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Iron in PDB 5jqu: Crystal Structure of Cytochrome P450 BM3 Heme Domain G265F/T269V/L272W/L322I/F405M/A406S (Wivs-Fm) Variant with Iron(III) Deuteroporphyrin IX Bound

Enzymatic activity of Crystal Structure of Cytochrome P450 BM3 Heme Domain G265F/T269V/L272W/L322I/F405M/A406S (Wivs-Fm) Variant with Iron(III) Deuteroporphyrin IX Bound

All present enzymatic activity of Crystal Structure of Cytochrome P450 BM3 Heme Domain G265F/T269V/L272W/L322I/F405M/A406S (Wivs-Fm) Variant with Iron(III) Deuteroporphyrin IX Bound:
1.14.14.1; 1.6.2.4;

Protein crystallography data

The structure of Crystal Structure of Cytochrome P450 BM3 Heme Domain G265F/T269V/L272W/L322I/F405M/A406S (Wivs-Fm) Variant with Iron(III) Deuteroporphyrin IX Bound, PDB code: 5jqu was solved by E.W.Reynolds, M.W.Mchenry, F.Cannac, J.G.Gober, C.D.Snow, E.M.Brustad, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.85 / 2.16
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 106.057, 166.299, 229.331, 90.00, 90.00, 90.00
R / Rfree (%) 25.8 / 33.4

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Cytochrome P450 BM3 Heme Domain G265F/T269V/L272W/L322I/F405M/A406S (Wivs-Fm) Variant with Iron(III) Deuteroporphyrin IX Bound (pdb code 5jqu). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of Cytochrome P450 BM3 Heme Domain G265F/T269V/L272W/L322I/F405M/A406S (Wivs-Fm) Variant with Iron(III) Deuteroporphyrin IX Bound, PDB code: 5jqu:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 5jqu

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Iron binding site 1 out of 8 in the Crystal Structure of Cytochrome P450 BM3 Heme Domain G265F/T269V/L272W/L322I/F405M/A406S (Wivs-Fm) Variant with Iron(III) Deuteroporphyrin IX Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Cytochrome P450 BM3 Heme Domain G265F/T269V/L272W/L322I/F405M/A406S (Wivs-Fm) Variant with Iron(III) Deuteroporphyrin IX Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:0.2
occ:1.00
 FE A:FDE501 0.0 0.2 1.0
SG A:CYS400 2.0 10.8 1.0
NC A:FDE501 2.0 13.1 1.0
NA A:FDE501 2.1 14.6 1.0
NB A:FDE501 2.1 13.3 1.0
ND A:FDE501 2.1 11.9 1.0
O A:HOH675 2.3 34.8 1.0
C4A A:FDE501 3.0 11.7 1.0
C4C A:FDE501 3.1 9.7 1.0
C1A A:FDE501 3.1 7.1 1.0
C1C A:FDE501 3.1 11.4 1.0
C1B A:FDE501 3.1 10.7 1.0
C1D A:FDE501 3.1 12.8 1.0
C4B A:FDE501 3.1 17.9 1.0
C4D A:FDE501 3.1 10.0 1.0
CHB A:FDE501 3.1 11.9 1.0
CHD A:FDE501 3.1 11.2 1.0
CB A:CYS400 3.2 8.1 1.0
CHA A:FDE501 3.4 6.1 1.0
CHC A:FDE501 3.5 10.2 1.0
CA A:CYS400 4.0 7.6 1.0
CE2 A:PHE87 4.1 5.9 1.0
C3C A:FDE501 4.2 8.5 1.0
C3D A:FDE501 4.3 11.9 1.0
C2C A:FDE501 4.3 12.5 1.0
C2D A:FDE501 4.3 16.1 1.0
C3B A:FDE501 4.3 13.7 1.0
C2B A:FDE501 4.3 9.6 1.0
C2A A:FDE501 4.3 5.0 1.0
C3A A:FDE501 4.4 5.2 1.0
C A:CYS400 4.7 9.8 1.0
N A:ILE401 4.8 10.9 1.0
CD2 A:PHE87 4.8 5.9 1.0
N A:GLY402 5.0 14.4 1.0

