Atomistry » Iron » PDB 3fpv-3gcj » 3g5n
Atomistry »
  Iron »
    PDB 3fpv-3gcj »
      3g5n »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy