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Iron in PDB 6p73: Cytochrome-C-Nitrite Reductase

Enzymatic activity of Cytochrome-C-Nitrite Reductase

All present enzymatic activity of Cytochrome-C-Nitrite Reductase:
1.7.2.2;

Protein crystallography data

The structure of Cytochrome-C-Nitrite Reductase, PDB code: 6p73 was solved by M.Schmidt, A.Pacheco, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.78 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.180, 96.070, 222.600, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 21.2

Other elements in 6p73:

The structure of Cytochrome-C-Nitrite Reductase also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Cytochrome-C-Nitrite Reductase (pdb code 6p73). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 10 binding sites of Iron where determined in the Cytochrome-C-Nitrite Reductase, PDB code: 6p73:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 6p73

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Iron binding site 1 out of 10 in the Cytochrome-C-Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cytochrome-C-Nitrite Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:14.7
occ:1.00
FE A:HEC501 0.0 14.7 1.0
NB A:HEC501 2.0 13.0 1.0
NA A:HEC501 2.0 10.9 1.0
NC A:HEC501 2.0 15.5 1.0
NZ A:LYS123 2.1 13.8 1.0
ND A:HEC501 2.1 12.8 1.0
O A:HOH921 2.3 18.9 1.0
CE A:LYS123 3.0 14.9 1.0
C1B A:HEC501 3.0 11.7 1.0
C4B A:HEC501 3.0 12.1 1.0
C4A A:HEC501 3.0 12.7 1.0
C1A A:HEC501 3.0 13.9 1.0
C1C A:HEC501 3.1 13.4 1.0
C4C A:HEC501 3.1 13.8 1.0
C4D A:HEC501 3.1 12.8 1.0
C1D A:HEC501 3.1 13.1 1.0
CHB A:HEC501 3.4 11.6 1.0
CHC A:HEC501 3.4 14.1 1.0
CHA A:HEC501 3.4 12.9 1.0
CHD A:HEC501 3.5 12.2 1.0
O A:HOH690 4.2 16.3 1.0
C2B A:HEC501 4.2 14.9 1.0
C3B A:HEC501 4.2 12.9 1.0
C3A A:HEC501 4.3 11.5 1.0
C2A A:HEC501 4.3 10.8 1.0
C2C A:HEC501 4.3 12.6 1.0
C3C A:HEC501 4.3 11.8 1.0
O A:HOH639 4.3 25.8 1.0
NE2 A:HIS257 4.3 15.9 1.0
C3D A:HEC501 4.3 12.3 1.0
C2D A:HEC501 4.4 13.8 1.0
CD A:LYS123 4.4 16.4 1.0
CMD A:HEC503 4.8 12.8 1.0
O A:HOH800 4.9 18.4 1.0

Iron binding site 2 out of 10 in 6p73

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Iron binding site 2 out of 10 in the Cytochrome-C-Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cytochrome-C-Nitrite Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe502

b:18.4
occ:1.00
FE A:HEC502 0.0 18.4 1.0
NB A:HEC502 2.0 19.1 1.0
NE2 A:HIS294 2.0 18.0 1.0
NA A:HEC502 2.0 17.1 1.0
ND A:HEC502 2.0 19.6 1.0
NC A:HEC502 2.1 14.3 1.0
NE2 A:HIS161 2.1 17.2 1.0
CD2 A:HIS294 3.0 19.1 1.0
C1B A:HEC502 3.0 18.9 1.0
CD2 A:HIS161 3.0 17.6 1.0
C4B A:HEC502 3.0 18.1 1.0
CE1 A:HIS294 3.0 17.6 1.0
C4A A:HEC502 3.0 20.8 1.0
C1D A:HEC502 3.0 19.1 1.0
C1A A:HEC502 3.1 17.8 1.0
C4D A:HEC502 3.1 20.1 1.0
C4C A:HEC502 3.1 17.3 1.0
C1C A:HEC502 3.1 16.8 1.0
CE1 A:HIS161 3.1 17.0 1.0
CHB A:HEC502 3.4 16.4 1.0
CHD A:HEC502 3.4 17.0 1.0
CHC A:HEC502 3.4 18.1 1.0
CHA A:HEC502 3.4 19.6 1.0
ND1 A:HIS294 4.1 20.3 1.0
CG A:HIS294 4.1 17.0 1.0
CG A:HIS161 4.2 17.2 1.0
C2B A:HEC502 4.2 19.6 1.0
ND1 A:HIS161 4.2 18.1 1.0
C3B A:HEC502 4.2 20.0 1.0
C3A A:HEC502 4.3 19.7 1.0
C2A A:HEC502 4.3 18.3 1.0
C2D A:HEC502 4.3 20.8 1.0
C3D A:HEC502 4.3 21.2 1.0
C2C A:HEC502 4.3 16.7 1.0
C3C A:HEC502 4.3 16.8 1.0
CE A:MET280 4.6 18.9 1.0

