Atomistry » Iron » PDB 3r1a-3rmk » 3r1b
Atomistry »
  Iron »
    PDB 3r1a-3rmk »
      3r1b »

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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy