Iron in PDB 3g93: Single Ligand Occupancy Crystal Structure of Cytochrome P450 2B4 in Complex with the Inhibitor 1-Biphenyl-4-Methyl-1H-Imidazole
Enzymatic activity of Single Ligand Occupancy Crystal Structure of Cytochrome P450 2B4 in Complex with the Inhibitor 1-Biphenyl-4-Methyl-1H-Imidazole
All present enzymatic activity of Single Ligand Occupancy Crystal Structure of Cytochrome P450 2B4 in Complex with the Inhibitor 1-Biphenyl-4-Methyl-1H-Imidazole:
1.14.14.1;
Protein crystallography data
The structure of Single Ligand Occupancy Crystal Structure of Cytochrome P450 2B4 in Complex with the Inhibitor 1-Biphenyl-4-Methyl-1H-Imidazole, PDB code: 3g93
was solved by
S.C.Gay,
L.Sun,
K.Maekawa,
J.R.Halpert,
C.D.Stout,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.75 /
3.20
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
86.910,
151.815,
181.583,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
23.7 /
27
|
Iron Binding Sites:
The binding sites of Iron atom in the Single Ligand Occupancy Crystal Structure of Cytochrome P450 2B4 in Complex with the Inhibitor 1-Biphenyl-4-Methyl-1H-Imidazole
(pdb code 3g93). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Single Ligand Occupancy Crystal Structure of Cytochrome P450 2B4 in Complex with the Inhibitor 1-Biphenyl-4-Methyl-1H-Imidazole, PDB code: 3g93:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 3g93
Go back to
Iron Binding Sites List in 3g93
Iron binding site 1 out
of 4 in the Single Ligand Occupancy Crystal Structure of Cytochrome P450 2B4 in Complex with the Inhibitor 1-Biphenyl-4-Methyl-1H-Imidazole
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Single Ligand Occupancy Crystal Structure of Cytochrome P450 2B4 in Complex with the Inhibitor 1-Biphenyl-4-Methyl-1H-Imidazole within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe500
b:22.6
occ:1.00
|
FE
|
A:HEM500
|
0.0
|
22.6
|
1.0
|
NC
|
A:HEM500
|
1.7
|
23.9
|
1.0
|
ND
|
A:HEM500
|
1.9
|
34.8
|
1.0
|
NB
|
A:HEM500
|
1.9
|
28.2
|
1.0
|
NA
|
A:HEM500
|
1.9
|
25.4
|
1.0
|
NAD
|
A:PB2501
|
2.1
|
21.7
|
1.0
|
SG
|
A:CYS436
|
2.3
|
28.8
|
1.0
|
CAE
|
A:PB2501
|
2.6
|
24.5
|
1.0
|
C4C
|
A:HEM500
|
2.7
|
21.7
|
1.0
|
C1D
|
A:HEM500
|
2.8
|
30.8
|
1.0
|
C1C
|
A:HEM500
|
2.9
|
26.6
|
1.0
|
C1B
|
