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Iron in PDB 3ben: Structure of N-(12-Imidazolyl-Dodecanoyl)-L-Leucine Inhibitor Bound to the Heme Domain of Cytochrome P450-BM3

Enzymatic activity of Structure of N-(12-Imidazolyl-Dodecanoyl)-L-Leucine Inhibitor Bound to the Heme Domain of Cytochrome P450-BM3

All present enzymatic activity of Structure of N-(12-Imidazolyl-Dodecanoyl)-L-Leucine Inhibitor Bound to the Heme Domain of Cytochrome P450-BM3:
1.14.14.1;

Protein crystallography data

The structure of Structure of N-(12-Imidazolyl-Dodecanoyl)-L-Leucine Inhibitor Bound to the Heme Domain of Cytochrome P450-BM3, PDB code: 3ben was solved by D.R.Tomchick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.820, 148.209, 63.792, 90.00, 98.32, 90.00
R / Rfree (%) 16.1 / 19.1

Other elements in 3ben:

The structure of Structure of N-(12-Imidazolyl-Dodecanoyl)-L-Leucine Inhibitor Bound to the Heme Domain of Cytochrome P450-BM3 also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Structure of N-(12-Imidazolyl-Dodecanoyl)-L-Leucine Inhibitor Bound to the Heme Domain of Cytochrome P450-BM3 (pdb code 3ben). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of N-(12-Imidazolyl-Dodecanoyl)-L-Leucine Inhibitor Bound to the Heme Domain of Cytochrome P450-BM3, PDB code: 3ben:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3ben

Go back to Iron Binding Sites List in 3ben
Iron binding site 1 out of 4 in the Structure of N-(12-Imidazolyl-Dodecanoyl)-L-Leucine Inhibitor Bound to the Heme Domain of Cytochrome P450-BM3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of N-(12-Imidazolyl-Dodecanoyl)-L-Leucine Inhibitor Bound to the Heme Domain of Cytochrome P450-BM3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe470

b:12.3
occ:0.50
FE A:HEM470 0.0 12.3 0.5
FE A:HEM470 0.4 10.2 0.5
NC A:HEM470 1.8 8.9 0.5
ND A:HEM470 2.0 10.4 0.5
NC A:HEM470 2.0 13.1 0.5
NB A:HEM470 2.0 11.3 0.5
NA A:HEM470 2.1 12.9 0.5
ND A:HEM470 2.1 12.4 0.5
SG A:CYS400 2.1 8.9 1.0
NB A:HEM470 2.2 10.6 0.5
NA A:HEM470 2.3 10.8 0.5
N3 A:LEH500 2.3 15.6 1.0
C4C A:HEM470 2.8 9.0 0.5
C1D A:HEM470 2.9 9.6 0.5
C1C A:HEM470 2.9 9.3 0.5
C4B A:HEM470 3.0 12.2 0.5
C1C A:HEM470 3.0 12.5 0.5
C4C A:HEM470 3.1 12.4 0.5
C1D A:HEM470 3.1 12.3 0.5
C1B A:HEM470 3.1 11.4 0.5
C1A A:HEM470 3.1 11.2 0.5
C4A A:HEM470 3.1 11.5 0.5
C4D A:HEM470 3.1 11.4 0.5
C4B A:HEM470 3.1 9.9 0.5
C4D A:HEM470 3.1 9.0 0.5
CHD A:HEM470 3.1 9.2 0.5
C21 A:LEH500 3.2 19.8 1.0
CB A:CYS400 3.2 6.9 1.0
C1B A:HEM470 3.3 10.2 0.5
C1A A:HEM470 3.3 9.1 0.5
C19 A:LEH500 3.3 21.7 1.0
C4A A:HEM470 3.3 11.0 0.5
CHC A:HEM470 3.4 10.2 0.5
CHC A:HEM470 3.4 12.4 0.5
CHD A:HEM470 3.4 12.5 0.5
CHA A:HEM470 3.5 11.6 0.5
CHB A:HEM470 3.5 11.4 0.5
CHA A:HEM470 3.6 9.2 0.5
CHB A:HEM470 3.7 10.2 0.5
CA A:CYS400 3.9 6.5 1.0
C3C A:HEM470 4.0 9.6 0.5
C2C A:HEM470 4.1 8.9 0.5
C2D A:HEM470 4.1 9.1 0.5
C3B A:HEM470 4.2 12.0 0.5
C2C A:HEM470 4.3 12.7 0.5
C2B A:HEM470 4.3 11.7 0.5
C20 A:LEH500 4.3 21.9 1.0
C3D A:HEM470 4.3 9.4 0.5
C3C A:HEM470 4.3 12.4 0.5
C3A A:HEM470 4.3 11.4 0.5
C2A A:HEM470 4.3 11.8 0.5
C2D A:HEM470 4.3 11.4 0.5
C3D A:HEM470 4.3 10.5 0.5
N2 A:LEH500 4.3 20.6 1.0
C3B A:HEM470 4.4 10.9 0.5
C2B A:HEM470 4.4 9.7 0.5
C2A A:HEM470 4.5 9.0 0.5
C3A A:HEM470 4.5 9.7 0.5
C A:CYS400 4.7 8.4 1.0
N A:GLY402 4.8 7.5 1.0
N A:ILE401 4.9 7.7 1.0

