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

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

All present enzymatic activity of Crystal Structure of Cytochrome P450 BM3 Heme Domain T269V/L272W/L322I/A406S (Wivs) 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 T269V/L272W/L322I/A406S (Wivs) Variant with Iron(III) Deuteroporphyrin IX Bound, PDB code: 5jqv 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) 32.97 / 2.34
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 106.708, 167.405, 228.471, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 28.4

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Cytochrome P450 BM3 Heme Domain T269V/L272W/L322I/A406S (Wivs) Variant with Iron(III) Deuteroporphyrin IX Bound (pdb code 5jqv). 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 T269V/L272W/L322I/A406S (Wivs) Variant with Iron(III) Deuteroporphyrin IX Bound, PDB code: 5jqv:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 5jqv

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Iron binding site 1 out of 8 in the Crystal Structure of Cytochrome P450 BM3 Heme Domain T269V/L272W/L322I/A406S (Wivs) 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 T269V/L272W/L322I/A406S (Wivs) Variant with Iron(III) Deuteroporphyrin IX Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:19.3
occ:1.00
 FE A:FDE501 0.0 19.3 1.0
NA A:FDE501 2.0 14.8 1.0
NC A:FDE501 2.1 20.8 1.0
NB A:FDE501 2.1 12.5 1.0
ND A:FDE501 2.1 19.2 1.0
SG A:CYS400 2.3 24.3 1.0
O A:HOH654 2.7 16.0 1.0
C1A A:FDE501 3.0 17.9 1.0
C4A A:FDE501 3.1 15.6 1.0
C4C A:FDE501 3.1 17.9 1.0
C1C A:FDE501 3.1 20.2 1.0
C4B A:FDE501 3.1 16.4 1.0
C1B A:FDE501 3.1 12.8 1.0
C4D A:FDE501 3.1 15.9 1.0
CHB A:FDE501 3.1 11.5 1.0
C1D A:FDE501 3.1 15.3 1.0
CHD A:FDE501 3.2 13.1 1.0
CB A:CYS400 3.2 13.8 1.0
CHA A:FDE501 3.4 15.5 1.0
CHC A:FDE501 3.4 18.4 1.0
CA A:CYS400 3.9 20.4 1.0
C3C A:FDE501 4.2 18.9 1.0
C2C A:FDE501 4.3 17.8 1.0
C3B A:FDE501 4.3 15.7 1.0
C2A A:FDE501 4.3 11.5 1.0
C3D A:FDE501 4.3 14.3 1.0
C3A A:FDE501 4.4 16.7 1.0
C2B A:FDE501 4.4 15.0 1.0
C2D A:FDE501 4.4 12.6 1.0
CE2 A:PHE87 4.5 16.0 1.0
C A:CYS400 4.7 22.7 1.0
N A:ILE401 4.7 22.8 1.0
O A:ALA264 4.8 21.6 1.0
OG1 A:THR268 5.0 15.4 1.0
N A:GLY402 5.0 19.3 1.0

Iron binding site 2 out of 8 in 5jqv

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Iron binding site 2 out of 8 in the Crystal Structure of Cytochrome P450 BM3 Heme Domain T269V/L272W/L322I/A406S (Wivs) 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 T269V/L272W/L322I/A406S (Wivs) Variant with Iron(III) Deuteroporphyrin IX Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:12.9
occ:1.00
 FE B:FDE501 0.0 12.9 1.0
NC B:FDE501 2.1 7.8 1.0
NA B:FDE501 2.1 8.7 1.0
NB B:FDE501 2.1 7.0 1.0
ND B:FDE501 2.1 8.7 1.0
SG B:CYS400 2.3 9.9 1.0
O B:HOH731 2.9 16.0 1.0
C4C B:FDE501 3.0 14.3 1.0
CB B:CYS400 3.0 9.6 1.0
C4A B:FDE501 3.1 10.9 1.0
C1C B:FDE501 3.1 7.3 1.0
C4B B:FDE501 3.1 12.7 1.0
C1A B:FDE501 3.1 8.8 1.0
C1B B:FDE501 3.1 9.7 1.0
C1D B:FDE501 3.1 9.1 1.0
CHB B:FDE501 3.1 11.3 1.0
CHD B:FDE501 3.1 9.8 1.0
C4D B:FDE501 3.1 10.8 1.0
CHA B:FDE501 3.4 8.0 1.0
CHC B:FDE501 3.5 10.8 1.0
CA B:CYS400 3.9 9.6 1.0
C3C B:FDE501 4.2 10.9 1.0
C2C B:FDE501 4.3 8.0 1.0
C3B B:FDE501 4.3 8.9 1.0
C2D B:FDE501 4.4 10.4 1.0
C2B B:FDE501 4.4 11.8 1.0
C3D B:FDE501 4.4 9.8 1.0
C2A B:FDE501 4.4 6.9 1.0
C3A B:FDE501 4.4 8.8 1.0
CE2 B:PHE87 4.6 8.7 1.0
O B:HOH641 4.7 20.1 1.0
O B:ALA264 4.7 14.4 1.0
C B:CYS400 4.7 14.0 1.0
N B:ILE401 4.9 17.8 1.0
N B:CYS400 5.0 13.3 1.0

