Iron in PDB 4nkz: Human Steroidogenic Cytochrome P450 17A1 Mutant A105L with Substrate 17ALPHA-Hydroxypregnenolone
Enzymatic activity of Human Steroidogenic Cytochrome P450 17A1 Mutant A105L with Substrate 17ALPHA-Hydroxypregnenolone
All present enzymatic activity of Human Steroidogenic Cytochrome P450 17A1 Mutant A105L with Substrate 17ALPHA-Hydroxypregnenolone:
1.14.99.9;
4.1.2.30;
Protein crystallography data
The structure of Human Steroidogenic Cytochrome P450 17A1 Mutant A105L with Substrate 17ALPHA-Hydroxypregnenolone, PDB code: 4nkz
was solved by
E.E.Scott,
E.M.Petrunak,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
38.70 /
3.00
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
85.820,
151.093,
170.342,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
19.1 /
26.1
|
Iron Binding Sites:
The binding sites of Iron atom in the Human Steroidogenic Cytochrome P450 17A1 Mutant A105L with Substrate 17ALPHA-Hydroxypregnenolone
(pdb code 4nkz). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Human Steroidogenic Cytochrome P450 17A1 Mutant A105L with Substrate 17ALPHA-Hydroxypregnenolone, PDB code: 4nkz:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 4nkz
Go back to
Iron Binding Sites List in 4nkz
Iron binding site 1 out
of 4 in the Human Steroidogenic Cytochrome P450 17A1 Mutant A105L with Substrate 17ALPHA-Hydroxypregnenolone
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Human Steroidogenic Cytochrome P450 17A1 Mutant A105L with Substrate 17ALPHA-Hydroxypregnenolone within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe600
b:56.5
occ:1.00
|
FE
|
A:HEM600
|
0.0
|
56.5
|
1.0
|
|
NB
|
A:HEM600
|
2.0
|
51.6
|
1.0
|
|
NA
|
A:HEM600
|
2.0
|
59.6
|
1.0
|
|
ND
|
A:HEM600
|
2.1
|
56.4
|
1.0
|
|
NC
|
A:HEM600
|
2.1
|
64.8
|
1.0
|
|
SG
|
A:CYS442
|
2.7
|
77.2
|
1.0
|
|
HB2
|
A:CYS442
|
3.0
|
67.4
|
1.0
|
|
C1B
|
A:HEM600
|
3.0
|
56.6
|
1.0
|
|
C1A
|
A:HEM600
|
3.0
|
60.3
|
1.0
|
|
C4A
|
A:HEM600
|
3.0
|
55.7
|
1.0
|
|
C4B
|
A:HEM600
|
3.0
|
53.5
|
1.0
|
|
HA5
|
A:LZZ601
|
3.1
|
81.6
|
1.0
|
|
C4D
|
A:HEM600
|
3.1
|
51.8
|
1.0
|
|
C1C
|
A:HEM600
|
3.1
|
57.4
|
1.0
|
|
C1D
|
A:HEM600
|
3.1
|
57.2
|
1.0
|
|
C4C
|
A:HEM600
|
3.1
|
58.6
|
1.0
|
|
CB
|