Iron binding site 3 out of 10 in 6p73

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Iron binding site 3 out of 10 in the Cytochrome-C-Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cytochrome-C-Nitrite Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe503

b:13.9
occ:1.00
FE A:HEC503 0.0 13.9 1.0
NB A:HEC503 2.0 12.5 1.0
ND A:HEC503 2.0 17.0 1.0
NE2 A:HIS203 2.0 12.5 1.0
NE2 A:HIS91 2.0 14.8 1.0
NC A:HEC503 2.1 15.7 1.0
NA A:HEC503 2.1 13.5 1.0
CE1 A:HIS91 2.9 14.1 1.0
C1B A:HEC503 3.0 13.2 1.0
CE1 A:HIS203 3.0 13.6 1.0
C1D A:HEC503 3.0 13.2 1.0
CD2 A:HIS203 3.0 13.6 1.0
C4C A:HEC503 3.0 14.7 1.0
C4B A:HEC503 3.1 14.9 1.0
C4A A:HEC503 3.1 12.8 1.0
C4D A:HEC503 3.1 11.5 1.0
C1C A:HEC503 3.1 13.7 1.0
C1A A:HEC503 3.1 12.1 1.0
CD2 A:HIS91 3.1 14.2 1.0
CHD A:HEC503 3.4 13.2 1.0
CHB A:HEC503 3.4 14.7 1.0
CHC A:HEC503 3.4 14.0 1.0
CHA A:HEC503 3.5 9.6 1.0
ND1 A:HIS91 4.1 14.6 1.0
ND1 A:HIS203 4.1 11.8 1.0
CG A:HIS203 4.2 13.1 1.0
CG A:HIS91 4.2 16.1 1.0
C2B A:HEC503 4.2 15.0 1.0
C3B A:HEC503 4.3 14.8 1.0
C2D A:HEC503 4.3 11.9 1.0
C3C A:HEC503 4.3 12.7 1.0
C3D A:HEC503 4.3 12.3 1.0
C2C A:HEC503 4.3 15.5 1.0
C3A A:HEC503 4.3 11.0 1.0
C2A A:HEC503 4.3 13.4 1.0
CG1 A:VAL296 4.9 17.6 1.0

Iron binding site 4 out of 10 in 6p73

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Iron binding site 4 out of 10 in the Cytochrome-C-Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cytochrome-C-Nitrite Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe504

b:13.7
occ:1.00
FE A:HEC504 0.0 13.7 1.0
NC A:HEC504 2.0 15.0 1.0
NA A:HEC504 2.0 15.1 1.0
NB A:HEC504 2.0 13.4 1.0
ND A:HEC504 2.0 14.5 1.0
NE2 A:HIS386 2.1 14.3 1.0
NE2 A:HIS279 2.1 14.7 1.0
CE1 A:HIS386 2.9 13.8 1.0
C4C A:HEC504 3.0 15.2 1.0
C1C A:HEC504 3.0 13.8 1.0
C4B A:HEC504 3.0 13.6 1.0
CE1 A:HIS279 3.0 14.9 1.0
C1D A:HEC504 3.0 15.9 1.0
C4A A:HEC504 3.0 14.1 1.0
C1B A:HEC504 3.0 13.0 1.0
C1A A:HEC504 3.1 14.3 1.0
C4D A:HEC504 3.1 16.9 1.0
CD2 A:HIS279 3.1 15.0 1.0
CD2 A:HIS386 3.2 16.6 1.0
CHC A:HEC504 3.4 14.3 1.0
CHD A:HEC504 3.4 14.6 1.0
CHB A:HEC504 3.4 15.3 1.0
CHA A:HEC504 3.4 14.0 1.0
ND1 A:HIS386 4.1 15.2 1.0
ND1 A:HIS279 4.2 14.2 1.0
CG A:HIS386 4.2 17.0 1.0
C3C A:HEC504 4.2 14.9 1.0
C2C A:HEC504 4.2 16.0 1.0
C3B A:HEC504 4.2 11.4 1.0
CG A:HIS279 4.2 14.3 1.0
C2B A:HEC504 4.3 13.6 1.0
C3A A:HEC504 4.3 17.1 1.0
C2A A:HEC504 4.3 16.8 1.0
C2D A:HEC504 4.3 16.3 1.0
C3D A:HEC504 4.3 17.6 1.0

