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Iron in PDB 2q6n: Structure of Cytochrome P450 2B4 with Bound 1-(4- Cholorophenyl)Imidazole

Enzymatic activity of Structure of Cytochrome P450 2B4 with Bound 1-(4- Cholorophenyl)Imidazole

All present enzymatic activity of Structure of Cytochrome P450 2B4 with Bound 1-(4- Cholorophenyl)Imidazole:
1.14.14.1;

Protein crystallography data

The structure of Structure of Cytochrome P450 2B4 with Bound 1-(4- Cholorophenyl)Imidazole, PDB code: 2q6n was solved by Y.Zhao, L.Sun, B.K.Muralidhara, S.Kumar, M.A.White, C.D.Stout, J.R.Halpert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 3.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 140.000, 147.310, 238.490, 90.00, 90.00, 90.00
R / Rfree (%) 23.3 / 31.1

Other elements in 2q6n:

The structure of Structure of Cytochrome P450 2B4 with Bound 1-(4- Cholorophenyl)Imidazole also contains other interesting chemical elements:

Chlorine (Cl) 7 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Cytochrome P450 2B4 with Bound 1-(4- Cholorophenyl)Imidazole (pdb code 2q6n). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 7 binding sites of Iron where determined in the Structure of Cytochrome P450 2B4 with Bound 1-(4- Cholorophenyl)Imidazole, PDB code: 2q6n:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7;

Iron binding site 1 out of 7 in 2q6n

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Iron binding site 1 out of 7 in the Structure of Cytochrome P450 2B4 with Bound 1-(4- Cholorophenyl)Imidazole


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Cytochrome P450 2B4 with Bound 1-(4- Cholorophenyl)Imidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:78.8
occ:1.00
 FE A:HEM500 0.0 78.8 1.0
NA A:HEM500 2.0 78.8 1.0
ND A:HEM500 2.1 78.8 1.0
NC A:HEM500 2.1 78.8 1.0
NB A:HEM500 2.1 78.8 1.0
N3 A:1CI501 2.1 0.0 1.0
SG A:CYS436 2.3 67.4 1.0
C1D A:HEM500 3.0 78.8 1.0
C1C A:HEM500 3.0 78.8 1.0
C4B A:HEM500 3.0 78.8 1.0
C4A A:HEM500 3.0 78.8 1.0
C1B A:HEM500 3.0 78.8 1.0
C4D A:HEM500 3.0 78.8 1.0
C4C A:HEM500 3.1 78.8 1.0
C1A A:HEM500 3.1 78.8 1.0
C4 A:1CI501 3.1 0.0 1.0
C2 A:1CI501 3.1 0.0 1.0
CHB A:HEM500 3.3 78.8 1.0
CHC A:HEM500 3.3 78.8 1.0
CHD A:HEM500 3.3 78.8 1.0
CHA A:HEM500 3.4 78.8 1.0
CB A:CYS436 3.4 67.4 1.0
CA A:CYS436 4.2 85.2 1.0
C2D A:HEM500 4.2 78.8 1.0
C2C A:HEM500 4.2 78.8 1.0
C3A A:HEM500 4.2 78.8 1.0
C5 A:1CI501 4.2 0.0 1.0
N1 A:1CI501 4.2 0.0 1.0
C2A A:HEM500 4.2 78.8 1.0
C3B A:HEM500 4.3 78.8 1.0
C3D A:HEM500 4.3 78.8 1.0
C3C A:HEM500 4.3 78.8 1.0
C2B A:HEM500 4.3 78.8 1.0
CB A:ALA298 4.7 39.1 1.0
C A:CYS436 4.9 85.2 1.0
N A:LEU437 5.0 92.4 1.0

Iron binding site 2 out of 7 in 2q6n

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Iron binding site 2 out of 7 in the Structure of Cytochrome P450 2B4 with Bound 1-(4- Cholorophenyl)Imidazole


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Cytochrome P450 2B4 with Bound 1-(4- Cholorophenyl)Imidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe500