A:HEM500
|
2.9
|
27.1
|
1.0
|
C4A
|
A:HEM500
|
3.0
|
18.1
|
1.0
|
C4D
|
A:HEM500
|
3.0
|
26.3
|
1.0
|
C4B
|
A:HEM500
|
3.0
|
24.1
|
1.0
|
C1A
|
A:HEM500
|
3.0
|
29.7
|
1.0
|
CHD
|
A:HEM500
|
3.1
|
18.3
|
1.0
|
CB
|
A:CYS436
|
3.3
|
26.5
|
1.0
|
CHB
|
A:HEM500
|
3.3
|
20.1
|
1.0
|
CAC
|
A:PB2501
|
3.4
|
28.2
|
1.0
|
CHC
|
A:HEM500
|
3.4
|
18.2
|
1.0
|
CHA
|
A:HEM500
|
3.5
|
24.3
|
1.0
|
CAF
|
A:PB2501
|
3.9
|
33.0
|
1.0
|
C3C
|
A:HEM500
|
3.9
|
29.4
|
1.0
|
C2C
|
A:HEM500
|
4.0
|
29.7
|
1.0
|
CA
|
A:CYS436
|
4.0
|
28.8
|
1.0
|
C2D
|
A:HEM500
|
4.1
|
30.5
|
1.0
|
C2B
|
A:HEM500
|
4.1
|
25.2
|
1.0
|
C3A
|
A:HEM500
|
4.2
|
20.6
|
1.0
|
C3D
|
A:HEM500
|
4.2
|
18.2
|
1.0
|
C3B
|
A:HEM500
|
4.2
|
20.6
|
1.0
|
C2A
|
A:HEM500
|
4.2
|
23.1
|
1.0
|
NAB
|
A:PB2501
|
4.3
|
28.3
|
1.0
|
N
|
A:GLY438
|
4.5
|
26.0
|
1.0
|
N
|
A:LEU437
|
4.6
|
23.2
|
1.0
|
C
|
A:CYS436
|
4.7
|
26.9
|
1.0
|
CA
|
A:GLY438
|
4.9
|
25.7
|
1.0
|
CA
|
A:GLY299
|
4.9
|
30.6
|
1.0
|
|
Iron binding site 2 out
of 4 in 3g93
Go back to
Iron Binding Sites List in 3g93
Iron binding site 2 out
of 4 in the Single Ligand Occupancy Crystal Structure of Cytochrome P450 2B4 in Complex with the Inhibitor 1-Biphenyl-4-Methyl-1H-Imidazole
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Single Ligand Occupancy Crystal Structure of Cytochrome P450 2B4 in Complex with the Inhibitor 1-Biphenyl-4-Methyl-1H-Imidazole within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe500
b:20.1
occ:1.00
|
FE
|
B:HEM500
|
0.0
|
20.1
|
1.0
|
NC
|
B:HEM500
|
1.6
|
19.6
|
1.0
|
NB
|
B:HEM500
|
1.6
|
19.7
|
1.0
|
ND
|
B:HEM500
|
2.0
|
27.8
|
1.0
|
NA
|
B:HEM500
|
2.1
|
18.6
|
1.0
|
NAD
|
A:PB2496
|
2.1
|
16.3
|
1.0
|
SG
|
B:CYS436
|
2.3
|
24.0
|
1.0
|
C1C
|
B:HEM500
|
2.6
|
19.5
|
1.0
|
C4B
|
B:HEM500
|
2.6
|
20.8
|
1.0
|
C4C
|
B:HEM500
|
2.7
|
22.5
|
1.0
|
C1B
|
B:HEM500
|
2.8
|
17.9
|
1.0
|
C1D
|
B:HEM500
|
3.0
|
28.5
|
1.0
|
C4A
|
B:HEM500
|
3.0
|
18.2
|
1.0
|
CHC
|
B:HEM500
|
3.1
|
16.3
|
1.0
|
CAE
|
A:PB2496
|
3.1
|
19.5
|
1.0
|
CAC
|
A:PB2496
|
3.1
|
26.1
|
1.0
|
C1A
|
B:HEM500
|
3.2
|
25.0
|
1.0
|
C4D
|
B:HEM500
|
3.2
|
20.4
|
1.0
|
CHD
|
B:HEM500
|
3.2
|
24.0
|
1.0
|
CHB
|
B:HEM500
|
3.3
|
18.5
|
1.0
|
CB
|
B:CYS436
|
3.4
|
27.2
|
1.0
|
CHA
|
B:HEM500
|
3.6
|
25.4
|
1.0
|
C2C
|