Iron binding site 2 out of 8 in 5jqu

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Iron binding site 2 out of 8 in the Crystal Structure of Cytochrome P450 BM3 Heme Domain G265F/T269V/L272W/L322I/F405M/A406S (Wivs-Fm) Variant with Iron(III) Deuteroporphyrin IX Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Cytochrome P450 BM3 Heme Domain G265F/T269V/L272W/L322I/F405M/A406S (Wivs-Fm) Variant with Iron(III) Deuteroporphyrin IX Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:2.0
occ:1.00
 FE B:FDE501 0.0 2.0 1.0
NA B:FDE501 2.0 9.8 1.0
NC B:FDE501 2.1 5.9 1.0
NB B:FDE501 2.1 12.2 1.0
ND B:FDE501 2.1 11.6 1.0
SG B:CYS400 2.4 2.0 1.0
C4A B:FDE501 3.0 5.1 1.0
C1B B:FDE501 3.0 2.7 1.0
CHB B:FDE501 3.0 9.1 1.0
C1A B:FDE501 3.0 2.3 1.0
C4C B:FDE501 3.1 2.2 1.0
C4B B:FDE501 3.1 3.7 1.0
C1D B:FDE501 3.1 3.7 1.0
C4D B:FDE501 3.1 4.9 1.0
C1C B:FDE501 3.1 2.0 1.0
CHD B:FDE501 3.1 3.9 1.0
CB B:CYS400 3.2 3.1 1.0
CHA B:FDE501 3.4 6.8 1.0
CHC B:FDE501 3.5 2.6 1.0
CA B:CYS400 4.0 2.4 1.0
C3C B:FDE501 4.3 2.4 1.0
CE2 B:PHE87 4.3 2.9 1.0
C2B B:FDE501 4.3 2.0 1.0
C3B B:FDE501 4.3 5.0 1.0
C2C B:FDE501 4.3 2.0 1.0
C2A B:FDE501 4.3 2.2 1.0
C3D B:FDE501 4.3 2.5 1.0
C3A B:FDE501 4.3 2.0 1.0
C2D B:FDE501 4.3 4.3 1.0
N B:GLY402 4.8 5.4 1.0
C B:CYS400 4.8 3.3 1.0
N B:ILE401 4.9 4.4 1.0
CD2 B:PHE87 5.0 2.1 1.0

Iron binding site 3 out of 8 in 5jqu

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Iron binding site 3 out of 8 in the Crystal Structure of Cytochrome P450 BM3 Heme Domain G265F/T269V/L272W/L322I/F405M/A406S (Wivs-Fm) Variant with Iron(III) Deuteroporphyrin IX Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Cytochrome P450 BM3 Heme Domain G265F/T269V/L272W/L322I/F405M/A406S (Wivs-Fm) Variant with Iron(III) Deuteroporphyrin IX Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:2.0
occ:1.00
 FE C:FDE501 0.0 2.0 1.0
NC C:FDE501 2.0 6.8 1.0
ND C:FDE501 2.0 2.0 1.0
NA C:FDE501 2.1 4.8 1.0
NB C:FDE501 2.1 5.0 1.0
SG C:CYS400 2.3 20.1 1.0
O C:HOH685 2.9 22.6 1.0
C1D C:FDE501 3.0 2.3 1.0
C4C C:FDE501 3.0 4.4 1.0
CHD C:FDE501 3.0 8.1 1.0
C4D C:FDE501 3.1 2.0 1.0
C1C C:FDE501 3.1 3.0 1.0
C4A C:FDE501 3.1 4.0 1.0
C1A C:FDE501 3.1 2.3 1.0
CB C:CYS400 3.1 3.9 1.0
C4B C:FDE501 3.1 2.7 1.0
C1B C:FDE501 3.1 2.6 1.0
CHB C:FDE501 3.1 2.8 1.0
CHA C:FDE501 3.4 2.0 1.0
CHC C:FDE501 3.5 3.5 1.0
CA C:CYS400 3.9 2.0 1.0
C3C C:FDE501 4.2 2.5 1.0
C2D C:FDE501 4.2 2.0 1.0
C3D C:FDE501 4.3 2.0 1.0
C2C C:FDE501 4.3 2.6 1.0
C3B C:FDE501 4.3 3.0 1.0
C2B C:FDE501 4.4 3.3 1.0
C2A C:FDE501 4.4 2.0 1.0
C3A C:FDE501 4.4 2.0 1.0
CE1 C:PHE87 4.5 2.1 1.0
C C:CYS400 4.8 2.0 1.0