Iron binding site 5 out of 10 in 6p73

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Iron binding site 5 out of 10 in the Cytochrome-C-Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Cytochrome-C-Nitrite Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe505

b:15.6
occ:1.00
FE A:HEC505 0.0 15.6 1.0
NB A:HEC505 2.0 15.3 1.0
NA A:HEC505 2.0 15.3 1.0
ND A:HEC505 2.0 15.3 1.0
NE2 A:HIS311 2.0 17.6 1.0
NE2 A:HIS268 2.1 16.1 1.0
NC A:HEC505 2.1 14.6 1.0
CE1 A:HIS311 2.9 21.2 1.0
C1B A:HEC505 3.0 16.4 1.0
CE1 A:HIS268 3.0 15.9 1.0
C4A A:HEC505 3.0 16.6 1.0
C1A A:HEC505 3.0 15.5 1.0
C4B A:HEC505 3.0 14.9 1.0
C4D A:HEC505 3.0 14.7 1.0
C1D A:HEC505 3.1 15.3 1.0
CD2 A:HIS268 3.1 17.5 1.0
C1C A:HEC505 3.1 14.9 1.0
C4C A:HEC505 3.1 15.4 1.0
CD2 A:HIS311 3.1 17.8 1.0
CHB A:HEC505 3.4 15.4 1.0
CHA A:HEC505 3.4 14.4 1.0
CHC A:HEC505 3.5 15.8 1.0
CHD A:HEC505 3.5 16.8 1.0
ND1 A:HIS311 4.1 21.9 1.0
ND1 A:HIS268 4.1 16.6 1.0
CG A:HIS268 4.2 15.8 1.0
CG A:HIS311 4.2 19.2 1.0
C2B A:HEC505 4.2 16.6 1.0
C2A A:HEC505 4.2 18.5 1.0
C3A A:HEC505 4.2 20.7 1.0
C3B A:HEC505 4.3 15.9 1.0
C3D A:HEC505 4.3 17.2 1.0
C2D A:HEC505 4.3 17.6 1.0
C2C A:HEC505 4.3 15.2 1.0
C3C A:HEC505 4.3 17.1 1.0
CBC A:HEC504 4.7 15.1 1.0

Iron binding site 6 out of 10 in 6p73

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Iron binding site 6 out of 10 in the Cytochrome-C-Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Cytochrome-C-Nitrite Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:12.7
occ:1.00
FE B:HEC501 0.0 12.7 1.0
NB B:HEC501 2.0 10.9 1.0
NA B:HEC501 2.0 14.0 1.0
NC B:HEC501 2.0 12.8 1.0
NZ B:LYS123 2.1 12.3 1.0
ND B:HEC501 2.1 11.7 1.0
O B:HOH866 2.4 18.6 1.0
CE B:LYS123 3.0 14.5 1.0
C4B B:HEC501 3.0 11.2 1.0
C1B B:HEC501 3.0 12.8 1.0
C1A B:HEC501 3.0 11.7 1.0
C1C B:HEC501 3.0 13.2 1.0
C4A B:HEC501 3.0 13.1 1.0
C4D B:HEC501 3.1 11.1 1.0
C4C B:HEC501 3.1 12.8 1.0
C1D B:HEC501 3.1 12.1 1.0
CHC B:HEC501 3.4 11.1 1.0
CHA B:HEC501 3.4 10.7 1.0
CHB B:HEC501 3.4 12.2 1.0
CHD B:HEC501 3.5 10.5 1.0
O B:HOH762 4.1 14.5 1.0
C2B B:HEC501 4.2 14.3 1.0
C3B B:HEC501 4.2 13.2 1.0
C2A B:HEC501 4.3 12.7 1.0
C3A B:HEC501 4.3 11.6 1.0
NE2 B:HIS257 4.3 15.5 1.0
C2C B:HEC501 4.3 11.2 1.0
C3C B:HEC501 4.3 11.9 1.0
O B:HOH673 4.3 24.4 1.0
C3D B:HEC501 4.3 11.3 1.0
C2D B:HEC501 4.3 12.6 1.0
CD B:LYS123 4.4 13.2 1.0
O B:HOH713 4.7 18.5 1.0
CMD B:HEC503 4.7 12.3 1.0

