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Iron in PDB 3r1a: Closed Crystal Structure of Cytochrome P450 2B4 Covalently Bound to the Mechanism-Based Inactivator Tert-Butylphenylacetylene

Enzymatic activity of Closed Crystal Structure of Cytochrome P450 2B4 Covalently Bound to the Mechanism-Based Inactivator Tert-Butylphenylacetylene

All present enzymatic activity of Closed Crystal Structure of Cytochrome P450 2B4 Covalently Bound to the Mechanism-Based Inactivator Tert-Butylphenylacetylene:
1.14.14.1;

Protein crystallography data

The structure of Closed Crystal Structure of Cytochrome P450 2B4 Covalently Bound to the Mechanism-Based Inactivator Tert-Butylphenylacetylene, PDB code: 3r1a was solved by S.C.Gay, H.Zhang, C.D.Stout, P.F.Hollenberg, J.R.Halpert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 115.93 / 3.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 134.381, 144.549, 229.275, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 28.5

Iron Binding Sites:

The binding sites of Iron atom in the Closed Crystal Structure of Cytochrome P450 2B4 Covalently Bound to the Mechanism-Based Inactivator Tert-Butylphenylacetylene (pdb code 3r1a). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Closed Crystal Structure of Cytochrome P450 2B4 Covalently Bound to the Mechanism-Based Inactivator Tert-Butylphenylacetylene, PDB code: 3r1a:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 3r1a

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Iron binding site 1 out of 8 in the Closed Crystal Structure of Cytochrome P450 2B4 Covalently Bound to the Mechanism-Based Inactivator Tert-Butylphenylacetylene


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Closed Crystal Structure of Cytochrome P450 2B4 Covalently Bound to the Mechanism-Based Inactivator Tert-Butylphenylacetylene within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:47.6
occ:1.00
 FE A:HEM500 0.0 47.6 1.0
NA A:HEM500 2.0 41.4 1.0
NB A:HEM500 2.1 55.4 1.0
NC A:HEM500 2.1 48.7 1.0
ND A:HEM500 2.1 52.4 1.0
SG A:CYS436 2.6 47.7 1.0
C1A A:HEM500 3.0 46.5 1.0
C4D A:HEM500 3.1 48.2 1.0
C4A A:HEM500 3.1 49.9 1.0
C1C A:HEM500 3.1 46.9 1.0
C4B A:HEM500 3.1 51.9 1.0
C4C A:HEM500 3.1 45.8 1.0
C1B A:HEM500 3.1 54.2 1.0
C1D A:HEM500 3.1 48.0 1.0
CHA A:HEM500 3.4 50.2 1.0
CHC A:HEM500 3.4 48.2 1.0
CHB A:HEM500 3.5 57.5 1.0
CHD A:HEM500 3.5 45.9 1.0
O A:HOH1 3.5 29.6 1.0
CB A:CYS436 3.8 52.6 1.0
C2A A:HEM500 4.2 48.0 1.0
C3A A:HEM500 4.3 50.5 1.0
C2C A:HEM500 4.3 50.6 1.0
C3D A:HEM500 4.3 45.4 1.0
C3C A:HEM500 4.3 49.6 1.0
C3B A:HEM500 4.3 50.8 1.0
C2B A:HEM500 4.3 50.4 1.0
C2D A:HEM500 4.3 50.6 1.0
CB A:ALA298 4.5 49.1 1.0
CA A:CYS436 4.6 54.4 1.0
N A:GLY438 4.7 59.9 1.0
N A:LEU437 5.0 49.8 1.0

Iron binding site 2 out of 8 in 3r1a

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Iron binding site 2 out of 8 in the Closed Crystal Structure of Cytochrome P450 2B4 Covalently Bound to the Mechanism-Based Inactivator Tert-Butylphenylacetylene