b:78.4
occ:1.00
 FE B:HEM500 0.0 78.4 1.0
NB B:HEM500 2.0 78.4 1.0
NC B:HEM500 2.1 78.4 1.0
NA B:HEM500 2.1 78.4 1.0
ND B:HEM500 2.1 78.4 1.0
SG B:CYS436 2.3 70.2 1.0
N3 B:1CI501 2.7 0.0 1.0
C4B B:HEM500 3.0 78.4 1.0
C1C B:HEM500 3.0 78.4 1.0
C1D B:HEM500 3.0 78.4 1.0
C4A B:HEM500 3.0 78.4 1.0
C1B B:HEM500 3.0 78.4 1.0
C4C B:HEM500 3.1 78.4 1.0
C4D B:HEM500 3.1 78.4 1.0
C1A B:HEM500 3.1 78.4 1.0
CHC B:HEM500 3.3 78.4 1.0
CHB B:HEM500 3.3 78.4 1.0
CHD B:HEM500 3.3 78.4 1.0
CHA B:HEM500 3.4 78.4 1.0
CB B:CYS436 3.5 70.2 1.0
C4 B:1CI501 3.5 0.0 1.0
C2 B:1CI501 3.7 0.0 1.0
CA B:CYS436 4.1 92.4 1.0
C2C B:HEM500 4.2 78.4 1.0
C2D B:HEM500 4.2 78.4 1.0
C3B B:HEM500 4.2 78.4 1.0
C3A B:HEM500 4.3 78.4 1.0
C3C B:HEM500 4.3 78.4 1.0
C2B B:HEM500 4.3 78.4 1.0
C3D B:HEM500 4.3 78.4 1.0
C2A B:HEM500 4.3 78.4 1.0
C B:CYS436 4.7 92.4 1.0
C5 B:1CI501 4.7 0.0 1.0
N B:GLY438 4.7 80.1 1.0
N B:LEU437 4.8 91.8 1.0
N1 B:1CI501 4.8 0.0 1.0
OG1 B:THR302 4.9 0.8 1.0

Iron binding site 3 out of 7 in 2q6n

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Iron binding site 3 out of 7 in the Structure of Cytochrome P450 2B4 with Bound 1-(4- Cholorophenyl)Imidazole


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Cytochrome P450 2B4 with Bound 1-(4- Cholorophenyl)Imidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe500

b:93.6
occ:1.00
 FE C:HEM500 0.0 93.6 1.0
ND C:HEM500 2.1 93.6 1.0
NC C:HEM500 2.1 93.6 1.0
NA C:HEM500 2.1 93.6 1.0
NB C:HEM500 2.1 93.6 1.0
SG C:CYS436 2.5 0.6 1.0
N3 C:1CI501 2.5 0.0 1.0
C1D C:HEM500 3.0 93.6 1.0
C4 C:1CI501 3.0 0.0 1.0
C1C C:HEM500 3.0 93.6 1.0
C4B C:HEM500 3.0 93.6 1.0
C4D C:HEM500 3.0 93.6 1.0
C4A C:HEM500 3.0 93.6 1.0
C1B C:HEM500 3.0 93.6 1.0
C4C C:HEM500 3.1 93.6 1.0
C1A C:HEM500 3.1 93.6 1.0
CHC C:HEM500 3.3 93.6 1.0
CHD C:HEM500 3.3 93.6 1.0
CHB C:HEM500 3.3 93.6 1.0
CHA C:HEM500 3.4 93.6 1.0
CB C:CYS436 3.5 0.6 1.0
C2 C:1CI501 3.6 0.0 1.0
CA C:CYS436 4.2 0.4 1.0
C2D C:HEM500 4.2 93.6 1.0
C2C C:HEM500 4.2 93.6 1.0
C5 C:1CI501 4.2 0.0 1.0
C3A C:HEM500 4.3 93.6 1.0
C3D C:HEM500 4.3 93.6 1.0
C3B C:HEM500 4.3 93.6 1.0
C3C C:HEM500 4.3 93.6 1.0
C2B C:HEM500 4.3 93.6 1.0
C2A C:HEM500 4.3 93.6 1.0
N1 C:1CI501 4.5 0.0 1.0
CB C:ALA298 4.6 0.5 1.0
C C:CYS436 4.8 0.4 1.0
OG1 C:THR302 4.9 0.3 1.0
N C:GLY438 4.9 0.1 1.0
N C:LEU437 5.0 0.2 1.0
O C:ALA298 5.0 87.2 1.0

Iron binding site 4 out of 7 in 2q6n

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Iron binding site 4 out of 7 in the Structure of Cytochrome P450 2B4 with Bound 1-(4- Cholorophenyl)Imidazole