Iron binding site 2 out of 4 in 3ben

Go back to Iron Binding Sites List in 3ben
Iron binding site 2 out of 4 in the Structure of N-(12-Imidazolyl-Dodecanoyl)-L-Leucine Inhibitor Bound to the Heme Domain of Cytochrome P450-BM3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of N-(12-Imidazolyl-Dodecanoyl)-L-Leucine Inhibitor Bound to the Heme Domain of Cytochrome P450-BM3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe470

b:10.2
occ:0.50
FE A:HEM470 0.0 10.2 0.5
FE A:HEM470 0.4 12.3 0.5
ND A:HEM470 1.8 12.4 0.5
NC A:HEM470 1.9 13.1 0.5
NC A:HEM470 2.0 8.9 0.5
NB A:HEM470 2.0 10.6 0.5
ND A:HEM470 2.0 10.4 0.5
NA A:HEM470 2.0 10.8 0.5
N3 A:LEH500 2.1 15.6 1.0
NA A:HEM470 2.2 12.9 0.5
NB A:HEM470 2.3 11.3 0.5
SG A:CYS400 2.4 8.9 1.0
C1D A:HEM470 2.8 12.3 0.5
C4C A:HEM470 2.9 12.4 0.5
C4D A:HEM470 2.9 11.4 0.5
C19 A:LEH500 3.0 21.7 1.0
C4C A:HEM470 3.0 9.0 0.5
C21 A:LEH500 3.0 19.8 1.0
C1C A:HEM470 3.0 12.5 0.5
C1D A:HEM470 3.0 9.6 0.5
C4B A:HEM470 3.1 9.9 0.5
C1B A:HEM470 3.1 10.2 0.5
C4A A:HEM470 3.1 11.0 0.5
C1A A:HEM470 3.1 9.1 0.5
C1C A:HEM470 3.1 9.3 0.5
C4D A:HEM470 3.1 9.0 0.5
C1A A:HEM470 3.1 11.2 0.5
CHD A:HEM470 3.2 12.5 0.5
C4B A:HEM470 3.2 12.2 0.5
C4A A:HEM470 3.3 11.5 0.5
C1B A:HEM470 3.3 11.4 0.5
CHD A:HEM470 3.4 9.2 0.5
CHA A:HEM470 3.4 11.6 0.5
CHB A:HEM470 3.4 10.2 0.5
CB A:CYS400 3.5 6.9 1.0
CHC A:HEM470 3.5 10.2 0.5
CHA A:HEM470 3.5 9.2 0.5
CHC A:HEM470 3.5 12.4 0.5
CHB A:HEM470 3.7 11.4 0.5
C20 A:LEH500 4.1 21.9 1.0
N2 A:LEH500 4.1 20.6 1.0
C2D A:HEM470 4.1 11.4 0.5
CA A:CYS400 4.1 6.5 1.0
C3D A:HEM470 4.1 10.5 0.5
C3C A:HEM470 4.2 12.4 0.5
C2C A:HEM470 4.2 12.7 0.5
C3C A:HEM470 4.2 9.6 0.5
C2C A:HEM470 4.3 8.9 0.5
C2D A:HEM470 4.3 9.1 0.5
C3B A:HEM470 4.3 10.9 0.5
C2A A:HEM470 4.3 9.0 0.5
C3A A:HEM470 4.3 9.7 0.5
C2B A:HEM470 4.3 9.7 0.5
C3D A:HEM470 4.3 9.4 0.5
C2A A:HEM470 4.4 11.8 0.5
C3A A:HEM470 4.4 11.4 0.5
C3B A:HEM470 4.5 12.0 0.5
C2B A:HEM470 4.5 11.7 0.5
CB A:ALA264 4.8 15.1 1.0
N A:GLY402 4.8 7.5 1.0
C A:CYS400 4.8 8.4 1.0
N A:ILE401 4.9 7.7 1.0

