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
|