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Iron in PDB 3r1b: Open Crystal Structure of Cytochrome P450 2B4 Covalently Bound to the Mechanism-Based Inactivator Tert-Butylphenylacetylene

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

All present enzymatic activity of Open 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 Open Crystal Structure of Cytochrome P450 2B4 Covalently Bound to the Mechanism-Based Inactivator Tert-Butylphenylacetylene, PDB code: 3r1b 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) 53.43 / 3.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 193.924, 153.691, 129.665, 90.00, 122.22, 90.00
R / Rfree (%) 24.2 / 28.8

Iron Binding Sites:

The binding sites of Iron atom in the Open Crystal Structure of Cytochrome P450 2B4 Covalently Bound to the Mechanism-Based Inactivator Tert-Butylphenylacetylene (pdb code 3r1b). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Open Crystal Structure of Cytochrome P450 2B4 Covalently Bound to the Mechanism-Based Inactivator Tert-Butylphenylacetylene, PDB code: 3r1b:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3r1b

Go back to Iron Binding Sites List in 3r1b
Iron binding site 1 out of 4 in the Open 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 Open 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:56.1
occ:1.00
 FE A:HEM500 0.0 56.1 1.0
NC A:HEM500 2.0 48.7 1.0
NA A:HEM500 2.1 51.7 1.0
NB A:HEM500 2.1 54.0 1.0
ND A:HEM500 2.1 54.6 1.0
SG A:CYS436 2.5 58.7 1.0
C4C A:HEM500 3.0 53.3 1.0
C1A A:HEM500 3.1 55.3 1.0
C1C A:HEM500 3.1 53.3 1.0
C4A A:HEM500 3.1 56.3 1.0
C1D A:HEM500 3.1 48.5 1.0
C1B A:HEM500 3.1 50.4 1.0
C4D A:HEM500 3.1 56.9 1.0
C4B A:HEM500 3.1 55.0 1.0
CHD A:HEM500 3.4 48.1 1.0
CHA A:HEM500 3.4 60.7 1.0
CHB A:HEM500 3.5 54.8 1.0
CHC A:HEM500 3.5 58.4 1.0
CB A:CYS436 3.6 58.1 1.0
O1 A:TB2501 3.7 67.0 1.0
C3C A:HEM500 4.3 52.0 1.0
C2A A:HEM500 4.3 58.3 1.0
C3A A:HEM500 4.3 56.9 1.0
C2C A:HEM500 4.3 49.7 1.0
C2B A:HEM500 4.3 45.6 1.0
C2D A:HEM500 4.3 52.4 1.0
C3B A:HEM500 4.3 52.4 1.0
CA A:CYS436 4.3 57.1 1.0
C3D A:HEM500 4.3 49.8 1.0
CA A:GLY299 4.5 66.4 1.0
C4 A:TB2501 4.6 62.5 1.0
C5 A:TB2501 4.6 60.5 1.0
C1 A:TB2501 4.9 61.6 1.0
N A:GLY438 4.9 53.2 1.0
C A:CYS436 5.0 57.3 1.0
N A:LEU437 5.0 59.2 1.0

Iron binding site 2 out of 4 in 3r1b

Go back to Iron Binding Sites List in 3r1b
Iron binding site 2 out of 4 in the Open 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 Open 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:58.2
occ:1.00
 FE B:HEM500 0.0 58.2 1.0
NA B:HEM500 2.0 60.8 1.0
NC B:HEM500 2.0 61.2 1.0
NB B:HEM500 2.1 52.9 1.0
ND B:HEM500 2.1 53.9 1.0
SG B:CYS436 2.5 59.8 1.0
C4C B:HEM500 3.0 55.1 1.0
C1A B:HEM500 3.1 59.5 1.0
C4A B:HEM500 3.1 62.8 1.0
C1D B:HEM500 3.1 51.5 1.0
C1B B:HEM500 3.1 56.5 1.0
C1C B:HEM500 3.1 65.2 1.0
C4B B:HEM500 3.1 62.1 1.0
C4D B:HEM500 3.1 57.3 1.0
CB B:CYS436 3.4 60.2 1.0
CHD B:HEM500 3.4 54.0 1.0
CHB B:HEM500 3.4 55.9 1.0
CHA B:HEM500 3.4 62.4 1.0
CHC B:HEM500 3.5 62.9 1.0
O1 B:TB2501 3.9 74.9 1.0
CA B:CYS436 4.1 60.0 1.0
C3C B:HEM500 4.3 56.1 1.0
C2A B:HEM500 4.3 60.7 1.0
C3A B:HEM500 4.3 64.4 1.0
C2C B:HEM500 4.3 60.4 1.0
C2B B:HEM500 4.3 59.3 1.0
C3B B:HEM500 4.3 65.1 1.0
C2D B:HEM500 4.3 60.1 1.0
C7 B:TB2501 4.3 70.8 1.0
C8 B:TB2501 4.3 70.7 1.0
C3D B:HEM500 4.3 60.5 1.0
CB B:ALA298 4.6 84.6 1.0
C B:CYS436 4.7 58.6 1.0
N B:LEU437 4.8 52.7 1.0
CA B:GLY299 4.9 75.7 1.0
N B:GLY438 4.9 54.8 1.0