Iron binding site 3 out of 8 in 5jqv

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Iron binding site 3 out of 8 in the Crystal Structure of Cytochrome P450 BM3 Heme Domain T269V/L272W/L322I/A406S (Wivs) 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 T269V/L272W/L322I/A406S (Wivs) Variant with Iron(III) Deuteroporphyrin IX Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:8.6
occ:1.00
 FE C:FDE501 0.0 8.6 1.0
NC C:FDE501 2.1 13.2 1.0
ND C:FDE501 2.1 9.5 1.0
NA C:FDE501 2.1 10.5 1.0
NB C:FDE501 2.1 13.7 1.0
SG C:CYS400 2.4 19.7 1.0
O C:HOH683 2.7 15.8 1.0
C4C C:FDE501 3.0 14.1 1.0
C1C C:FDE501 3.1 13.8 1.0
C4D C:FDE501 3.1 11.2 1.0
C1A C:FDE501 3.1 8.2 1.0
C1D C:FDE501 3.1 8.9 1.0
C4B C:FDE501 3.1 13.0 1.0
C4A C:FDE501 3.1 10.9 1.0
C1B C:FDE501 3.1 8.3 1.0
CHD C:FDE501 3.2 10.4 1.0
CHB C:FDE501 3.2 8.2 1.0
CB C:CYS400 3.3 10.0 1.0
CHA C:FDE501 3.4 12.8 1.0
CHC C:FDE501 3.4 12.0 1.0
CA C:CYS400 4.0 13.9 1.0
C3C C:FDE501 4.2 15.3 1.0
C2C C:FDE501 4.3 15.0 1.0
C3D C:FDE501 4.3 12.6 1.0
C2D C:FDE501 4.3 9.8 1.0
C3B C:FDE501 4.4 14.9 1.0
C2B C:FDE501 4.4 11.6 1.0
C2A C:FDE501 4.4 7.2 1.0
C3A C:FDE501 4.4 9.4 1.0
C C:CYS400 4.8 15.3 1.0
O C:ALA264 4.8 26.2 1.0
CE2 C:PHE87 4.8 11.4 1.0
N C:ILE401 4.8 10.6 1.0

Iron binding site 4 out of 8 in 5jqv

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Iron binding site 4 out of 8 in the Crystal Structure of Cytochrome P450 BM3 Heme Domain T269V/L272W/L322I/A406S (Wivs) 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 T269V/L272W/L322I/A406S (Wivs) Variant with Iron(III) Deuteroporphyrin IX Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:21.8
occ:1.00
 FE D:FDE501 0.0 21.8 1.0
NA D:FDE501 2.1 15.0 1.0
NC D:FDE501 2.1 19.8 1.0
ND D:FDE501 2.1 18.7 1.0
NB D:FDE501 2.1 26.7 1.0
SG D:CYS400 2.3 28.4 1.0
CB D:CYS400 2.9 26.7 1.0
C1A D:FDE501 3.1 23.2 1.0
C4A D:FDE501 3.1 20.3 1.0
C4C D:FDE501 3.1 20.1 1.0
C1C D:FDE501 3.1 18.2 1.0
C4D D:FDE501 3.1 16.8 1.0
C1D D:FDE501 3.1 27.6 1.0
C4B D:FDE501 3.1 19.9 1.0
C1B D:FDE501 3.1 21.1 1.0
CHB D:FDE501 3.2 21.7 1.0
CHD D:FDE501 3.2 25.0 1.0
CHA D:FDE501 3.4 26.1 1.0
CHC D:FDE501 3.5 19.4 1.0
CA D:CYS400 3.8 23.1 1.0
C3C D:FDE501 4.3 23.6 1.0
C3D D:FDE501 4.3 20.0 1.0
C2C D:FDE501 4.3 20.0 1.0
C3B D:FDE501 4.4 24.1 1.0
C2D D:FDE501 4.4 27.1 1.0
C2A D:FDE501 4.4 22.6 1.0
C2B D:FDE501 4.4 18.6 1.0
C3A D:FDE501 4.4 20.9 1.0
C D:CYS400 4.7 28.7 1.0
CE2 D:PHE87 4.7 21.2 1.0
N D:ILE401 4.9 25.4 1.0
O D:ALA264 4.9 33.3 1.0
N D:CYS400 4.9 19.9 1.0