A:CYS442
|
3.4
|
56.1
|
1.0
|
|
CHB
|
A:HEM600
|
3.4
|
55.1
|
1.0
|
|
CHA
|
A:HEM600
|
3.4
|
51.5
|
1.0
|
|
CHC
|
A:HEM600
|
3.5
|
50.3
|
1.0
|
|
CHD
|
A:HEM600
|
3.5
|
52.2
|
1.0
|
|
HA
|
A:CYS442
|
3.6
|
65.3
|
1.0
|
|
HAS
|
A:LZZ601
|
3.7
|
82.5
|
1.0
|
|
OAX
|
A:LZZ601
|
3.9
|
68.0
|
1.0
|
|
CA
|
A:CYS442
|
4.0
|
54.5
|
1.0
|
|
H
|
A:ILE443
|
4.1
|
55.7
|
1.0
|
|
H
|
A:GLY444
|
4.2
|
79.5
|
1.0
|
|
HB3
|
A:CYS442
|
4.2
|
67.4
|
1.0
|
|
HB1
|
A:ALA302
|
4.2
|
78.7
|
1.0
|
|
C2B
|
A:HEM600
|
4.3
|
50.3
|
1.0
|
|
C2A
|
A:HEM600
|
4.3
|
64.0
|
1.0
|
|
C3B
|
A:HEM600
|
4.3
|
50.8
|
1.0
|
|
C3A
|
A:HEM600
|
4.3
|
58.4
|
1.0
|
|
C2C
|
A:HEM600
|
4.3
|
57.6
|
1.0
|
|
C3C
|
A:HEM600
|
4.3
|
62.2
|
1.0
|
|
C3D
|
A:HEM600
|
4.3
|
56.1
|
1.0
|
|
HG21
|
A:THR306
|
4.3
|
75.0
|
1.0
|
|
C2D
|
A:HEM600
|
4.3
|
56.5
|
1.0
|
|
HHB
|
A:HEM600
|
4.4
|
66.1
|
1.0
|
|
HHA
|
A:HEM600
|
4.4
|
61.8
|
1.0
|
|
HHC
|
A:HEM600
|
4.4
|
60.4
|
1.0
|
|
HHD
|
A:HEM600
|
4.5
|
62.7
|
1.0
|
|
HD1
|
A:PHE435
|
4.5
|
70.4
|
1.0
|
|
HAP
|
A:LZZ601
|
4.5
|
75.0
|
1.0
|
|
CAP
|
A:LZZ601
|
4.5
|
68.7
|
1.0
|
|
CAN
|
A:LZZ601
|
4.6
|
66.1
|
1.0
|
|
N
|
A:ILE443
|
4.7
|
46.4
|
1.0
|
|
CAM
|
A:LZZ601
|
4.8
|
65.2
|
1.0
|
|
C
|
A:CYS442
|
4.9
|
54.4
|
1.0
|
|
HAQ
|
A:LZZ601
|
5.0
|
82.5
|
1.0
|
|
N
|
A:GLY444
|
5.0
|
66.2
|
1.0
|
|
OAO
|
A:LZZ601
|
5.0
|
63.5
|
1.0
|
|
Iron binding site 2 out
of 4 in 4nkz
Go back to
Iron Binding Sites List in 4nkz
Iron binding site 2 out
of 4 in the Human Steroidogenic Cytochrome P450 17A1 Mutant A105L with Substrate 17ALPHA-Hydroxypregnenolone
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Human Steroidogenic Cytochrome P450 17A1 Mutant A105L with Substrate 17ALPHA-Hydroxypregnenolone within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe600
b:58.9
occ:1.00
|
FE
|
B:HEM600
|
0.0
|
58.9
|
1.0
|
|
NC
|
B:HEM600
|
2.0
|
58.8
|
1.0
|
|
NA
|
B:HEM600
|
2.1
|
51.7
|
1.0
|
|
ND
|
B:HEM600
|
2.1
|
52.2
|
1.0
|
|
NB
|
B:HEM600
|
2.1
|
57.6
|
1.0
|
|
SG
|
B:CYS442
|
2.7
|
75.1
|
1.0
|
|
HA5
|
B:LZZ601
|
3.0
|
74.6
|
1.0
|
|
C4C
|
B:HEM600
|
3.0
|
56.3
|
1.0
|
|
C4A
|
B:HEM600
|
3.0
|
56.1
|
1.0
|
|
C1D
|
B:HEM600
|
3.1
|
50.0
|
1.0
|
|
C1C
|
B:HEM600
|
3.1
|
57.6
|
1.0
|
|
C1B
|