Iron binding site 3 out of 4 in 3r1b

Go back to Iron Binding Sites List in 3r1b
Iron binding site 3 out of 4 in the Open 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 Open 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:77.3
occ:1.00
 FE C:HEM500 0.0 77.3 1.0
NC C:HEM500 2.0 83.3 1.0
NA C:HEM500 2.1 80.6 1.0
NB C:HEM500 2.1 79.1 1.0
ND C:HEM500 2.1 90.3 1.0
SG C:CYS436 2.6 76.9 1.0
C1A C:HEM500 3.0 86.0 1.0
C4C C:HEM500 3.1 86.6 1.0
C1C C:HEM500 3.1 83.0 1.0
C4A C:HEM500 3.1 80.2 1.0
C4D C:HEM500 3.1 91.4 1.0
C1B C:HEM500 3.1 82.4 1.0
C1D C:HEM500 3.1 83.3 1.0
C4B C:HEM500 3.1 75.7 1.0
CHA C:HEM500 3.4 86.8 1.0
CHD C:HEM500 3.4 83.8 1.0
CHC C:HEM500 3.4 80.9 1.0
CHB C:HEM500 3.5 83.6 1.0
CB C:CYS436 3.6 80.1 1.0
O1 C:TB2501 3.8 83.9 1.0
C2A C:HEM500 4.2 88.0 1.0
C3A C:HEM500 4.3 83.6 1.0
C2C C:HEM500 4.3 81.5 1.0
C3C C:HEM500 4.3 83.2 1.0
C2B C:HEM500 4.3 73.5 1.0
C3D C:HEM500 4.3 90.8 1.0
C3B C:HEM500 4.3 73.3 1.0
C2D C:HEM500 4.3 83.8 1.0
C8 C:TB2501 4.5 82.4 1.0
C7 C:TB2501 4.5 85.3 1.0
CA C:CYS436 4.5 80.7 1.0
C1 C:TB2501 5.0 79.7 1.0

Iron binding site 4 out of 4 in 3r1b

Go back to Iron Binding Sites List in 3r1b
Iron binding site 4 out of 4 in the Open 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 Open 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:94.8
occ:1.00
 FE D:HEM500 0.0 94.8 1.0
NC D:HEM500 2.0 0.9 1.0
NA D:HEM500 2.1 0.6 1.0
NB D:HEM500 2.1 99.5 1.0
ND D:HEM500 2.1 1.0 1.0
SG D:CYS436 2.6 0.0 1.0
C4C D:HEM500 3.0 98.3 1.0
C4A D:HEM500 3.0 100.0 1.0
C1B D:HEM500 3.0 0.2 1.0
C1D D:HEM500 3.1 0.3 1.0
C1C D:HEM500 3.1 0.5 1.0
C1A D:HEM500 3.1 99.5 1.0
C4B D:HEM500 3.1 0.3 1.0
C4D D:HEM500 3.1 0.9 1.0
CB D:CYS436 3.2 0.3 1.0
CHD D:HEM500 3.4 96.8 1.0
CHB D:HEM500 3.4 0.3 1.0
CHA D:HEM500 3.5 99.7 1.0
CHC D:HEM500 3.5 0.0 1.0
O1 D:TB2501 4.1 0.6 1.0
CA D:CYS436 4.1 0.6 1.0
C3C D:HEM500 4.2 0.6 1.0
C2C D:HEM500 4.2 0.0 1.0
C3A D:HEM500 4.2 0.2 1.0
C2B D:HEM500 4.3 96.1 1.0
C2A D:HEM500 4.3 0.7 1.0
C3B D:HEM500 4.3 97.8 1.0
C2D D:HEM500 4.3 0.2 1.0
C3D D:HEM500 4.3 0.9 1.0
C5 D:TB2501 4.4 0.2 1.0
C4 D:TB2501 4.4 0.3 1.0
N D:GLY438 5.0 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 Aug 4 19:08:54 2024

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