Iron binding site 5 out of 8 in 5jqv

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Iron binding site 5 out of 8 in the Crystal Structure of Cytochrome P450 BM3 Heme Domain T269V/L272W/L322I/A406S (Wivs) 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 T269V/L272W/L322I/A406S (Wivs) Variant with Iron(III) Deuteroporphyrin IX Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:11.4
occ:1.00
 FE E:FDE501 0.0 11.4 1.0
NC E:FDE501 2.1 7.7 1.0
ND E:FDE501 2.1 8.8 1.0
NA E:FDE501 2.1 11.5 1.0
NB E:FDE501 2.1 12.0 1.0
SG E:CYS400 2.4 17.1 1.0
O E:HOH728 2.6 18.1 1.0
C1C E:FDE501 3.1 10.7 1.0
C4C E:FDE501 3.1 9.2 1.0
C4B E:FDE501 3.1 13.7 1.0
C1D E:FDE501 3.1 13.2 1.0
C4D E:FDE501 3.1 9.5 1.0
C1A E:FDE501 3.1 10.6 1.0
C4A E:FDE501 3.1 10.2 1.0
C1B E:FDE501 3.1 11.4 1.0
CHD E:FDE501 3.2 11.3 1.0
CB E:CYS400 3.2 11.8 1.0
CHB E:FDE501 3.2 9.8 1.0
CHC E:FDE501 3.4 14.6 1.0
CHA E:FDE501 3.4 9.7 1.0
CA E:CYS400 4.0 9.4 1.0
C3C E:FDE501 4.3 10.6 1.0
C2C E:FDE501 4.3 8.7 1.0
C3D E:FDE501 4.3 11.4 1.0
C3B E:FDE501 4.3 7.9 1.0
C2D E:FDE501 4.3 9.5 1.0
C2B E:FDE501 4.4 11.6 1.0
C2A E:FDE501 4.4 9.2 1.0
C3A E:FDE501 4.4 9.7 1.0
CE2 E:PHE87 4.7 17.1 1.0
O E:ALA264 4.8 14.0 1.0
C E:CYS400 4.8 13.7 1.0
N E:ILE401 4.9 12.7 1.0

Iron binding site 6 out of 8 in 5jqv

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Iron binding site 6 out of 8 in the Crystal Structure of Cytochrome P450 BM3 Heme Domain T269V/L272W/L322I/A406S (Wivs) 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 T269V/L272W/L322I/A406S (Wivs) Variant with Iron(III) Deuteroporphyrin IX Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:15.5
occ:1.00
 FE F:FDE501 0.0 15.5 1.0
NC F:FDE501 2.1 15.6 1.0
NA F:FDE501 2.1 10.6 1.0
ND F:FDE501 2.1 17.0 1.0
NB F:FDE501 2.1 15.1 1.0
SG F:CYS400 2.4 23.1 1.0
C4C F:FDE501 3.1 16.0 1.0
C1A F:FDE501 3.1 10.2 1.0
C4A F:FDE501 3.1 15.5 1.0
CB F:CYS400 3.1 17.4 1.0
C1C F:FDE501 3.1 19.4 1.0
C4D F:FDE501 3.1 15.0 1.0
C1D F:FDE501 3.1 13.6 1.0
C4B F:FDE501 3.1 20.2 1.0
C1B F:FDE501 3.1 13.8 1.0
CHB F:FDE501 3.1 18.4 1.0
CHD F:FDE501 3.2 15.1 1.0
CHA F:FDE501 3.4 14.0 1.0
CHC F:FDE501 3.5 23.4 1.0
CA F:CYS400 3.9 18.6 1.0
C3C F:FDE501 4.3 16.2 1.0
C2C F:FDE501 4.3 14.6 1.0
C3D F:FDE501 4.3 13.3 1.0
C3B F:FDE501 4.4 14.9 1.0
C2D F:FDE501 4.4 13.5 1.0
C2B F:FDE501 4.4 16.9 1.0
C2A F:FDE501 4.4 13.0 1.0
C3A F:FDE501 4.4 12.7 1.0
CE2 F:PHE87 4.7 13.7 1.0
C F:CYS400 4.8 22.0 1.0
O F:ALA264 4.8 23.5 1.0
N F:ILE401 5.0 22.3 1.0

