Atomistry » Iron » PDB 3b9j-3by0 » 3ben
Atomistry »
  Iron »
    PDB 3b9j-3by0 »
      3ben »

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: Sun Aug 4 07:51:47 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