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Closed Crystal Structure of Cytochrome P450 2B4 Covalently Bound to the Mechanism-Based Inactivator Tert-Butylphenylacetylene within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe500

b:61.1
occ:1.00
 FE B:HEM500 0.0 61.1 1.0
NC B:HEM500 2.0 59.1 1.0
NB B:HEM500 2.1 52.0 1.0
NA B:HEM500 2.1 57.4 1.0
ND B:HEM500 2.1 62.1 1.0
SG B:CYS436 2.6 49.4 1.0
C4C B:HEM500 3.0 60.9 1.0
O B:HOH2 3.1 40.7 1.0
C4A B:HEM500 3.1 52.9 1.0
C1C B:HEM500 3.1 59.6 1.0
C1D B:HEM500 3.1 63.5 1.0
C1B B:HEM500 3.1 51.6 1.0
C4B B:HEM500 3.1 57.8 1.0
C1A B:HEM500 3.1 55.2 1.0
C4D B:HEM500 3.1 60.8 1.0
CHD B:HEM500 3.4 61.3 1.0
CHB B:HEM500 3.4 54.5 1.0
CHC B:HEM500 3.4 60.3 1.0
CHA B:HEM500 3.5 59.1 1.0
CB B:CYS436 3.6 56.6 1.0
C3A B:HEM500 4.2 46.2 1.0
C3C B:HEM500 4.3 60.7 1.0
C2A B:HEM500 4.3 50.8 1.0
C2C B:HEM500 4.3 58.3 1.0
C2B B:HEM500 4.3 53.0 1.0
C3B B:HEM500 4.3 57.8 1.0
C2D B:HEM500 4.3 68.9 1.0
C3D B:HEM500 4.4 60.4 1.0
CA B:CYS436 4.4 60.6 1.0
CB B:ALA298 4.7 60.9 1.0
N B:GLY438 4.9 63.3 1.0
N B:LEU437 5.0 64.6 1.0

Iron binding site 3 out of 8 in 3r1a

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Iron binding site 3 out of 8 in the Closed Crystal Structure of Cytochrome P450 2B4 Covalently Bound to the Mechanism-Based Inactivator Tert-Butylphenylacetylene


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Closed Crystal Structure of Cytochrome P450 2B4 Covalently Bound to the Mechanism-Based Inactivator Tert-Butylphenylacetylene within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe500

b:52.5
occ:1.00
 FE C:HEM500 0.0 52.5 1.0
NA C:HEM500 2.0 56.7 1.0
NB C:HEM500 2.1 50.9 1.0
NC C:HEM500 2.1 65.7 1.0
ND C:HEM500 2.1 56.4 1.0
SG C:CYS436 2.6 57.8 1.0
C1A C:HEM500 3.0 55.4 1.0
C4A C:HEM500 3.0 52.9 1.0
C4D C:HEM500 3.1 55.4 1.0
C1B C:HEM500 3.1 55.8 1.0
C4C C:HEM500 3.1 65.1 1.0
C1D C:HEM500 3.1 65.5 1.0
C4B C:HEM500 3.1 52.2 1.0
C1C C:HEM500 3.1 64.0 1.0
CHA C:HEM500 3.4 58.2 1.0
O C:HOH4 3.4 40.9 1.0
CHB C:HEM500 3.4 50.8 1.0
CHD C:HEM500 3.4 66.9 1.0
CHC C:HEM500 3.5 58.1 1.0
CB C:CYS436 3.6 57.0 1.0
C2A C:HEM500 4.2 50.3 1.0
C3A C:HEM500 4.2 54.1 1.0
C2B C:HEM500 4.3 57.9 1.0
C3D C:HEM500 4.3 56.6 1.0
C3C C:HEM500 4.3 65.7 1.0
C2D C:HEM500 4.3 64.0 1.0
C3B C:HEM500 4.3 54.4 1.0
C2C C:HEM500 4.3 64.6 1.0
CA C:CYS436 4.5 60.6 1.0
CB C:ALA298 4.5 60.7 1.0
N C:GLY438 4.7 66.0 1.0
CA C:GLY438 5.0 68.6 1.0
N C:LEU437 5.0 66.2 1.0

Iron binding site 4 out of 8 in 3r1a

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Iron binding site 4 out of 8 in the Closed Crystal Structure of Cytochrome P450 2B4 Covalently Bound to the Mechanism-Based Inactivator Tert-Butylphenylacetylene


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Closed Crystal Structure of Cytochrome P450 2B4 Covalently Bound to the Mechanism-Based Inactivator Tert-Butylphenylacetylene within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe500

b:44.6
occ:1.00
 FE D:HEM500 0.0 44.6 1.0
NC D:HEM500 2.0 43.6 1.0
NA D:HEM500 2.1 42.6 1.0
ND D:HEM500 2.1 42.2 1.0
NB D:HEM500 2.1 46.3 1.0
SG D:CYS436 2.5 48.2 1.0
C4C D:HEM500 3.0 46.3 1.0
C1A D:HEM500 3.1 45.2 1.0
C1C D:HEM500 3.1 48.5 1.0
C1D D:HEM500 3.1 43.5 1.0
C4D D:HEM500 3.1 42.0 1.0
C4B D:HEM500 3.1 44.4 1.0
C4A D:HEM500 3.1 42.7 1.0
C1B D:HEM500 3.1 45.5 1.0
CHD D:HEM500 3.4 44.3 1.0
CHA D:HEM500 3.4 45.3 1.0
CHC D:HEM500 3.4 43.3 1.0
CHB D:HEM500 3.5 44.6 1.0
O D:HOH3 3.5 36.2 1.0
CB D:CYS436 3.6 46.5 1.0
C3C D:HEM500 4.3 49.9 1.0
C2C D:HEM500 4.3 53.3 1.0
C2A D:HEM500 4.3 43.0 1.0
C2D D:HEM500 4.3 45.4 1.0
C3D D:HEM500 4.3 39.1 1.0
C3B D:HEM500 4.3 43.6 1.0
C3A D:HEM500 4.3 39.2 1.0
C2B D:HEM500 4.3 42.1 1.0
CA D:CYS436 4.3 45.8 1.0
CB D:ALA298 4.8 46.5 1.0
O D:ALA298 4.8 53.6 1.0
N D:GLY438 5.0 50.0 1.0

Iron binding site 5 out of 8 in 3r1a

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Iron binding site 5 out of 8 in the Closed Crystal Structure of Cytochrome P450 2B4 Covalently Bound to the Mechanism-Based Inactivator Tert-Butylphenylacetylene


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Closed Crystal Structure of Cytochrome P450 2B4 Covalently Bound to the Mechanism-Based Inactivator Tert-Butylphenylacetylene within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe500

b:51.7
occ:1.00
 FE E:HEM500 0.0 51.7 1.0
NA E:HEM500 2.1 58.1 1.0
NC E:HEM500 2.1 56.4 1.0
ND E:HEM500 2.1 57.8 1.0
NB E:HEM500 2.1 59.2 1.0
O E:HOH5 2.5 39.6 1.0
SG E:CYS436 2.6 53.1 1.0
C1A E:HEM500 3.1 58.0 1.0
C4C E:HEM500 3.1 55.8 1.0
C1D E:HEM500 3.1 56.4 1.0
C1C E:HEM500 3.1 57.9 1.0
C4D E:HEM500 3.1 55.9 1.0
C4A E:HEM500 3.1 58.2 1.0
C1B E:HEM500 3.1 60.4 1.0
C4B E:HEM500 3.1 60.9 1.0
CHA E:HEM500 3.4 57.9 1.0
CHD E:HEM500 3.4 56.0 1.0
CHC E:HEM500 3.5 60.5 1.0
CHB E:HEM500 3.5 62.9 1.0
CB E:CYS436 3.7 63.6 1.0
C2A E:HEM500 4.3 52.3 1.0
C2C E:HEM500 4.3 57.2 1.0
C3A E:HEM500 4.3 49.3 1.0
C3C E:HEM500 4.3 53.5 1.0
C2D E:HEM500 4.3 51.7 1.0
C2B E:HEM500 4.3 57.6 1.0
C3D E:HEM500 4.3 54.7 1.0
C3B E:HEM500 4.3 58.6 1.0
CB E:ALA298 4.4 62.9 1.0
CA E:CYS436 4.5 61.6 1.0
N E:GLY438 4.5 64.9 1.0
N E:LEU437 4.8 62.0 1.0
O1 E:TB2501 4.8 52.2 1.0
CA E:GLY438 4.9 64.4 1.0

