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Iron in PDB 7p6l: Heme Domain of CYP505A30, A Fungal Hydroxylase From Myceliophthora Thermophila, Bound to Dodecanoic Acid

Enzymatic activity of Heme Domain of CYP505A30, A Fungal Hydroxylase From Myceliophthora Thermophila, Bound to Dodecanoic Acid

All present enzymatic activity of Heme Domain of CYP505A30, A Fungal Hydroxylase From Myceliophthora Thermophila, Bound to Dodecanoic Acid:
1.14.14.1; 1.6.2.4;

Protein crystallography data

The structure of Heme Domain of CYP505A30, A Fungal Hydroxylase From Myceliophthora Thermophila, Bound to Dodecanoic Acid, PDB code: 7p6l was solved by D.J.Opperman, J.C.Aschenbrenner, C.Tolmie, A.C.Ebrecht, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 61.43 / 2.33
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 171.49, 171.49, 175.647, 90, 90, 90
R / Rfree (%) 20.3 / 23.4

Iron Binding Sites:

The binding sites of Iron atom in the Heme Domain of CYP505A30, A Fungal Hydroxylase From Myceliophthora Thermophila, Bound to Dodecanoic Acid (pdb code 7p6l). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Heme Domain of CYP505A30, A Fungal Hydroxylase From Myceliophthora Thermophila, Bound to Dodecanoic Acid, PDB code: 7p6l:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 7p6l

Go back to Iron Binding Sites List in 7p6l
Iron binding site 1 out of 4 in the Heme Domain of CYP505A30, A Fungal Hydroxylase From Myceliophthora Thermophila, Bound to Dodecanoic Acid


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Heme Domain of CYP505A30, A Fungal Hydroxylase From Myceliophthora Thermophila, Bound to Dodecanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:79.3
occ:1.00
 FE B:HEM501 0.0 79.3 1.0
ND B:HEM501 1.9 84.6 1.0
NA B:HEM501 2.0 79.2 1.0
NB B:HEM501 2.1 82.0 1.0
NC B:HEM501 2.1 84.1 1.0
SG B:CYS411 2.3 78.6 1.0
O B:HOH610 2.8 76.6 1.0
C4D B:HEM501 2.9 79.2 1.0
C1D B:HEM501 2.9 80.9 1.0
C1A B:HEM501 3.0 78.2 1.0
C4B B:HEM501 3.1 76.8 1.0
C1B B:HEM501 3.1 80.3 1.0
C4C B:HEM501 3.1 82.5 1.0
C4A B:HEM501 3.1 77.6 1.0
C1C B:HEM501 3.1 80.0 1.0
CHA B:HEM501 3.3 78.4 1.0
CB B:CYS411 3.4 80.5 1.0
CHD B:HEM501 3.4 81.0 1.0
CHC B:HEM501 3.5 75.9 1.0
CHB B:HEM501 3.5 80.8 1.0
CA B:CYS411 4.1 80.2 1.0
C3D B:HEM501 4.2 80.9 1.0
C2D B:HEM501 4.2 80.2 1.0
C2A B:HEM501 4.2 77.9 1.0
C3A B:HEM501 4.2 77.8 1.0
C2B B:HEM501 4.3 69.8 1.0
C2C B:HEM501 4.3 79.6 1.0
C3C B:HEM501 4.3 79.2 1.0
C3B B:HEM501 4.3 77.5 1.0
O B:ALA270 4.5 71.6 1.0
CE2 B:PHE93 4.8 79.6 1.0
OG1 B:THR274 4.9 68.3 1.0
C B:CYS411 5.0 76.7 1.0
N B:GLY413 5.0 75.5 1.0
CB B:ALA270 5.0 71.7 1.0

Iron binding site 2 out of 4 in 7p6l

Go back to Iron Binding Sites List in 7p6l
Iron binding site 2 out of 4 in the Heme Domain of CYP505A30, A Fungal Hydroxylase From Myceliophthora Thermophila, Bound to Dodecanoic Acid


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Heme Domain of CYP505A30, A Fungal Hydroxylase From Myceliophthora Thermophila, Bound to Dodecanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:68.9
occ:1.00
 FE A:HEM501 0.0 68.9 1.0
ND A:HEM501 1.9 65.3 1.0
NB A:HEM501 2.0 62.6 1.0
NA A:HEM501 2.1 66.3 1.0
NC A:HEM501 2.1 63.2 1.0
SG A:CYS411 2.3 75.3 1.0
C4D A:HEM501 2.9 63.6 1.0
C1D A:HEM501 3.0 64.3 1.0
C4B A:HEM501 3.0 62.8 1.0
C1B A:HEM501 3.0 66.9 1.0
C1A A:HEM501 3.1 65.8 1.0
C1C A:HEM501 3.1 64.7 1.0
C4A A:HEM501 3.1 67.4 1.0
C4C A:HEM501 3.1 62.8 1.0
CB A:CYS411 3.2 72.4 1.0
O A:HOH605 3.3 58.7 1.0
CHC A:HEM501 3.4 62.7 1.0
CHA A:HEM501 3.4 65.7 1.0
CHB A:HEM501 3.5 68.6 1.0
CHD A:HEM501 3.5 64.1 1.0
CA A:CYS411 4.0 73.8 1.0
C3D A:HEM501 4.2 62.2 1.0
C2D A:HEM501 4.2 62.5 1.0
C2B A:HEM501 4.3 68.4 1.0
C3B A:HEM501 4.3 66.3 1.0
C2A A:HEM501 4.3 66.6 1.0
C3A A:HEM501 4.3 67.6 1.0
C2C A:HEM501 4.3 65.9 1.0
C3C A:HEM501 4.3 62.3 1.0
O A:ALA270 4.6 69.0 1.0
C A:CYS411 4.8 72.2 1.0
N A:GLY413 4.8 69.3 1.0
CE2 A:PHE93 4.9 65.7 1.0
OG1 A:THR274 4.9 58.9 1.0
N A:ILE412 5.0 71.8 1.0

