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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

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