B:HEM600
|
3.1
|
53.4
|
1.0
|
|
C4D
|
B:HEM600
|
3.1
|
54.3
|
1.0
|
|
C1A
|
B:HEM600
|
3.1
|
59.3
|
1.0
|
|
C4B
|
B:HEM600
|
3.1
|
62.7
|
1.0
|
|
HB2
|
B:CYS442
|
3.2
|
70.8
|
1.0
|
|
CHD
|
B:HEM600
|
3.4
|
50.5
|
1.0
|
|
CHB
|
B:HEM600
|
3.4
|
55.7
|
1.0
|
|
HAQ
|
B:LZZ601
|
3.5
|
87.1
|
1.0
|
|
CB
|
B:CYS442
|
3.5
|
59.0
|
1.0
|
|
CHA
|
B:HEM600
|
3.5
|
56.0
|
1.0
|
|
CHC
|
B:HEM600
|
3.5
|
58.3
|
1.0
|
|
HA
|
B:CYS442
|
3.6
|
62.3
|
1.0
|
|
OAX
|
B:LZZ601
|
3.8
|
62.2
|
1.0
|
|
CA
|
B:CYS442
|
4.1
|
51.9
|
1.0
|
|
C3C
|
B:HEM600
|
4.2
|
55.7
|
1.0
|
|
C2C
|
B:HEM600
|
4.3
|
55.3
|
1.0
|
|
C3A
|
B:HEM600
|
4.3
|
61.3
|
1.0
|
|
HB3
|
B:CYS442
|
4.3
|
70.8
|
1.0
|
|
C2D
|
B:HEM600
|
4.3
|
56.2
|
1.0
|
|
C2A
|
B:HEM600
|
4.3
|
67.2
|
1.0
|
|
CAP
|
B:LZZ601
|
4.3
|
72.6
|
1.0
|
|
C3D
|
B:HEM600
|
4.3
|
60.5
|
1.0
|
|
C2B
|
B:HEM600
|
4.3
|
50.5
|
1.0
|
|
C3B
|
B:HEM600
|
4.3
|
54.4
|
1.0
|
|
HHD
|
B:HEM600
|
4.4
|
60.6
|
1.0
|
|
H
|
B:GLY444
|
4.4
|
75.4
|
1.0
|
|
H
|
B:ILE443
|
4.4
|
60.5
|
1.0
|
|
HHB
|
B:HEM600
|
4.4
|
66.8
|
1.0
|
|
HB1
|
B:ALA302
|
4.4
|
76.1
|
1.0
|
|
HHA
|
B:HEM600
|
4.4
|
67.2
|
1.0
|
|
HHC
|
B:HEM600
|
4.5
|
70.0
|
1.0
|
|
HD1
|
B:PHE435
|
4.5
|
75.3
|
1.0
|
|
HG21
|
B:THR306
|
4.5
|
70.1
|
1.0
|
|
HAP
|
B:LZZ601
|
4.5
|
86.5
|
1.0
|
|
CAN
|
B:LZZ601
|
4.6
|
64.7
|
1.0
|
|
HAS
|
B:LZZ601
|
4.6
|
87.1
|
1.0
|
|
CAM
|
B:LZZ601
|
4.8
|
65.7
|
1.0
|
|
N
|
B:ILE443
|
4.9
|
50.4
|
1.0
|
|
C
|
B:CYS442
|
5.0
|
50.9
|
1.0
|
|
Iron binding site 3 out
of 4 in 4nkz
Go back to
Iron Binding Sites List in 4nkz
Iron binding site 3 out
of 4 in the Human Steroidogenic Cytochrome P450 17A1 Mutant A105L with Substrate 17ALPHA-Hydroxypregnenolone
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Human Steroidogenic Cytochrome P450 17A1 Mutant A105L with Substrate 17ALPHA-Hydroxypregnenolone within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe600
b:53.0
occ:1.00
|
FE
|
C:HEM600
|
0.0
|
53.0
|
1.0
|
|
NB
|
C:HEM600
|
2.0
|
63.0
|
1.0
|
|
NA
|
C:HEM600
|
2.1
|
69.4
|
1.0
|
|
ND
|
C:HEM600
|
2.1
|
70.9
|
1.0
|
|
NC
|
C:HEM600
|
2.1
|
67.0
|
1.0
|
|
SG
|
C:CYS442
|
2.5
|
59.9
|
1.0
|
|
C1B
|
C:HEM600
|
3.0
|
66.5
|
1.0
|
|
C4A
|
C:HEM600
|
3.1
|
62.1
|
1.0
|
|
C4B
|
C:HEM600
|
3.1
|
66.4
|
1.0
|
|
C1C
|
C:HEM600
|
3.1
|
61.0
|
1.0
|
|
C4D
|
C:HEM600
|
3.1
|
64.8
|
1.0
|
|
C1A
|
C:HEM600
|
3.1
|
60.7
|
1.0
|
|
C1D
|
C:HEM600
|
3.1
|
63.2
|
1.0
|
|
C4C
|
C:HEM600
|
3.1
|
66.9
|
1.0
|
|
HB2
|
C:CYS442
|
3.2
|
73.3
|
1.0
|
|
OAX
|
C:LZZ601
|
3.4
|
59.7
|
1.0
|
|
CHB
|
C:HEM600
|
3.4
|
67.3
|
1.0
|
|
CHC
|
C:HEM600
|
3.4
|
64.8
|
1.0
|
|
CB
|
C:CYS442
|
3.4
|
61.1
|
1.0
|
|
CHA
|
C:HEM600
|
3.5
|
57.9
|
1.0
|
|
CHD
|
C:HEM600
|
3.5
|
56.6
|
1.0
|
|
HAS
|
C:LZZ601
|
3.5
|
78.7
|
1.0
|
|
HA
|
C:CYS442
|
3.7
|
71.3
|
1.0
|
|
HA5
|
C:LZZ601
|
3.8
|
71.7
|
1.0
|
|
HAO
|
C:LZZ601
|
3.9
|
85.4
|
1.0
|
|
CA
|
C:CYS442
|
4.1
|
59.4
|
1.0
|
|
H
|
C:GLY444
|
4.2
|
65.3
|
1.0
|
|
HB3
|
C:CYS442
|
4.2
|
73.3
|
1.0
|
|
C2B
|
C:HEM600
|
4.2
|
64.7
|
1.0
|
|
HD1
|
C:PHE435
|
4.3
|
73.7
|
1.0
|
|
C3B
|
C:HEM600
|
4.3
|
65.1
|
1.0
|
|
C3A
|
C:HEM600
|
4.3
|
53.7
|
1.0
|
|
C2C
|
C:HEM600
|
4.3
|
64.9
|
1.0
|
|
CAP
|
C:LZZ601
|
4.3
|
65.6
|
1.0
|
|
C2A
|
C:HEM600
|
4.3
|
61.5
|
1.0
|
|
C3D
|
C:HEM600
|
4.3
|
59.6
|
1.0
|
|
C3C
|
C:HEM600
|
4.3
|
67.0
|
1.0
|
|
C2D
|
C:HEM600
|
4.4
|
58.8
|
1.0
|
|
CAM
|
C:LZZ601
|
4.4
|
65.4
|
1.0
|
|
HHB
|
C:HEM600
|
4.4
|
80.7
|
1.0
|
|
CAN
|
C:LZZ601
|
4.4
|
69.3
|
1.0
|
|
HHC
|
C:HEM600
|
4.4
|
77.8
|
1.0
|
|
HHA
|
C:HEM600
|
4.4
|
69.5
|
1.0
|
|
H
|
C:ILE443
|
4.4
|
66.7
|
1.0
|
|
HHD
|
C:HEM600
|
4.5
|
67.9
|
1.0
|
|
HG21
|
C:THR306
|
4.5
|
75.1
|
1.0
|
|
CAL
|
C:LZZ601
|
4.6
|
71.2
|
1.0
|
|
HB1
|
C:ALA302
|
4.6
|
74.3
|
1.0
|
|
HAR
|
C:LZZ601
|
4.6
|
78.7
|
1.0
|
|
N
|
C:ILE443
|
4.9
|
55.5
|
1.0
|
|
C
|
C:CYS442
|
5.0
|
57.7
|
1.0
|
|
OAO
|
C:LZZ601
|
5.0
|
74.5
|
1.0
|
|
Iron binding site 4 out
of 4 in 4nkz
Go back to
Iron Binding Sites List in 4nkz
Iron binding site 4 out
of 4 in the Human Steroidogenic Cytochrome P450 17A1 Mutant A105L with Substrate 17ALPHA-Hydroxypregnenolone
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Human Steroidogenic Cytochrome P450 17A1 Mutant A105L with Substrate 17ALPHA-Hydroxypregnenolone within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe600
b:58.0
occ:1.00
|
FE
|
D:HEM600
|
0.0
|
58.0
|
1.0
|
|
NB
|
D:HEM600
|
2.0
|
62.8
|
1.0
|
|
NA
|
D:HEM600
|
2.0
|
67.9
|
1.0
|
|
ND