Iron binding site 6 out of 8 in 3r1a

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Iron binding site 6 out of 8 in the Closed Crystal Structure of Cytochrome P450 2B4 Covalently Bound to the Mechanism-Based Inactivator Tert-Butylphenylacetylene


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Closed Crystal Structure of Cytochrome P450 2B4 Covalently Bound to the Mechanism-Based Inactivator Tert-Butylphenylacetylene within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe500

b:50.0
occ:1.00
 FE F:HEM500 0.0 50.0 1.0
NA F:HEM500 2.0 50.8 1.0
NC F:HEM500 2.1 50.2 1.0
ND F:HEM500 2.1 59.4 1.0
NB F:HEM500 2.1 56.0 1.0
SG F:CYS436 2.6 47.0 1.0
C1A F:HEM500 3.0 52.4 1.0
C4D F:HEM500 3.1 52.3 1.0
C4C F:HEM500 3.1 54.0 1.0
C1D F:HEM500 3.1 59.6 1.0
C1C F:HEM500 3.1 49.6 1.0
C4A F:HEM500 3.1 53.4 1.0
C4B F:HEM500 3.1 52.8 1.0
C1B F:HEM500 3.1 49.7 1.0
CHA F:HEM500 3.4 47.5 1.0
CHD F:HEM500 3.4 55.1 1.0
CHC F:HEM500 3.5 49.5 1.0
CHB F:HEM500 3.5 49.6 1.0
CB F:CYS436 3.6 49.5 1.0
O F:HOH6 3.6 31.0 1.0
C2A F:HEM500 4.3 54.2 1.0
C3C F:HEM500 4.3 56.0 1.0
C2C F:HEM500 4.3 50.6 1.0
C3A F:HEM500 4.3 53.2 1.0
C3D F:HEM500 4.3 53.0 1.0
C2D F:HEM500 4.3 61.2 1.0
C3B F:HEM500 4.3 50.2 1.0
C2B F:HEM500 4.3 48.6 1.0
CA F:CYS436 4.5 56.3 1.0
CB F:ALA298 4.5 51.1 1.0
N F:GLY438 4.7 54.2 1.0

Iron binding site 7 out of 8 in 3r1a

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Iron binding site 7 out of 8 in the Closed Crystal Structure of Cytochrome P450 2B4 Covalently Bound to the Mechanism-Based Inactivator Tert-Butylphenylacetylene


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Closed Crystal Structure of Cytochrome P450 2B4 Covalently Bound to the Mechanism-Based Inactivator Tert-Butylphenylacetylene within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe500