B:HEM500
|
3.8
|
20.7
|
1.0
|
C3C
|
B:HEM500
|
3.8
|
26.5
|
1.0
|
C3B
|
B:HEM500
|
3.9
|
19.0
|
1.0
|
C2B
|
B:HEM500
|
3.9
|
16.7
|
1.0
|
CA
|
B:CYS436
|
4.2
|
28.1
|
1.0
|
C2D
|
B:HEM500
|
4.3
|
24.2
|
1.0
|
CAF
|
A:PB2496
|
4.3
|
27.1
|
1.0
|
C3A
|
B:HEM500
|
4.3
|
32.3
|
1.0
|
NAB
|
A:PB2496
|
4.3
|
27.6
|
1.0
|
C2A
|
B:HEM500
|
4.4
|
31.6
|
1.0
|
C3D
|
B:HEM500
|
4.4
|
23.1
|
1.0
|
N
|
B:GLY438
|
4.7
|
25.2
|
1.0
|
CA
|
B:GLY299
|
4.7
|
36.5
|
1.0
|
N
|
B:LEU437
|
4.8
|
25.9
|
1.0
|
C
|
B:CYS436
|
4.9
|
30.7
|
1.0
|
|
Iron binding site 3 out
of 4 in 3g93
Go back to
Iron Binding Sites List in 3g93
Iron binding site 3 out
of 4 in the Single Ligand Occupancy Crystal Structure of Cytochrome P450 2B4 in Complex with the Inhibitor 1-Biphenyl-4-Methyl-1H-Imidazole
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Single Ligand Occupancy Crystal Structure of Cytochrome P450 2B4 in Complex with the Inhibitor 1-Biphenyl-4-Methyl-1H-Imidazole within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe500
b:30.3
occ:1.00
|
FE
|
C:HEM500
|
0.0
|
30.3
|
1.0
|
ND
|
C:HEM500
|
1.7
|
42.3
|
1.0
|
NC
|
C:HEM500
|
1.8
|
53.1
|
1.0
|
NA
|
C:HEM500
|
1.8
|
24.0
|
1.0
|
NAD
|
C:PB2501
|
1.9
|
27.1
|
1.0
|
NB
|
C:HEM500
|
2.1
|
43.7
|
1.0
|
SG
|
C:CYS436
|
2.3
|
28.1
|
1.0
|
CAE
|
C:PB2501
|
2.6
|
24.4
|
1.0
|
C1D
|
C:HEM500
|
2.7
|
47.9
|
1.0
|
C4D
|
C:HEM500
|
2.7
|
43.7
|
1.0
|
C4C
|
C:HEM500
|
2.8
|
39.1
|
1.0
|
C1A
|
C:HEM500
|
2.8
|
31.6
|
1.0
|
C1C
|
C:HEM500
|
2.9
|
41.6
|
1.0
|
C4A
|
C:HEM500
|
2.9
|
30.8
|
1.0
|
CAC
|
C:PB2501
|
3.0
|
35.5
|
1.0
|
C1B
|
C:HEM500
|
3.1
|
29.9
|
1.0
|
CHD
|
C:HEM500
|
3.1
|
31.2
|
1.0
|
C4B
|
C:HEM500
|
3.2
|
43.9
|
1.0
|
CHA
|
C:HEM500
|
3.2
|
40.8
|
1.0
|
CB
|
C:CYS436
|
3.3
|
29.9
|
1.0
|
CHB
|
C:HEM500
|
3.5
|
31.2
|
1.0
|
CHC
|
C:HEM500
|
3.5
|
34.6
|
1.0
|
CAF
|
C:PB2501
|
3.9
|
33.2
|
1.0
|
C2D
|
C:HEM500
|
3.9
|
44.4
|
1.0
|
C3D
|
C:HEM500
|
4.0
|
28.4
|
1.0
|
C3C
|
C:HEM500
|
4.0
|
32.3
|
1.0
|
C2C
|
C:HEM500
|
4.1
|
33.7
|
1.0
|
C2A
|
C:HEM500
|
4.1
|
32.6
|
1.0
|
NAB
|
C:PB2501
|
4.1
|
28.5
|
1.0
|
C3A
|
C:HEM500
|
4.1
|
37.8
|
1.0
|
CA
|
C:CYS436
|
4.2
|
29.2
|
1.0
|
C2B
|
C:HEM500
|
4.3
|
32.6
|
1.0
|
C3B
|
C:HEM500
|
4.3
|
45.4
|
1.0
|
N
|
C:GLY438
|
4.7
|
24.2
|
1.0
|
CA
|
C:GLY299
|
4.8
|
31.3
|
1.0
|
N
|
C:LEU437
|
4.8
|
28.1
|
1.0
|
C
|
C:CYS436
|
4.9
|
32.2
|
1.0
|
CA
|
C:GLY438
|
5.0
|
29.3
|
1.0
|
|
Iron binding site 4 out
of 4 in 3g93
Go back to
Iron Binding Sites List in 3g93
Iron binding site 4 out
of 4 in the Single Ligand Occupancy Crystal Structure of Cytochrome P450 2B4 in Complex with the Inhibitor 1-Biphenyl-4-Methyl-1H-Imidazole
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Single Ligand Occupancy Crystal Structure of Cytochrome P450 2B4 in Complex with the Inhibitor 1-Biphenyl-4-Methyl-1H-Imidazole within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe500
b:19.8
occ:1.00
|
FE
|
D:HEM500
|
0.0
|
19.8
|
1.0
|
NC
|
D:HEM500
|
2.0
|
25.9
|
1.0
|
ND
|
D:HEM500
|
2.0
|
17.1
|
1.0
|
NB
|
D:HEM500
|
2.0
|
24.2
|
1.0
|
NAD
|
D:PB2501
|
2.1
|
26.3
|
1.0
|
NA
|
D:HEM500
|
2.1
|
28.2
|
1.0
|
SG
|
D:CYS436
|
2.4
|
26.8
|
1.0
|
C4C
|
D:HEM500
|
2.9
|
28.1
|
1.0
|
C1D
|
D:HEM500
|
3.0
|
16.1
|
1.0
|
C1C
|
D:HEM500
|
3.0
|
24.7
|
1.0
|
CAC
|
D:PB2501
|
3.0
|
24.4
|
1.0
|
C1B
|
D:HEM500
|
3.1
|
24.2
|
1.0
|
C4B
|
D:HEM500
|
3.1
|
25.0
|
1.0
|
CAE
|
D:PB2501
|
3.1
|
27.1
|
1.0
|
C4A
|
D:HEM500
|
3.1
|
26.4
|
1.0
|
C4D
|
D:HEM500
|
3.1
|
26.0
|
1.0
|
C1A
|
D:HEM500
|
3.2
|
28.1
|
1.0
|
CHD
|
D:HEM500
|
3.3
|
23.1
|
1.0
|
CHC
|
D:HEM500
|
3.4
|
19.5
|
1.0
|
CHB
|
D:HEM500
|
3.5
|
23.1
|
1.0
|
CHA
|
D:HEM500
|
3.5
|
23.1
|
1.0
|
CB
|
D:CYS436
|
3.5
|
27.5
|
1.0
|
C3C
|
D:HEM500
|
4.2
|
23.2
|
1.0
|
C2C
|
D:HEM500
|
4.2
|
31.1
|
1.0
|
NAB
|
D:PB2501
|
4.2
|
39.6
|
1.0
|
C2D
|
D:HEM500
|
4.2
|
17.3
|
1.0
|
CAF
|
D:PB2501
|
4.3
|
28.3
|
1.0
|
C2B
|
D:HEM500
|
4.3
|
22.8
|
1.0
|
C3B
|
D:HEM500
|
4.3
|
37.4
|
1.0
|
C3D
|
D:HEM500
|
4.3
|
30.3
|
1.0
|
C3A
|
D:HEM500
|
4.3
|
26.1
|
1.0
|
C2A
|
D:HEM500
|
4.4
|
25.9
|
1.0
|
CA
|
D:CYS436
|
4.4
|
27.6
|
1.0
|
CA
|
D:GLY299
|
4.7
|
33.5
|
1.0
|
N
|
D:GLY438
|
4.9
|
25.6
|
1.0
|
|
Reference:
S.C.Gay,
L.Sun,
K.Maekawa,
J.R.Halpert,
C.D.Stout.
Crystal Structures of Cytochrome P450 2B4 in Complex with the Inhibitor 1-Biphenyl-4-Methyl-1H-Imidazole: Ligand-Induced Structural Response Through Alpha-Helical Repositioning. Biochemistry V. 48 4762 2009.
ISSN: ISSN 0006-2960
PubMed: 19397311
DOI: 10.1021/BI9003765
Page generated: Sun Aug 4 10:26:15 2024
|