Iron binding site 4 out of 8 in 5jqu

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Iron binding site 4 out of 8 in the Crystal Structure of Cytochrome P450 BM3 Heme Domain G265F/T269V/L272W/L322I/F405M/A406S (Wivs-Fm) Variant with Iron(III) Deuteroporphyrin IX Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Cytochrome P450 BM3 Heme Domain G265F/T269V/L272W/L322I/F405M/A406S (Wivs-Fm) Variant with Iron(III) Deuteroporphyrin IX Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:13.6
occ:1.00
 FE D:FDE501 0.0 13.6 1.0
NC D:FDE501 2.1 7.8 1.0
NA D:FDE501 2.1 10.9 1.0
NB D:FDE501 2.1 8.6 1.0
ND D:FDE501 2.1 8.4 1.0
SG D:CYS400 2.3 8.8 1.0
C4C D:FDE501 3.1 10.5 1.0
CB D:CYS400 3.1 13.3 1.0
C1A D:FDE501 3.1 12.7 1.0
C1C D:FDE501 3.1 6.9 1.0
C4A D:FDE501 3.1 10.0 1.0
C4B D:FDE501 3.1 7.8 1.0
C1D D:FDE501 3.1 8.1 1.0
C1B D:FDE501 3.1 9.0 1.0
C4D D:FDE501 3.1 8.6 1.0
CHB D:FDE501 3.1 10.6 1.0
CHD D:FDE501 3.1 8.6 1.0
CHA D:FDE501 3.4 10.8 1.0
CHC D:FDE501 3.4 6.8 1.0
CA D:CYS400 3.9 10.6 1.0
C3C D:FDE501 4.3 12.2 1.0
C2C D:FDE501 4.3 7.5 1.0
C3B D:FDE501 4.3 6.9 1.0
C2D D:FDE501 4.3 11.7 1.0
C3D D:FDE501 4.3 14.0 1.0
C2B D:FDE501 4.4 12.8 1.0
C2A D:FDE501 4.4 9.8 1.0
C3A D:FDE501 4.4 6.3 1.0
CE2 D:PHE87 4.7 11.2 1.0
C D:CYS400 4.8 12.2 1.0
N D:CYS400 5.0 17.8 1.0

Iron binding site 5 out of 8 in 5jqu

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Iron binding site 5 out of 8 in the Crystal Structure of Cytochrome P450 BM3 Heme Domain G265F/T269V/L272W/L322I/F405M/A406S (Wivs-Fm) Variant with Iron(III) Deuteroporphyrin IX Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Cytochrome P450 BM3 Heme Domain G265F/T269V/L272W/L322I/F405M/A406S (Wivs-Fm) Variant with Iron(III) Deuteroporphyrin IX Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:2.0
occ:1.00
 FE E:FDE501 0.0 2.0 1.0
NA E:FDE501 2.1 11.5 1.0
NC E:FDE501 2.1 3.9 1.0
NB E:FDE501 2.1 13.8 1.0
ND E:FDE501 2.1 3.8 1.0
SG E:CYS400 2.2 3.1 1.0
O E:HOH664 2.4 15.4 1.0
C1A E:FDE501 3.0 5.2 1.0
C4A E:FDE501 3.1 4.1 1.0
C4C E:FDE501 3.1 4.0 1.0
C1B E:FDE501 3.1 4.0 1.0
C4B E:FDE501 3.1 6.0 1.0
C1C E:FDE501 3.1 4.3 1.0
CHB E:FDE501 3.1 4.7 1.0
C1D E:FDE501 3.1 3.4 1.0
C4D E:FDE501 3.1 4.0 1.0
CB E:CYS400 3.1 4.3 1.0
CHD E:FDE501 3.1 5.3 1.0
CHA E:FDE501 3.4 3.9 1.0
CHC E:FDE501 3.4 5.3 1.0
CA E:CYS400 4.0 4.0 1.0
C3C E:FDE501 4.3 3.7 1.0
C3B E:FDE501 4.3 5.1 1.0
C2C E:FDE501 4.3 4.9 1.0
C2B E:FDE501 4.3 5.8 1.0
C3D E:FDE501 4.3 8.3 1.0
C2D E:FDE501 4.3 2.4 1.0
C2A E:FDE501 4.3 4.4 1.0
C3A E:FDE501 4.4 3.8 1.0
O E:HOH733 4.6 16.5 1.0
CE2 E:PHE87 4.8 9.6 1.0
C E:CYS400 4.9 5.0 1.0
CD1 E:PHE393 5.0 13.1 1.0