|
D:HEM600
|
2.1
|
64.4
|
1.0
|
|
NC
|
D:HEM600
|
2.2
|
65.2
|
1.0
|
|
SG
|
D:CYS442
|
2.6
|
56.6
|
1.0
|
|
HA5
|
D:LZZ601
|
2.9
|
76.4
|
1.0
|
|
C1B
|
D:HEM600
|
3.0
|
65.9
|
1.0
|
|
C4B
|
D:HEM600
|
3.0
|
67.7
|
1.0
|
|
C4A
|
D:HEM600
|
3.0
|
61.4
|
1.0
|
|
C1A
|
D:HEM600
|
3.1
|
67.6
|
1.0
|
|
C1C
|
D:HEM600
|
3.1
|
64.8
|
1.0
|
|
C4D
|
D:HEM600
|
3.1
|
57.4
|
1.0
|
|
C1D
|
D:HEM600
|
3.2
|
69.2
|
1.0
|
|
C4C
|
D:HEM600
|
3.2
|
62.4
|
1.0
|
|
CHB
|
D:HEM600
|
3.3
|
68.2
|
1.0
|
|
HB2
|
D:CYS442
|
3.4
|
79.8
|
1.0
|
|
CHC
|
D:HEM600
|
3.4
|
61.5
|
1.0
|
|
CHA
|
D:HEM600
|
3.5
|
61.4
|
1.0
|
|
CB
|
D:CYS442
|
3.5
|
66.5
|
1.0
|
|
CHD
|
D:HEM600
|
3.5
|
59.4
|
1.0
|
|
HA
|
D:CYS442
|
3.7
|
78.4
|
1.0
|
|
OAX
|
D:LZZ601
|
3.8
|
63.7
|
1.0
|
|
HAS
|
D:LZZ601
|
3.9
|
82.3
|
1.0
|
|
HAP
|
D:LZZ601
|
4.0
|
69.8
|
1.0
|
|
CA
|
D:CYS442
|
4.2
|
65.4
|
1.0
|
|
C3B
|
D:HEM600
|
4.2
|
69.8
|
1.0
|
|
C2B
|
D:HEM600
|
4.2
|
67.2
|
1.0
|
|
H
|
D:GLY444
|
4.2
|
74.5
|
1.0
|
|
HB1
|
D:ALA302
|
4.2
|
69.9
|
1.0
|
|
C3A
|
D:HEM600
|
4.2
|
53.6
|
1.0
|
|
C2A
|
D:HEM600
|
4.3
|
67.6
|
1.0
|
|
C2C
|
D:HEM600
|
4.3
|
70.4
|
1.0
|
|
HHB
|
D:HEM600
|
4.3
|
81.9
|
1.0
|
|
HD1
|
D:PHE435
|
4.3
|
80.4
|
1.0
|
|
HB3
|
D:CYS442
|
4.4
|
79.8
|
1.0
|
|
HHC
|
D:HEM600
|
4.4
|
73.8
|
1.0
|
|
C2D
|
D:HEM600
|
4.4
|
64.4
|
1.0
|
|
C3D
|
D:HEM600
|
4.4
|
56.4
|
1.0
|
|
C3C
|
D:HEM600
|
4.4
|
68.4
|
1.0
|
|
H
|
D:ILE443
|
4.4
|
74.9
|
1.0
|
|
HHA
|
D:HEM600
|
4.4
|
73.7
|
1.0
|
|
CAN
|
D:LZZ601
|
4.5
|
64.5
|
1.0
|
|
HG21
|
D:THR306
|
4.5
|
86.3
|
1.0
|
|
HHD
|
D:HEM600
|
4.5
|
71.2
|
1.0
|
|
CAM
|
D:LZZ601
|
4.6
|
61.3
|
1.0
|
|
CAP
|
D:LZZ601
|
4.6
|
68.6
|
1.0
|
|
CAL
|
D:LZZ601
|
4.7
|
58.2
|
1.0
|
|
OAO
|
D:LZZ601
|
4.8
|
65.3
|
1.0
|
|
HA3
|
D:GLY444
|
4.8
|
73.2
|
1.0
|
|
N
|
D:ILE443
|
4.9
|
62.4
|
1.0
|
|
HAO
|
D:LZZ601
|
4.9
|
69.8
|
1.0
|
|
N
|
D:GLY444
|
5.0
|
62.1
|
1.0
|
|
Reference:
E.M.Petrunak,
N.M.Devore,
P.R.Porubsky,
E.E.Scott.
Structures of Human Steroidogenic Cytochrome P450 17A1 with Substrates. J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X
PubMed: 25301938
DOI: 10.1074/JBC.M114.610998
Page generated: Mon Aug 5 07:55:27 2024
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