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Cytochrome P450 2B4 with Bound 1-(4- Cholorophenyl)Imidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe500

b:0.6
occ:1.00
 FE D:HEM500 0.0 0.6 1.0
ND D:HEM500 2.1 0.6 1.0
NA D:HEM500 2.1 0.6 1.0
NB D:HEM500 2.1 0.6 1.0
NC D:HEM500 2.1 0.6 1.0
SG D:CYS436 2.1 98.2 1.0
N3 D:1CI501 2.4 0.0 1.0
C4 D:1CI501 2.9 0.0 1.0
C1D D:HEM500 3.0 0.6 1.0
C1C D:HEM500 3.0 0.6 1.0
C4B D:HEM500 3.0 0.6 1.0
C4A D:HEM500 3.0 0.6 1.0
C1B D:HEM500 3.0 0.6 1.0
C4D D:HEM500 3.0 0.6 1.0
C4C D:HEM500 3.1 0.6 1.0
C1A D:HEM500 3.1 0.6 1.0
CHC D:HEM500 3.3 0.6 1.0
CHB D:HEM500 3.3 0.6 1.0
CHD D:HEM500 3.3 0.6 1.0
CHA D:HEM500 3.4 0.6 1.0
CB D:CYS436 3.4 98.2 1.0
C2 D:1CI501 3.6 0.0 1.0
C5 D:1CI501 4.2 0.0 1.0
CA D:CYS436 4.2 0.9 1.0
C2D D:HEM500 4.2 0.6 1.0
C2C D:HEM500 4.2 0.6 1.0
C3A D:HEM500 4.2 0.6 1.0
C3D D:HEM500 4.3 0.6 1.0
C3B D:HEM500 4.3 0.6 1.0
C3C D:HEM500 4.3 0.6 1.0
C2B D:HEM500 4.3 0.6 1.0
C2A D:HEM500 4.3 0.6 1.0
N1 D:1CI501 4.5 0.0 1.0
N D:GLY438 4.6 0.3 1.0
N D:LEU437 4.7 93.5 1.0
C D:CYS436 4.8 0.9 1.0
CB D:ALA298 4.9 86.7 1.0

Iron binding site 5 out of 7 in 2q6n

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Iron binding site 5 out of 7 in the Structure of Cytochrome P450 2B4 with Bound 1-(4- Cholorophenyl)Imidazole


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of Cytochrome P450 2B4 with Bound 1-(4- Cholorophenyl)Imidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe500

b:69.9
occ:1.00
 FE E:HEM500 0.0 69.9 1.0
NA E:HEM500 2.0 69.9 1.0
ND E:HEM500 2.1 69.9 1.0
NB E:HEM500 2.1 69.9 1.0
NC E:HEM500 2.1 69.9 1.0
SG E:CYS436 2.8 0.2 1.0
N3 E:1CI501 2.9 0.0 1.0
C1D E:HEM500 3.0 69.9 1.0
C4B E:HEM500 3.0 69.9 1.0
C4A E:HEM500 3.0 69.9 1.0
C1C E:HEM500 3.0 69.9 1.0
C4D E:HEM500 3.0 69.9 1.0
C1B E:HEM500 3.0 69.9 1.0
C4C E:HEM500 3.1 69.9 1.0
C1A E:HEM500 3.1 69.9 1.0
CHB E:HEM500 3.3 69.9 1.0
CHC E:HEM500 3.3 69.9 1.0
CHD E:HEM500 3.3 69.9 1.0
CHA E:HEM500 3.4 69.9 1.0
CB E:CYS436 3.6 0.2 1.0
C2 E:1CI501 3.6 0.0 1.0
C4 E:1CI501 4.0 0.0 1.0
CA E:CYS436 4.1 0.6 1.0
C2D E:HEM500 4.2 69.9 1.0
C2C E:HEM500 4.2 69.9 1.0
C3A E:HEM500 4.2 69.9 1.0
C3D E:HEM500 4.2 69.9 1.0
C3B E:HEM500 4.3 69.9 1.0
C2A E:HEM500 4.3 69.9 1.0
C3C E:HEM500 4.3 69.9 1.0
C2B E:HEM500 4.3 69.9 1.0
N E:GLY438 4.7 83.1 1.0
N E:LEU437 4.7 0.8 1.0
C E:CYS436 4.8 0.6 1.0
N1 E:1CI501 4.8 0.0 1.0
CB E:ALA298 5.0 66.0 1.0

Iron binding site 6 out of 7 in 2q6n

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Iron binding site 6 out of 7 in the Structure of Cytochrome P450 2B4 with Bound 1-(4- Cholorophenyl)Imidazole