Iron binding site 6 out of 8 in 5jqu

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Iron binding site 6 out of 8 in the Crystal Structure of Cytochrome P450 BM3 Heme Domain G265F/T269V/L272W/L322I/F405M/A406S (Wivs-Fm) Variant with Iron(III) Deuteroporphyrin IX Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Cytochrome P450 BM3 Heme Domain G265F/T269V/L272W/L322I/F405M/A406S (Wivs-Fm) Variant with Iron(III) Deuteroporphyrin IX Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:8.9
occ:1.00
 FE F:FDE501 0.0 8.9 1.0
NC F:FDE501 2.0 7.6 1.0
ND F:FDE501 2.1 4.6 1.0
NA F:FDE501 2.1 5.0 1.0
NB F:FDE501 2.1 9.3 1.0
SG F:CYS400 2.3 11.7 1.0
CB F:CYS400 2.8 7.3 1.0
C4C F:FDE501 3.0 7.3 1.0
C4D F:FDE501 3.1 5.4 1.0
C1D F:FDE501 3.1 4.8 1.0
C1C F:FDE501 3.1 9.9 1.0
C1A F:FDE501 3.1 5.4 1.0
C4A F:FDE501 3.1 7.6 1.0
CHD F:FDE501 3.1 5.0 1.0
C4B F:FDE501 3.1 8.4 1.0
C1B F:FDE501 3.1 9.2 1.0
CHB F:FDE501 3.2 8.2 1.0
CHA F:FDE501 3.4 7.0 1.0
CHC F:FDE501 3.5 12.8 1.0
CA F:CYS400 3.7 6.7 1.0
C3C F:FDE501 4.2 8.6 1.0
C3D F:FDE501 4.3 9.2 1.0
C2C F:FDE501 4.3 7.6 1.0
C2D F:FDE501 4.3 7.6 1.0
C3B F:FDE501 4.4 12.8 1.0
C2B F:FDE501 4.4 13.6 1.0
C2A F:FDE501 4.4 6.1 1.0
CE2 F:PHE87 4.4 13.0 1.0
C3A F:FDE501 4.4 9.9 1.0
C F:CYS400 4.7 12.7 1.0
N F:CYS400 4.8 9.0 1.0

Iron binding site 7 out of 8 in 5jqu

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Iron binding site 7 out of 8 in the Crystal Structure of Cytochrome P450 BM3 Heme Domain G265F/T269V/L272W/L322I/F405M/A406S (Wivs-Fm) Variant with Iron(III) Deuteroporphyrin IX Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Cytochrome P450 BM3 Heme Domain G265F/T269V/L272W/L322I/F405M/A406S (Wivs-Fm) Variant with Iron(III) Deuteroporphyrin IX Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe501

