG A:CYS379 2.3 21.2 1.0
S2 A:SF4501 2.3 6.6 1.0
S1 A:SF4501 2.3 17.6 1.0
S3 A:SF4501 2.3 18.2 1.0
FE2 A:SF4501 2.7 22.4 1.0
FE1 A:SF4501 2.7 31.9 1.0
FE3 A:SF4501 2.7 31.1 1.0
CB A:CYS379 3.6 14.7 1.0
N A:GLN381 3.7 8.5 1.0
N A:GLY380 3.7 13.4 1.0
S4 A:SF4501 3.9 28.1 1.0
N A:CYS379 3.9 14.3 1.0
CB A:GLN381 4.1 4.6 1.0
CA A:CYS379 4.1 11.2 1.0
C A:CYS379 4.2 11.0 1.0
CD A:PRO223 4.4 14.6 1.0
CA A:GLN381 4.5 2.1 1.0
CA A:GLY380 4.6 5.3 1.0
N A:CYS382 4.6 12.6 1.0
C A:GLY380 4.6 7.2 1.0
SG A:CYS382 4.8 23.1 1.0
SG A:CYS425 4.8 20.4 1.0
OE1 A:GLN381 4.9 19.4 1.0
CG1 A:ILE205 4.9 24.1 1.0
SG A:CYS385 4.9 27.5 1.0
CD1 A:ILE205 5.0 25.9 1.0

Iron binding site 5 out of 28 in 7w35

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Iron binding site 5 out of 28 in the Deactive 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 Deactive State Ci From Dq-Nadh Dataset, Subclass 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:28.0
occ:1.00
 FE1 B:SF4301 0.0 28.0 1.0
SG B:CYS113 2.3 15.5 1.0
S2 B:SF4301 2.3 4.0 1.0
S4 B:SF4301 2.3 0.0 1.0
S3 B:SF4301 2.3 4.3 1.0
FE3 B:SF4301 2.7 31.5 1.0
FE2 B:SF4301 2.7 25.8 1.0
FE4 B:SF4301 2.7 38.3 1.0
CB B:CYS113 3.4 16.2 1.0
CA B:CYS113 3.7 7.9 1.0
N B:ALA115 3.8 23.9 1.0
N B:ILE114 3.9 24.3 1.0
S1 B:SF4301 3.9 14.0 1.0
C B:CYS113 4.2 18.3 1.0
CE2 B:TYR145 4.2 31.0 1.0
CA B:ALA115 4.4 13.4 1.0
CB B:ALA166 4.5 11.9 1.0
N B:CYS116 4.6 12.2 1.0
C B:ILE114 4.8 11.6 1.0
SG B:CYS119 4.8 0.0 1.0
SG B:CYS162 4.9 0.0 1.0
SG B:CYS116 4.9 9.7 1.0
CA B:ILE114 4.9 4.3 1.0
CD2 B:TYR145 5.0 33.4 1.0

Iron binding site 6 out of 28 in 7w35

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Iron binding site 6 out of 28 in the Deactive 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 Deactive State Ci From Dq-Nadh Dataset, Subclass 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:25.8
occ:1.00
 FE2 B:SF4301 0.0 25.8 1.0
SG B:CYS116 2.3 9.7 1.0
S1 B:SF4301 2.3 14.0 1.0
S3 B:SF4301 2.3 4.3 1.0
S4 B:SF4301 2.3 0.0 1.0
FE4 B:SF4301 2.7 38.3 1.0
FE3 B:SF4301 2.7 31.5 1.0
FE1 B:SF4301 2.7 28.0 1.0
N B:CYS116 3.4 12.2 1.0
CB B:CYS116 3.5 12.1 1.0
N B:LYS117 3.5 25.5 1.0
CA B:CYS116 3.8 14.6 1.0
S2 B:SF4301 3.9 4.0 1.0
C B:CYS116 4.0 20.2 1.0
N B:LEU118 4.1 4.2 1.0
N B:ALA115 4.4 23.9 1.0
C B:ALA115 4.5 27.2 1.0
CA B:LYS117 4.5 8.0 1.0
CD B:PRO163 4.5 20.0 1.0
SG B:CYS162 4.7 0.0 1.0
CA B:ALA115 4.7 13.4 1.0
SG B:CYS119 4.7 0.0 1.0
C B:LYS117 4.8 8.2 1.0
CG1 B:ILE114 4.8 19.5 1.0
SG B:CYS113 4.8 15.5 1.0
CB B:LEU118 4.9 14.7 1.0
N B:CYS119 4.9 10.4 1.0
N B:ILE114 5.0 24.3 1.0

Iron binding site 7 out of 28 in 7w35

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Iron binding site 7 out of 28 in the Deactive 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 Deactive State Ci From Dq-Nadh Dataset, Subclass 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:31.5
occ:1.00
 FE3 B:SF4301 0.0 31.5 1.0
SG B:CYS119 2.3 0.0 1.0
S1 B:SF4301 2.3 14.0 1.0
S4 B:SF4301 2.3 0.0 1.0
S2 B:SF4301 2.3 4.0 1.0
FE2 B:SF4301 2.7 25.8 1.0
FE1 B:SF4301 2.7 28.0 1.0
FE4 B:SF4301 2.7 38.3 1.0
CB B:CYS119 3.4 19.4 1.0
OH B:TYR145 3.7 26.1 1.0
S3 B:SF4301 3.9 4.3 1.0
N B:CYS119 4.0 10.4 1.0
CE2 B:TYR145 4.1 31.0 1.0
CA B:CYS119 4.3 6.2 1.0
CD1 B:ILE130 4.3 15.5 1.0
CZ B:TYR145 4.4 15.2 1.0
CG2 B:ILE167 4.5 22.6 1.0
N B:LYS117 4.6 25.5 1.0
N B:LEU118 4.6 4.2 1.0
SG B:CYS116 4.7 9.7 1.0
SG B:CYS113 4.7 15.5 1.0
SG B:CYS162 4.7 0.0 1.0
CA B:LYS117 4.8 8.0 1.0
C B:LYS117 5.0 8.2 1.0

Iron binding site 8 out of 28 in 7w35

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Iron binding site 8 out of 28 in the Deactive 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 Deactive State Ci From Dq-Nadh Dataset, Subclass 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:38.3
occ:1.00
 FE4 B:SF4301 0.0 38.3 1.0
SG B:CYS162 2.3 0.0 1.0
S1 B:SF4301 2.3 14.0 1.0
S3 B:SF4301 2.3 4.3 1.0
S2 B:SF4301 2.3 4.0 1.0
FE2 B:SF4301 2.7 25.8 1.0
FE3 B:SF4301 2.7 31.5 1.0
FE1 B:SF4301 2.7 28.0 1.0
CB B:CYS162 3.5 3.7 1.0
CB B:ALA166 3.8 11.9 1.0
S4 B:SF4301 3.9 0.0 1.0
CA B:CYS162 4.1 5.8 1.0
CG2 B:ILE167 4.2 22.6 1.0
CG2 B:VAL164 4.4 16.3 1.0
N B:ILE167 4.4 33.8 1.0
CD B:PRO163 4.5 20.0 1.0
SG B:CYS116 4.6 9.7 1.0
N B:ALA166 4.6 15.0 1.0
CA B:ALA166 4.7 1.5 1.0
SG B:CYS119 4.7 0.0 1.0
SG B:CYS113 4.8 15.5 1.0
CB B:ILE167 4.9 29.6 1.0
C B:CYS162 4.9 13.1 1.0
N B:PRO163 5.0 17.1 1.0

Iron binding site 9 out of 28 in 7w35

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Iron binding site 9 out of 28 in the Deactive 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 Deactive State Ci From Dq-Nadh Dataset, Subclass 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:32.5
occ:1.00
 FE1 B:SF4302 0.0 32.5 1.0
SG B:CYS123 2.3 1.0 1.0
S3 B:SF4302 2.3 0.0 1.0
S4 B:SF4302 2.3 0.0 1.0
S2 B:SF4302 2.3 16.9 1.0
FE4 B:SF4302 2.7 20.3 1.0
FE2 B:SF4302 2.7 20.4 1.0
FE3 B:SF4302 2.7 28.1 1.0
CB B:CYS123 3.4 12.1 1.0
CA B:CYS123 3.8 14.2 1.0
S1 B:SF4302 3.9 2.5 1.0
CD B:PRO124 4.1 15.3 1.0
CD1 B:ILE128 4.4 0.0 1.0
C B:CYS123 4.4 19.9 1.0
N B:PRO124 4.5 17.7 1.0
CB B:ALA127 4.5 12.9 1.0
CG1 B:ILE128 4.6 6.8 1.0
SG B:CYS155 4.8 7.6 1.0
SG B:CYS152 4.8 2.4 1.0
SG B:CYS158 4.8 11.2 1.0
N B:ALA125 4.9 26.0 1.0
N B:ALA127 5.0 31.3 1.0
CB B:CYS158 5.0 14.4 1.0

Iron binding site 10 out of 28 in 7w35

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Iron binding site 10 out of 28 in the Deactive 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 Deactive State Ci From Dq-Nadh Dataset, Subclass 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:20.4
occ:1.00
 FE2 B:SF4302 0.0 20.4 1.0
SG B:CYS152 2.3 2.4 1.0
S1 B:SF4302 2.3 2.5 1.0
S3 B:SF4302 2.3 0.0 1.0
S4 B:SF4302 2.3 0.0 1.0
FE1 B:SF4302 2.7 32.5 1.0
FE4 B:SF4302 2.7 20.3 1.0
FE3 B:SF4302 2.7 28.1 1.0
CB B:CYS152 3.5 11.0 1.0
NE2 B:HIS101 3.8 26.4 1.0
N B:TYR154 3.8 27.4 1.0
S2 B:SF4302 3.9 16.9 1.0
CA B:CYS152 3.9 14.9 1.0
N B:ILE153 4.0 31.8 1.0
CE1 B:HIS101 4.2 14.3 1.0
CA B:TYR154 4.3 15.4 1.0
C B:CYS152 4.4 27.6 1.0
N B:CYS155 4.6 32.4 1.0
SG B:CYS123 4.7 1.0 1.0
SG B:CYS158 4.8 11.2 1.0
SG B:CYS155 4.8 7.6 1.0
C B:ILE153 4.8 20.9 1.0
CD2 B:HIS101 4.9 11.8 1.0
CA B:ILE153 5.0 16.0 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
PubMed: 35145322
DOI: 10.1038/S41594-022-00722-W
Page generated: Fri Aug 9 08:56:53 2024

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