Iron binding site 7 out of 10 in 6p73

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Iron binding site 7 out of 10 in the Cytochrome-C-Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Cytochrome-C-Nitrite Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:17.8
occ:1.00
FE B:HEC502 0.0 17.8 1.0
NE2 B:HIS294 2.0 15.9 1.0
NB B:HEC502 2.0 17.0 1.0
NA B:HEC502 2.0 19.2 1.0
NE2 B:HIS161 2.1 16.0 1.0
ND B:HEC502 2.1 18.9 1.0
NC B:HEC502 2.1 14.6 1.0
CE1 B:HIS294 3.0 17.2 1.0
C1B B:HEC502 3.0 17.5 1.0
CD2 B:HIS294 3.0 17.2 1.0
C4A B:HEC502 3.0 18.2 1.0
CD2 B:HIS161 3.0 17.3 1.0
CE1 B:HIS161 3.0 16.5 1.0
C1D B:HEC502 3.1 17.3 1.0
C1A B:HEC502 3.1 18.3 1.0
C4B B:HEC502 3.1 18.1 1.0
C4C B:HEC502 3.1 15.7 1.0
C4D B:HEC502 3.1 18.7 1.0
C1C B:HEC502 3.1 15.2 1.0
CHB B:HEC502 3.4 17.2 1.0
CHD B:HEC502 3.4 14.4 1.0
CHA B:HEC502 3.5 18.4 1.0
CHC B:HEC502 3.5 17.9 1.0
ND1 B:HIS294 4.1 18.6 1.0
CG B:HIS294 4.1 19.0 1.0
ND1 B:HIS161 4.1 17.8 1.0
CG B:HIS161 4.2 16.5 1.0
C2B B:HEC502 4.2 19.9 1.0
C3A B:HEC502 4.2 20.9 1.0
C3B B:HEC502 4.3 16.7 1.0
C2A B:HEC502 4.3 21.5 1.0
C2D B:HEC502 4.3 18.9 1.0
C3D B:HEC502 4.3 22.0 1.0
C3C B:HEC502 4.3 16.7 1.0
C2C B:HEC502 4.3 15.4 1.0
CE B:MET280 4.6 15.4 1.0

Iron binding site 8 out of 10 in 6p73

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Iron binding site 8 out of 10 in the Cytochrome-C-Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Cytochrome-C-Nitrite Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe503

b:12.2
occ:1.00
FE B:HEC503 0.0 12.2 1.0
NE2 B:HIS203 2.0 14.6 1.0
NB B:HEC503 2.0 12.3 1.0
ND B:HEC503 2.0 13.1 1.0
NA B:HEC503 2.1 11.4 1.0
NC B:HEC503 2.1 12.2 1.0
NE2 B:HIS91 2.1 11.9 1.0
CE1 B:HIS203 2.9 13.8 1.0
C1B B:HEC503 3.0 14.0 1.0
CD2 B:HIS203 3.0 12.8 1.0
C4C B:HEC503 3.0 13.1 1.0
C1D B:HEC503 3.0 12.5 1.0
C4D B:HEC503 3.0 12.2 1.0
C4A B:HEC503 3.0 13.3 1.0
CE1 B:HIS91 3.1 13.8 1.0
C4B B:HEC503 3.1 12.4 1.0
C1A B:HEC503 3.1 11.1 1.0
CD2 B:HIS91 3.1 12.8 1.0
C1C B:HEC503 3.1 11.3 1.0
CHD B:HEC503 3.4 12.9 1.0
CHB B:HEC503 3.4 12.7 1.0
CHA B:HEC503 3.4 13.0 1.0
CHC B:HEC503 3.5 13.5 1.0
ND1 B:HIS203 4.0 11.0 1.0
CG B:HIS203 4.1 13.6 1.0
ND1 B:HIS91 4.2 15.4 1.0
CG B:HIS91 4.2 13.7 1.0
C2B B:HEC503 4.2 14.7 1.0
C3C B:HEC503 4.2 12.5 1.0
C3B B:HEC503 4.3 15.7 1.0
C2C B:HEC503 4.3 11.2 1.0
C2A B:HEC503 4.3 14.2 1.0
C3A B:HEC503 4.3 13.0 1.0
C2D B:HEC503 4.3 14.8 1.0
C3D B:HEC503 4.3 11.3 1.0
CG1 B:VAL296 4.9 14.1 1.0
CMD B:HEC501 5.0 9.9 1.0