Iron binding site 3 out of 4 in 3ben

Go back to Iron Binding Sites List in 3ben
Iron binding site 3 out of 4 in the Structure of N-(12-Imidazolyl-Dodecanoyl)-L-Leucine Inhibitor Bound to the Heme Domain of Cytochrome P450-BM3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of N-(12-Imidazolyl-Dodecanoyl)-L-Leucine Inhibitor Bound to the Heme Domain of Cytochrome P450-BM3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe471

b:12.3
occ:0.50
FE B:HEM471 0.0 12.3 0.5
FE B:HEM471 0.3 12.1 0.5
NC B:HEM471 1.9 13.0 0.5
NB B:HEM471 2.0 12.2 0.5
NB B:HEM471 2.0 12.2 0.5
NA B:HEM471 2.0 12.4 0.5
ND B:HEM471 2.1 12.6 0.5
NC B:HEM471 2.1 12.2 0.5
ND B:HEM471 2.1 12.3 0.5
SG B:CYS400 2.1 9.1 1.0
NA B:HEM471 2.2 13.0 0.5
N3 B:LEH500 2.4 18.0 1.0
C1C B:HEM471 2.9 11.3 0.5
C4C B:HEM471 3.0 12.6 0.5
C4B B:HEM471 3.0 12.0 0.5
C1B B:HEM471 3.0 12.2 0.5
C4B B:HEM471 3.0 12.4 0.5
C4A B:HEM471 3.0 11.5 0.5
C1D B:HEM471 3.1 11.5 0.5
C1C B:HEM471 3.1 12.4 0.5
C1B B:HEM471 3.1 12.4 0.5
C1A B:HEM471 3.1 10.9 0.5
C1D B:HEM471 3.1 11.8 0.5
C4D B:HEM471 3.1 11.2 0.5
C4C B:HEM471 3.1 12.5 0.5
C4D B:HEM471 3.1 10.9 0.5
C1A B:HEM471 3.2 11.9 0.5
C4A B:HEM471 3.2 12.5 0.5
CB B:CYS400 3.2 8.7 1.0
C19 B:LEH500 3.2 21.3 1.0
CHC B:HEM471 3.4 12.0 0.5
C21 B:LEH500 3.4 21.9 1.0
CHB B:HEM471 3.4 11.4 0.5
CHD B:HEM471 3.4 11.6 0.5
CHC B:HEM471 3.4 12.4 0.5
CHD B:HEM471 3.5 11.7 0.5
CHA B:HEM471 3.5 11.6 0.5
CHA B:HEM471 3.5 11.3 0.5
CHB B:HEM471 3.5 12.4 0.5
CA B:CYS400 3.9 7.0 1.0
C2C B:HEM471 4.1 12.0 0.5
C3C B:HEM471 4.2 12.3 0.5
C2B B:HEM471 4.2 11.8 0.5
C3B B:HEM471 4.2 11.8 0.5
C3B B:HEM471 4.2 12.8 0.5
C2B B:HEM471 4.2 10.8 0.5
C3A B:HEM471 4.3 11.1 0.5
C2A B:HEM471 4.3 11.0 0.5
C2C B:HEM471 4.3 10.9 0.5
C2D B:HEM471 4.3 11.8 0.5
C3C B:HEM471 4.3 11.9 0.5
C3D B:HEM471 4.3 11.4 0.5
C2D B:HEM471 4.3 10.1 0.5
N2 B:LEH500 4.4 22.3 1.0
C3D B:HEM471 4.4 10.4 0.5
C20 B:LEH500 4.4 22.0 1.0
C2A B:HEM471 4.4 12.3 0.5
C3A B:HEM471 4.4 11.5 0.5
N B:GLY402 4.7 8.6 1.0
C B:CYS400 4.7 9.7 1.0
N B:ILE401 4.8 7.9 1.0
CB B:ALA264 5.0 18.2 1.0

Iron binding site 4 out of 4 in 3ben

Go back to Iron Binding Sites List in 3ben
Iron binding site 4 out of 4 in the Structure of N-(12-Imidazolyl-Dodecanoyl)-L-Leucine Inhibitor Bound to the Heme Domain of Cytochrome P450-BM3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of N-(12-Imidazolyl-Dodecanoyl)-L-Leucine Inhibitor Bound to the Heme Domain of Cytochrome P450-BM3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe471

b:12.1
occ:0.50
FE B:HEM471 0.0 12.1 0.5
FE B:HEM471 0.3 12.3 0.5
ND B:HEM471 2.0 12.3 0.5
NB B:HEM471 2.0 12.2 0.5
NA B:HEM471 2.0 13.0 0.5
NC B:HEM471 2.0 12.2 0.5
NC B:HEM471 2.1 13.0 0.5
NA B:HEM471 2.1 12.4 0.5
NB B:HEM471 2.1 12.2 0.5
N3 B:LEH500 2.1 18.0 1.0
ND B:HEM471 2.1 12.6 0.5
SG B:CYS400 2.4 9.1 1.0
C19 B:LEH500 2.9 21.3 1.0
C1D B:HEM471 2.9 11.8 0.5
C4B B:HEM471 3.0 12.0 0.5
C1B B:HEM471 3.0 12.4 0.5
C4C B:HEM471 3.0 12.5 0.5
C1A B:HEM471 3.0 11.9 0.5
C4D B:HEM471 3.0 10.9 0.5
C4A B:HEM471 3.0 12.5 0.5
C1C B:HEM471 3.1 12.4 0.5
C1C B:HEM471 3.1 11.3 0.5
C1A B:HEM471 3.1 10.9 0.5
C4D B:HEM471 3.1 11.2 0.5
C1B B:HEM471 3.1 12.2 0.5
C4A B:HEM471 3.1 11.5 0.5
C4C B:HEM471 3.1 12.6 0.5
C4B B:HEM471 3.1 12.4 0.5
C21 B:LEH500 3.1 21.9 1.0
C1D B:HEM471 3.1 11.5 0.5
CHD B:HEM471 3.4 11.7 0.5
CHB B:HEM471 3.4 12.4 0.5
CHA B:HEM471 3.4 11.6 0.5
CHC B:HEM471 3.4 12.0 0.5
CHA B:HEM471 3.5 11.3 0.5
CHB B:HEM471 3.5 11.4 0.5
CHC B:HEM471 3.5 12.4 0.5
CHD B:HEM471 3.5 11.6 0.5
CB B:CYS400 3.5 8.7 1.0
N2 B:LEH500 4.0 22.3 1.0
C20 B:LEH500 4.1 22.0 1.0
CA B:CYS400 4.1 7.0 1.0
C2D B:HEM471 4.2 10.1 0.5
C2B B:HEM471 4.2 10.8 0.5
C3B B:HEM471 4.2 11.8 0.5
C3D B:HEM471 4.2 10.4 0.5
C3C B:HEM471 4.2 11.9 0.5
C3A B:HEM471 4.3 11.5 0.5
C2A B:HEM471 4.3 12.3 0.5
C2C B:HEM471 4.3 10.9 0.5
C2A B:HEM471 4.3 11.0 0.5
C2C B:HEM471 4.3 12.0 0.5
C3A B:HEM471 4.3 11.1 0.5
C3C B:HEM471 4.3 12.3 0.5
C2B B:HEM471 4.3 11.8 0.5
C3B B:HEM471 4.3 12.8 0.5
C3D B:HEM471 4.3 11.4 0.5
C2D B:HEM471 4.4 11.8 0.5
CB B:ALA264 4.8 18.2 1.0
N B:GLY402 4.8 8.6 1.0
C B:CYS400 4.9 9.7 1.0
N B:ILE401 5.0 7.9 1.0

Reference:

D.C.Haines, B.Chen, D.R.Tomchick, M.Bondlela, A.Hegde, M.Machius, J.A.Peterson. Crystal Structure of Inhibitor-Bound P450BM-3 Reveals Open Conformation of Substrate Access Channel. Biochemistry V. 47 3662 2008.
ISSN: ISSN 0006-2960
PubMed: 18298086
DOI: 10.1021/BI7023964
Page generated: Mon Aug 4 23:52:59 2025

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