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Iron in PDB 3g5n: Triple Ligand Occupancy Crystal Structure of Cytochrome P450 2B4 in Complex with the Inhibitor 1-Biphenyl-4-Methyl-1H-Imidazole

Enzymatic activity of Triple Ligand Occupancy Crystal Structure of Cytochrome P450 2B4 in Complex with the Inhibitor 1-Biphenyl-4-Methyl-1H-Imidazole

All present enzymatic activity of Triple 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 Triple Ligand Occupancy Crystal Structure of Cytochrome P450 2B4 in Complex with the Inhibitor 1-Biphenyl-4-Methyl-1H-Imidazole, PDB code: 3g5n 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) 45.48 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.696, 152.526, 181.903, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 24.7

Iron Binding Sites:

The binding sites of Iron atom in the Triple Ligand Occupancy Crystal Structure of Cytochrome P450 2B4 in Complex with the Inhibitor 1-Biphenyl-4-Methyl-1H-Imidazole (pdb code 3g5n). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Triple Ligand Occupancy Crystal Structure of Cytochrome P450 2B4 in Complex with the Inhibitor 1-Biphenyl-4-Methyl-1H-Imidazole, PDB code: 3g5n:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3g5n

Go back to Iron Binding Sites List in 3g5n
Iron binding site 1 out of 4 in the Triple 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 Triple 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:37.6
occ:1.00
 FE A:HEM500 0.0 37.6 1.0
NB A:HEM500 1.8 42.6 1.0
ND A:HEM500 1.9 41.4 1.0
NC A:HEM500 1.9 49.0 1.0
NA A:HEM500 1.9 44.5 1.0
NAD A:PB2501 2.2 35.8 1.0
SG A:CYS436 2.3 40.3 1.0
C4B A:HEM500 2.9 44.0 1.0
C1B A:HEM500 2.9 41.7 1.0
C4D A:HEM500 2.9 43.9 1.0
C1C A:HEM500 2.9 45.5 1.0
C4A A:HEM500 3.0 42.2 1.0
C1D A:HEM500 3.0 42.5 1.0
C1A A:HEM500 3.0 43.8 1.0
C4C A:HEM500 3.0 45.4 1.0
CAC A:PB2501 3.1 36.4 1.0
CAE A:PB2501 3.2 39.1 1.0
CHC A:HEM500 3.3 44.0 1.0
CHB A:HEM500 3.3 46.9 1.0
CHA A:HEM500 3.4 52.9 1.0
CHD A:HEM500 3.4 49.0 1.0
CB A:CYS436 3.4 36.0 1.0
CA A:CYS436 4.0 45.4 1.0
C3B A:HEM500 4.1 39.2 1.0
C2B A:HEM500 4.1 44.3 1.0
C3D A:HEM500 4.2 46.9 1.0
C2C A:HEM500 4.2 50.1 1.0
C3A A:HEM500 4.2 45.2 1.0
C2D A:HEM500 4.2 34.9 1.0
C2A A:HEM500 4.2 44.5 1.0
C3C A:HEM500 4.2 41.5 1.0
NAB A:PB2501 4.3 36.3 1.0
CAF A:PB2501 4.3 34.0 1.0
CA A:GLY299 4.5 46.2 1.0
N A:GLY438 4.6 49.0 1.0
C A:CYS436 4.6 41.4 1.0
N A:LEU437 4.7 47.2 1.0

Iron binding site 2 out of 4 in 3g5n

Go back to Iron Binding Sites List in 3g5n
Iron binding site 2 out of 4 in the Triple 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 Triple 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:39.1
occ:1.00
 FE B:HEM500 0.0 39.1 1.0
NC B:HEM500 1.8 58.1 1.0
NB B:HEM500 1.9 43.1 1.0
ND B:HEM500 2.0 48.8 1.0
NAD B:PB2501 2.0 40.8 1.0
NA B:HEM500 2.1 41.5 1.0
SG B:CYS436 2.2 44.1 1.0
C4C B:HEM500 2.8 42.7 1.0
C1C B:HEM500 2.8 47.6 1.0
CAE B:PB2501 2.9 46.6 1.0
C4B B:HEM500 2.9 49.7 1.0
C1D B:HEM500 2.9 49.8 1.0
C1B B:HEM500 3.0 37.0 1.0
C4D B:HEM500 3.1 43.3 1.0
C4A B:HEM500 3.1 45.3 1.0
CAC B:PB2501 3.1 37.8 1.0
C1A B:HEM500 3.1 43.7 1.0
CHD B:HEM500 3.3 43.9 1.0
CHC B:HEM500 3.3 42.7 1.0
CHB B:HEM500 3.4 52.9 1.0
CB B:CYS436 3.4 40.7 1.0
CHA B:HEM500 3.5 49.1 1.0
C2C B:HEM500 4.0 49.9 1.0
C3C B:HEM500 4.0 50.5 1.0
CA B:CYS436 4.1 47.8 1.0
C3B B:HEM500 4.1 41.4 1.0
CAF B:PB2501 4.1 45.9 1.0
C2B B:HEM500 4.2 46.0 1.0
C2D B:HEM500 4.2 51.4 1.0
NAB B:PB2501 4.2 37.4 1.0
C3D B:HEM500 4.2 46.6 1.0
C3A B:HEM500 4.3 42.4 1.0
C2A B:HEM500 4.3 44.0 1.0
CA B:GLY299 4.4 46.8 1.0
N B:GLY438 4.7 52.2 1.0
C B:CYS436 4.7 50.6 1.0
N B:LEU437 4.8 51.1 1.0