Iron binding site 9 out of 10 in 6p73

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Iron binding site 9 out of 10 in the Cytochrome-C-Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Cytochrome-C-Nitrite Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe504

b:12.5
occ:1.00
FE B:HEC504 0.0 12.5 1.0
NA B:HEC504 2.0 12.2 1.0
NC B:HEC504 2.0 14.6 1.0
NE2 B:HIS386 2.0 13.3 1.0
NB B:HEC504 2.0 13.1 1.0
ND B:HEC504 2.0 10.4 1.0
NE2 B:HIS279 2.1 11.6 1.0
CE1 B:HIS386 2.8 13.9 1.0
C4A B:HEC504 3.0 13.2 1.0
C4B B:HEC504 3.0 12.7 1.0
C4C B:HEC504 3.0 11.8 1.0
C1B B:HEC504 3.0 11.9 1.0
C1D B:HEC504 3.0 13.3 1.0
CD2 B:HIS279 3.0 12.4 1.0
C1A B:HEC504 3.1 14.2 1.0
C4D B:HEC504 3.1 15.8 1.0
C1C B:HEC504 3.1 13.3 1.0
CE1 B:HIS279 3.1 15.1 1.0
CD2 B:HIS386 3.1 11.3 1.0
CHD B:HEC504 3.4 13.5 1.0
CHB B:HEC504 3.4 12.4 1.0
CHC B:HEC504 3.4 13.6 1.0
CHA B:HEC504 3.4 12.8 1.0
ND1 B:HIS386 4.0 12.2 1.0
ND1 B:HIS279 4.2 11.9 1.0
CG B:HIS386 4.2 12.0 1.0
CG B:HIS279 4.2 13.3 1.0
C3A B:HEC504 4.2 13.8 1.0
C3B B:HEC504 4.2 12.5 1.0
C2B B:HEC504 4.2 12.8 1.0
C2A B:HEC504 4.2 13.8 1.0
C3C B:HEC504 4.3 14.1 1.0
C2D B:HEC504 4.3 17.5 1.0
C2C B:HEC504 4.3 14.2 1.0
C3D B:HEC504 4.3 16.2 1.0

Iron binding site 10 out of 10 in 6p73

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Iron binding site 10 out of 10 in the Cytochrome-C-Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Cytochrome-C-Nitrite Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe505

b:16.0
occ:1.00
FE B:HEC505 0.0 16.0 1.0
NB B:HEC505 2.0 15.2 1.0
ND B:HEC505 2.0 14.1 1.0
NA B:HEC505 2.0 13.9 1.0
NE2 B:HIS268 2.0 15.6 1.0
NE2 B:HIS311 2.1 14.8 1.0
NC B:HEC505 2.1 16.0 1.0
CE1 B:HIS311 2.9 20.9 1.0
CE1 B:HIS268 3.0 17.3 1.0
C4B B:HEC505 3.0 17.6 1.0
C4D B:HEC505 3.0 15.7 1.0
C1B B:HEC505 3.0 16.8 1.0
C1A B:HEC505 3.0 17.0 1.0
CD2 B:HIS268 3.0 15.3 1.0
C4A B:HEC505 3.1 13.6 1.0
C1C B:HEC505 3.1 15.3 1.0
C1D B:HEC505 3.1 13.7 1.0
C4C B:HEC505 3.1 15.9 1.0
CD2 B:HIS311 3.1 17.7 1.0
CHA B:HEC505 3.4 15.1 1.0
CHC B:HEC505 3.4 17.7 1.0
CHB B:HEC505 3.4 16.1 1.0
CHD B:HEC505 3.5 16.5 1.0
ND1 B:HIS311 4.1 21.2 1.0
ND1 B:HIS268 4.1 16.2 1.0
CG B:HIS268 4.2 15.6 1.0
CG B:HIS311 4.2 21.1 1.0
C3B B:HEC505 4.2 17.0 1.0
C2B B:HEC505 4.2 17.3 1.0
C2A B:HEC505 4.2 18.2 1.0
C3D B:HEC505 4.3 15.9 1.0
C3A B:HEC505 4.3 17.3 1.0
C2D B:HEC505 4.3 17.4 1.0
C2C B:HEC505 4.3 15.7 1.0
C3C B:HEC505 4.3 16.5 1.0
CBC B:HEC504 4.7 16.8 1.0

Reference:

M.Ali, N.Stein, Y.Mao, S.Shahid, M.Schmidt, B.Bennett, A.A.Pacheco. Trapping of A Putative Intermediate in the Cytochromecnitrite Reductase (Ccnir)-Catalyzed Reduction of Nitrite: Implications For the Ccnir Reaction Mechanism. J.Am.Chem.Soc. V. 141 13358 2019.
ISSN: ESSN 1520-5126
PubMed: 31381304
DOI: 10.1021/JACS.9B03036
Page generated: Wed Aug 7 05:39:48 2024

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