b:10.1
occ:1.00
 FE G:FDE501 0.0 10.1 1.0
NA G:FDE501 2.0 3.9 1.0
NC G:FDE501 2.0 4.2 1.0
ND G:FDE501 2.1 5.0 1.0
NB G:FDE501 2.1 6.8 1.0
SG G:CYS400 2.4 10.4 1.0
C1A G:FDE501 3.0 7.5 1.0
C1C G:FDE501 3.1 5.1 1.0
C4C G:FDE501 3.1 5.2 1.0
C4A G:FDE501 3.1 4.0 1.0
C1D G:FDE501 3.1 9.7 1.0
C4B G:FDE501 3.1 4.2 1.0
C4D G:FDE501 3.1 5.1 1.0
C1B G:FDE501 3.1 6.9 1.0
CHD G:FDE501 3.1 6.0 1.0
CHB G:FDE501 3.2 4.0 1.0
CHA G:FDE501 3.4 7.3 1.0
CB G:CYS400 3.4 5.9 1.0
CHC G:FDE501 3.4 4.3 1.0
CA G:CYS400 4.1 7.9 1.0
C3C G:FDE501 4.3 7.2 1.0
C2C G:FDE501 4.3 4.6 1.0
C3D G:FDE501 4.3 6.1 1.0
C2D G:FDE501 4.3 5.9 1.0
C3B G:FDE501 4.3 7.6 1.0
C2A G:FDE501 4.3 9.8 1.0
C3A G:FDE501 4.4 6.8 1.0
C2B G:FDE501 4.4 11.4 1.0
CE2 G:PHE87 4.5 4.8 1.0
N G:GLY402 4.6 12.0 1.0
C G:CYS400 4.8 5.8 1.0
N G:ILE401 4.9 4.9 1.0
CA G:GLY402 4.9 6.9 1.0
CD2 G:PHE87 5.0 7.7 1.0

Iron binding site 8 out of 8 in 5jqu

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Iron binding site 8 out of 8 in the Crystal Structure of Cytochrome P450 BM3 Heme Domain G265F/T269V/L272W/L322I/F405M/A406S (Wivs-Fm) Variant with Iron(III) Deuteroporphyrin IX Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Cytochrome P450 BM3 Heme Domain G265F/T269V/L272W/L322I/F405M/A406S (Wivs-Fm) Variant with Iron(III) Deuteroporphyrin IX Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe501

b:2.0
occ:1.00
 FE H:FDE501 0.0 2.0 1.0
NC H:FDE501 2.0 2.0 1.0
NA H:FDE501 2.0 2.0 1.0
NB H:FDE501 2.1 6.2 1.0
ND H:FDE501 2.1 2.0 1.0
SG H:CYS400 2.4 10.1 1.0
C1A H:FDE501 3.0 2.0 1.0
C1C H:FDE501 3.0 2.0 1.0
C4A H:FDE501 3.0 2.8 1.0
C4C H:FDE501 3.0 2.0 1.0
CB H:CYS400 3.1 6.0 1.0
C4B H:FDE501 3.1 7.9 1.0
C1B H:FDE501 3.1 2.5 1.0
C4D H:FDE501 3.1 2.7 1.0
C1D H:FDE501 3.1 2.0 1.0
CHB H:FDE501 3.1 2.0 1.0
CHD H:FDE501 3.2 2.5 1.0
O H:HOH687 3.2 10.2 1.0
CHC H:FDE501 3.4 7.8 1.0
CHA H:FDE501 3.4 2.3 1.0
CA H:CYS400 3.8 7.2 1.0
C3C H:FDE501 4.2 2.5 1.0
C2C H:FDE501 4.3 5.6 1.0
C3B H:FDE501 4.3 2.4 1.0
C2A H:FDE501 4.3 6.4 1.0
C3D H:FDE501 4.3 2.0 1.0
C2B H:FDE501 4.3 2.3 1.0
C3A H:FDE501 4.3 2.0 1.0
C2D H:FDE501 4.4 2.0 1.0
CE2 H:PHE87 4.4 7.4 1.0
C H:CYS400 4.7 3.5 1.0
N H:ILE401 4.9 3.3 1.0
N H:CYS400 5.0 6.7 1.0

Reference:

E.W.Reynolds, M.W.Mchenry, F.Cannac, J.G.Gober, C.D.Snow, E.M.Brustad. An Evolved Orthogonal Enzyme/Cofactor Pair. J.Am.Chem.Soc. V. 138 12451 2016.
ISSN: ESSN 1520-5126
PubMed: 27575374
DOI: 10.1021/JACS.6B05847
Page generated: Tue Aug 6 02:36:00 2024

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