Iron binding site 3 out of 4 in 3g5n

Go back to Iron Binding Sites List in 3g5n
Iron binding site 3 out of 4 in the Triple 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 Triple 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:50.2
occ:1.00
 FE C:HEM500 0.0 50.2 1.0
NB C:HEM500 1.7 61.9 1.0
NC C:HEM500 1.9 51.2 1.0
NA C:HEM500 1.9 47.1 1.0
ND C:HEM500 2.1 46.1 1.0
SG C:CYS436 2.2 42.5 1.0
NAD C:PB2501 2.3 32.5 1.0
C4B C:HEM500 2.7 61.2 1.0
C1B C:HEM500 2.8 50.3 1.0
C1C C:HEM500 2.9 56.3 1.0
C4A C:HEM500 3.0 51.9 1.0
C4C C:HEM500 3.0 53.5 1.0
C1A C:HEM500 3.0 49.9 1.0
CAC C:PB2501 3.0 50.8 1.0
C1D C:HEM500 3.1 56.1 1.0
C4D C:HEM500 3.1 49.2 1.0
CHC C:HEM500 3.2 51.5 1.0
CHB C:HEM500 3.3 58.3 1.0
CB C:CYS436 3.4 44.0 1.0
CAE C:PB2501 3.4 52.7 1.0
CHA C:HEM500 3.4 51.4 1.0
CHD C:HEM500 3.5 62.2 1.0
C3B C:HEM500 3.9 58.3 1.0
CA C:CYS436 4.0 49.9 1.0
C2B C:HEM500 4.0 59.8 1.0
C2C C:HEM500 4.1 60.2 1.0
C3C C:HEM500 4.2 59.1 1.0
C3A C:HEM500 4.2 37.3 1.0
C2A C:HEM500 4.2 45.4 1.0
C2D C:HEM500 4.3 52.6 1.0
NAB C:PB2501 4.3 35.6 1.0
C3D C:HEM500 4.3 52.1 1.0
CAF C:PB2501 4.5 52.2 1.0
N C:GLY438 4.5 52.0 1.0
CA C:GLY299 4.5 46.4 1.0
C C:CYS436 4.6 49.0 1.0
N C:LEU437 4.6 53.2 1.0
CA C:GLY438 5.0 53.1 1.0
CD1 C:PHE429 5.0 45.0 1.0

Iron binding site 4 out of 4 in 3g5n

Go back to Iron Binding Sites List in 3g5n
Iron binding site 4 out of 4 in the Triple 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 Triple 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:40.4
occ:1.00
 FE D:HEM500 0.0 40.4 1.0
NC D:HEM500 1.8 60.5 1.0
NA D:HEM500 1.9 53.3 1.0
NB D:HEM500 2.0 56.8 1.0
ND D:HEM500 2.0 47.4 1.0
NAD D:PB2501 2.0 35.1 1.0
SG D:CYS436 2.3 38.5 1.0
C4C D:HEM500 2.9 49.9 1.0
CAE D:PB2501 2.9 44.3 1.0
C1C D:HEM500 2.9 55.6 1.0
C4A D:HEM500 3.0 51.4 1.0
C1D D:HEM500 3.0 54.5 1.0
C1B D:HEM500 3.0 54.2 1.0
C4B D:HEM500 3.0 56.2 1.0
C1A D:HEM500 3.0 58.6 1.0
C4D D:HEM500 3.0 52.1 1.0
CAC D:PB2501 3.2 43.0 1.0
CHD D:HEM500 3.3 51.1 1.0
CHC D:HEM500 3.4 55.9 1.0
CB D:CYS436 3.4 40.3 1.0
CHB D:HEM500 3.4 51.1 1.0
CHA D:HEM500 3.4 54.2 1.0
C3C D:HEM500 4.1 49.5 1.0
C2C D:HEM500 4.1 60.0 1.0
CA D:CYS436 4.1 49.0 1.0
CAF D:PB2501 4.2 32.2 1.0
C3A D:HEM500 4.2 45.2 1.0
C2B D:HEM500 4.2 61.9 1.0
C2A D:HEM500 4.2 43.8 1.0
C3B D:HEM500 4.2 56.0 1.0
C2D D:HEM500 4.2 48.9 1.0
C3D D:HEM500 4.3 49.4 1.0
NAB D:PB2501 4.3 36.8 1.0
CA D:GLY299 4.4 45.2 1.0
N D:GLY438 4.6 51.4 1.0
C D:CYS436 4.7 48.8 1.0
N D:LEU437 4.7 51.9 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 10:25:29 2024

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