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of Cytochrome P450 2B4 with Bound 1-(4- Cholorophenyl)Imidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe500

b:0.3
occ:1.00
 FE F:HEM500 0.0 0.3 1.0
NB F:HEM500 2.1 0.3 1.0
ND F:HEM500 2.1 0.3 1.0
NA F:HEM500 2.1 0.3 1.0
NC F:HEM500 2.1 0.3 1.0
SG F:CYS436 2.3 0.0 1.0
N3 F:1CI501 2.5 0.0 1.0
C4B F:HEM500 3.0 0.3 1.0
C1D F:HEM500 3.0 0.3 1.0
C1C F:HEM500 3.0 0.3 1.0
C1B F:HEM500 3.0 0.3 1.0
C4A F:HEM500 3.0 0.3 1.0
C4D F:HEM500 3.0 0.3 1.0
C1A F:HEM500 3.1 0.3 1.0
C4C F:HEM500 3.1 0.3 1.0
C4 F:1CI501 3.1 0.0 1.0
CHC F:HEM500 3.3 0.3 1.0
CHB F:HEM500 3.3 0.3 1.0
CHD F:HEM500 3.3 0.3 1.0
CHA F:HEM500 3.4 0.3 1.0
CB F:CYS436 3.6 0.0 1.0
C2 F:1CI501 3.6 0.0 1.0
C2D F:HEM500 4.2 0.3 1.0
C2C F:HEM500 4.2 0.3 1.0
C3A F:HEM500 4.2 0.3 1.0
C3B F:HEM500 4.2 0.3 1.0
C3D F:HEM500 4.3 0.3 1.0
CA F:CYS436 4.3 0.1 1.0
C2B F:HEM500 4.3 0.3 1.0
C2A F:HEM500 4.3 0.3 1.0
C3C F:HEM500 4.3 0.3 1.0
C5 F:1CI501 4.3 0.0 1.0
N1 F:1CI501 4.5 0.0 1.0
CB F:ALA298 4.6 59.7 1.0
C F:CYS436 4.9 0.1 1.0
N F:LEU437 4.9 0.7 1.0
CD1 F:PHE429 4.9 0.9 1.0

Iron binding site 7 out of 7 in 2q6n

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Iron binding site 7 out of 7 in the Structure of Cytochrome P450 2B4 with Bound 1-(4- Cholorophenyl)Imidazole


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of Cytochrome P450 2B4 with Bound 1-(4- Cholorophenyl)Imidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe500

b:0.3
occ:1.00
 FE G:HEM500 0.0 0.3 1.0
ND G:HEM500 2.1 0.3 1.0
NA G:HEM500 2.1 0.3 1.0
NB G:HEM500 2.1 0.3 1.0
NC G:HEM500 2.1 0.3 1.0
SG G:CYS436 2.2 0.3 1.0
N3 G:1CI501 2.4 0.0 1.0
C4 G:1CI501 2.9 0.0 1.0
C4A G:HEM500 3.0 0.3 1.0
C1D G:HEM500 3.0 0.3 1.0
C1C G:HEM500 3.0 0.3 1.0
C4B G:HEM500 3.0 0.3 1.0
C4D G:HEM500 3.0 0.3 1.0
C1B G:HEM500 3.0 0.3 1.0
C4C G:HEM500 3.1 0.3 1.0
C1A G:HEM500 3.1 0.3 1.0
CHC G:HEM500 3.3 0.3 1.0
CHB G:HEM500 3.3 0.3 1.0
CB G:CYS436 3.3 0.3 1.0
CHA G:HEM500 3.3 0.3 1.0
CHD G:HEM500 3.3 0.3 1.0
C2 G:1CI501 3.6 0.0 1.0
CA G:CYS436 4.1 87.8 1.0
C5 G:1CI501 4.2 0.0 1.0
C3A G:HEM500 4.2 0.3 1.0
C2C G:HEM500 4.2 0.3 1.0
C2D G:HEM500 4.2 0.3 1.0
C2A G:HEM500 4.2 0.3 1.0
C3D G:HEM500 4.2 0.3 1.0
C3C G:HEM500 4.3 0.3 1.0
C3B G:HEM500 4.3 0.3 1.0
C2B G:HEM500 4.3 0.3 1.0
N1 G:1CI501 4.5 0.0 1.0
N G:LEU437 4.7 0.5 1.0
C G:CYS436 4.8 87.8 1.0
N G:GLY438 5.0 0.6 1.0

Reference:

Y.Zhao, L.Sun, B.K.Muralidhara, S.Kumar, M.A.White, C.D.Stout, J.R.Halpert. Structural and Thermodynamic Consequences of 1-(4-Chlorophenyl)Imidazole Binding to Cytochrome P450 2B4. Biochemistry V. 46 11559 2007.
ISSN: ISSN 0006-2960
PubMed: 17887776
DOI: 10.1021/BI7011614
Page generated: Sun Aug 4 01:37:05 2024

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