Iron binding site 7 out of 8 in 5jqv

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Iron binding site 7 out of 8 in the Crystal Structure of Cytochrome P450 BM3 Heme Domain T269V/L272W/L322I/A406S (Wivs) 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 T269V/L272W/L322I/A406S (Wivs) Variant with Iron(III) Deuteroporphyrin IX Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe501

b:16.9
occ:1.00
 FE G:FDE501 0.0 16.9 1.0
NC G:FDE501 2.1 16.8 1.0
ND G:FDE501 2.1 17.5 1.0
NA G:FDE501 2.1 12.9 1.0
NB G:FDE501 2.1 17.5 1.0
SG G:CYS400 2.3 16.6 1.0
C4C G:FDE501 3.1 16.1 1.0
C1C G:FDE501 3.1 15.6 1.0
C4D G:FDE501 3.1 17.3 1.0
C1D G:FDE501 3.1 15.8 1.0
C1A G:FDE501 3.1 14.1 1.0
C4A G:FDE501 3.1 11.1 1.0
C1B G:FDE501 3.1 12.5 1.0
C4B G:FDE501 3.1 15.2 1.0
CHD G:FDE501 3.2 16.2 1.0
CHB G:FDE501 3.2 14.6 1.0
CB G:CYS400 3.2 13.9 1.0
CHA G:FDE501 3.4 14.2 1.0
CHC G:FDE501 3.5 10.9 1.0
CA G:CYS400 4.0 14.6 1.0
C3C G:FDE501 4.3 17.6 1.0
C2C G:FDE501 4.3 14.7 1.0
C3D G:FDE501 4.3 16.1 1.0
C2D G:FDE501 4.4 14.9 1.0
C3B G:FDE501 4.4 16.3 1.0
C2B G:FDE501 4.4 12.4 1.0
C2A G:FDE501 4.4 17.8 1.0
C3A G:FDE501 4.4 11.5 1.0
CE2 G:PHE87 4.6 23.8 1.0
C G:CYS400 4.8 14.6 1.0
N G:ILE401 4.9 15.0 1.0
O G:ALA264 4.9 22.8 1.0

Iron binding site 8 out of 8 in 5jqv

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Iron binding site 8 out of 8 in the Crystal Structure of Cytochrome P450 BM3 Heme Domain T269V/L272W/L322I/A406S (Wivs) 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 T269V/L272W/L322I/A406S (Wivs) Variant with Iron(III) Deuteroporphyrin IX Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe501

b:13.6
occ:1.00
 FE H:FDE501 0.0 13.6 1.0
NC H:FDE501 2.1 7.8 1.0
NA H:FDE501 2.1 13.3 1.0
ND H:FDE501 2.1 11.8 1.0
NB H:FDE501 2.1 10.5 1.0
SG H:CYS400 2.4 23.3 1.0
C4C H:FDE501 3.0 10.9 1.0
C4A H:FDE501 3.1 11.7 1.0
CB H:CYS400 3.1 16.0 1.0
C1C H:FDE501 3.1 8.2 1.0
C1D H:FDE501 3.1 11.5 1.0
C1B H:FDE501 3.1 8.8 1.0
C1A H:FDE501 3.1 11.2 1.0
C4B H:FDE501 3.1 8.2 1.0
CHB H:FDE501 3.1 8.7 1.0
C4D H:FDE501 3.1 13.3 1.0
CHD H:FDE501 3.1 10.9 1.0
CHA H:FDE501 3.5 10.5 1.0
CHC H:FDE501 3.5 7.0 1.0
O H:HOH760 3.9 18.3 1.0
CA H:CYS400 4.0 12.7 1.0
C3C H:FDE501 4.2 9.4 1.0
C2C H:FDE501 4.3 6.4 1.0
C3D H:FDE501 4.4 10.3 1.0
C2D H:FDE501 4.4 14.2 1.0
C2B H:FDE501 4.4 8.6 1.0
C3B H:FDE501 4.4 8.5 1.0
C2A H:FDE501 4.4 10.1 1.0
C3A H:FDE501 4.4 14.0 1.0
CE2 H:PHE87 4.6 22.8 1.0
O H:HOH672 4.7 22.1 1.0
O H:ALA264 4.9 16.9 1.0
C H:CYS400 4.9 13.1 1.0
OG1 H:THR268 4.9 9.7 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 02:36:24 2024

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