b:59.5
occ:1.00
 FE G:HEM500 0.0 59.5 1.0
NA G:HEM500 2.0 62.3 1.0
NC G:HEM500 2.1 76.7 1.0
ND G:HEM500 2.1 82.2 1.0
NB G:HEM500 2.1 69.6 1.0
SG G:CYS436 2.6 73.8 1.0
O G:HOH7 2.9 46.2 1.0
C4D G:HEM500 3.1 82.4 1.0
C1A G:HEM500 3.1 60.2 1.0
C1D G:HEM500 3.1 82.2 1.0
C4A G:HEM500 3.1 68.0 1.0
C1B G:HEM500 3.1 69.1 1.0
C4C G:HEM500 3.1 78.8 1.0
C4B G:HEM500 3.1 68.8 1.0
C1C G:HEM500 3.1 73.1 1.0
CHA G:HEM500 3.4 75.1 1.0
CHD G:HEM500 3.4 82.2 1.0
CHB G:HEM500 3.4 71.4 1.0
CHC G:HEM500 3.5 70.1 1.0
CB G:CYS436 3.7 82.9 1.0
C2B G:HEM500 4.3 67.0 1.0
C2A G:HEM500 4.3 59.7 1.0
C3B G:HEM500 4.3 68.6 1.0
C3A G:HEM500 4.3 63.4 1.0
C3D G:HEM500 4.3 79.8 1.0
C2D G:HEM500 4.3 75.0 1.0
C3C G:HEM500 4.3 72.7 1.0
C2C G:HEM500 4.3 68.2 1.0
CA G:CYS436 4.6 83.2 1.0
CB G:ALA298 4.6 61.9 1.0
N G:GLY438 4.7 88.3 1.0
O G:ALA298 4.8 69.2 1.0
N G:LEU437 4.9 78.5 1.0

Iron binding site 8 out of 8 in 3r1a

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Iron binding site 8 out of 8 in the Closed Crystal Structure of Cytochrome P450 2B4 Covalently Bound to the Mechanism-Based Inactivator Tert-Butylphenylacetylene


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Closed Crystal Structure of Cytochrome P450 2B4 Covalently Bound to the Mechanism-Based Inactivator Tert-Butylphenylacetylene within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe500

b:0.4
occ:1.00
 FE H:HEM500 0.0 0.4 1.0
NA H:HEM500 2.1 0.4 1.0
NC H:HEM500 2.1 0.6 1.0
ND H:HEM500 2.1 0.4 1.0
NB H:HEM500 2.1 0.9 1.0
SG H:CYS436 2.9 0.3 1.0
C1A H:HEM500 3.1 0.1 1.0
C1D H:HEM500 3.1 100.0 1.0
C4C H:HEM500 3.1 0.6 1.0
C4D H:HEM500 3.1 0.8 1.0
C4A H:HEM500 3.1 0.5 1.0
C1C H:HEM500 3.1 0.6 1.0
C1B H:HEM500 3.1 0.6 1.0
C4B H:HEM500 3.1 0.3 1.0
CHA H:HEM500 3.4 0.8 1.0
CHD H:HEM500 3.4 97.5 1.0
CHB H:HEM500 3.5 0.2 1.0
CHC H:HEM500 3.5 0.2 1.0
CB H:CYS436 3.8 0.4 1.0
O H:HOH8 3.8 81.8 1.0
C2A H:HEM500 4.3 0.0 1.0
C3C H:HEM500 4.3 1.0 1.0
C3A H:HEM500 4.3 0.1 1.0
C2C H:HEM500 4.3 0.3 1.0
C2D H:HEM500 4.3 99.5 1.0
C3D H:HEM500 4.3 0.2 1.0
C2B H:HEM500 4.3 0.3 1.0
C3B H:HEM500 4.3 0.5 1.0
CA H:CYS436 4.4 0.4 1.0
CB H:ALA298 4.6 94.9 1.0
N H:LEU437 4.7 0.7 1.0
N H:GLY438 4.9 0.6 1.0

Reference:

S.C.Gay, H.Zhang, P.R.Wilderman, A.G.Roberts, T.Liu, S.Li, H.L.Lin, Q.Zhang, V.L.Woods, C.D.Stout, P.F.Hollenberg, J.R.Halpert. Structural Analysis of Mammalian Cytochrome P450 2B4 Covalently Bound to the Mechanism-Based Inactivator Tert-Butylphenylacetylene: Insight Into Partial Enzymatic Activity. Biochemistry V. 50 4903 2011.
ISSN: ISSN 0006-2960
PubMed: 21510666
DOI: 10.1021/BI200482G
Page generated: Sun Dec 13 15:19:43 2020

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