Iron binding site 3 out of 4 in 7p6l

Go back to Iron Binding Sites List in 7p6l
Iron binding site 3 out of 4 in the Heme Domain of CYP505A30, A Fungal Hydroxylase From Myceliophthora Thermophila, Bound to Dodecanoic Acid


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Heme Domain of CYP505A30, A Fungal Hydroxylase From Myceliophthora Thermophila, Bound to Dodecanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:73.2
occ:1.00
 FE C:HEM501 0.0 73.2 1.0
ND C:HEM501 1.9 74.6 1.0
NA C:HEM501 2.0 74.8 1.0
NB C:HEM501 2.1 67.9 1.0
NC C:HEM501 2.1 73.4 1.0
SG C:CYS411 2.3 74.7 1.0
C4D C:HEM501 2.9 74.9 1.0
C1D C:HEM501 3.0 72.7 1.0
O C:HOH626 3.0 73.8 1.0
C1A C:HEM501 3.0 74.2 1.0
C4B C:HEM501 3.0 67.1 1.0
C1B C:HEM501 3.1 69.7 1.0
C4A C:HEM501 3.1 72.0 1.0
C4C C:HEM501 3.1 71.1 1.0
C1C C:HEM501 3.1 68.2 1.0
CB C:CYS411 3.2 71.9 1.0
CHA C:HEM501 3.4 75.3 1.0
CHC C:HEM501 3.5 67.3 1.0
CHB C:HEM501 3.5 70.1 1.0
CHD C:HEM501 3.5 72.0 1.0
CA C:CYS411 3.9 74.8 1.0
C3D C:HEM501 4.2 70.1 1.0
C2D C:HEM501 4.2 71.9 1.0
C2A C:HEM501 4.2 71.3 1.0
C3A C:HEM501 4.3 70.8 1.0
C3B C:HEM501 4.3 66.3 1.0
C2B C:HEM501 4.3 68.0 1.0
C2C C:HEM501 4.3 68.8 1.0
C3C C:HEM501 4.4 70.3 1.0
O C:ALA270 4.6 78.0 1.0
C C:CYS411 4.8 74.6 1.0
CE2 C:PHE93 4.8 81.0 1.0
N C:GLY413 4.9 68.9 1.0
OG1 C:THR274 4.9 74.9 1.0
CB C:ALA270 4.9 74.2 1.0

Iron binding site 4 out of 4 in 7p6l

Go back to Iron Binding Sites List in 7p6l
Iron binding site 4 out of 4 in the Heme Domain of CYP505A30, A Fungal Hydroxylase From Myceliophthora Thermophila, Bound to Dodecanoic Acid


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Heme Domain of CYP505A30, A Fungal Hydroxylase From Myceliophthora Thermophila, Bound to Dodecanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:78.4
occ:1.00
 FE D:HEM501 0.0 78.4 1.0
ND D:HEM501 1.9 81.8 1.0
NA D:HEM501 2.0 87.8 1.0
NB D:HEM501 2.1 81.4 1.0
NC D:HEM501 2.1 82.5 1.0
SG D:CYS411 2.2 73.1 1.0
O D:HOH607 2.9 70.1 1.0
C1D D:HEM501 2.9 77.6 1.0
C4D D:HEM501 3.0 78.6 1.0
C1A D:HEM501 3.0 86.3 1.0
C1B D:HEM501 3.1 86.1 1.0
C4C D:HEM501 3.1 76.1 1.0
C4B D:HEM501 3.1 83.8 1.0
C4A D:HEM501 3.1 83.1 1.0
C1C D:HEM501 3.2 83.3 1.0
CB D:CYS411 3.2 79.9 1.0
CHA D:HEM501 3.3 85.4 1.0
CHD D:HEM501 3.4 74.0 1.0
CHB D:HEM501 3.5 84.9 1.0
CHC D:HEM501 3.5 86.1 1.0
CA D:CYS411 3.9 81.1 1.0
C2D D:HEM501 4.2 76.1 1.0
C3D D:HEM501 4.2 75.4 1.0
C2A D:HEM501 4.3 83.8 1.0
C2B D:HEM501 4.3 84.7 1.0
C3A D:HEM501 4.3 86.3 1.0
C3C D:HEM501 4.3 84.4 1.0
C3B D:HEM501 4.3 81.7 1.0
C2C D:HEM501 4.3 85.7 1.0
O D:ALA270 4.6 64.0 1.0
C D:CYS411 4.7 84.9 1.0
N D:GLY413 4.8 76.7 1.0
CE2 D:PHE93 4.9 77.0 1.0
N D:ILE412 4.9 81.5 1.0
OG1 D:THR274 5.0 66.8 1.0

Reference:

J.C.Aschenbrenner, A.C.Ebrecht, C.Tolmie, M.S.Smit, D.J.Opperman. Structure of the Fungal Hydroxylase, CYP505A30, and Rational Transfer of Mutation Data From CYP102A1 to Alter Regioselectivity Catalysis Science and V. 11 7359 2021TECHNOLOGY.
ISSN: ESSN 2044-4761
DOI: 10.1039/D1CY01348C
Page generated: Thu Aug 8 15:04:25 2024

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