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Iron in PDB 3a4z: Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution

Protein crystallography data

The structure of Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution, PDB code: 3a4z was solved by Y.Yasutake, Y.Fujii, W.K.Cheon, A.Arisawa, T.Tamura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.27 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 77.378, 172.467, 189.873, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 24.4

Other elements in 3a4z:

The structure of Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution also contains other interesting chemical elements:

Calcium (Ca) 6 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution (pdb code 3a4z). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution, PDB code: 3a4z:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 3a4z

Go back to Iron Binding Sites List in 3a4z
Iron binding site 1 out of 5 in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution


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 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe412

b:18.3
occ:1.00
 FE A:HEM412 0.0 18.3 1.0
NC A:HEM412 2.1 20.0 1.0
NB A:HEM412 2.1 19.9 1.0
NA A:HEM412 2.1 19.1 1.0
ND A:HEM412 2.1 20.0 1.0
SG A:CYS347 2.2 18.1 1.0
C4C A:HEM412 3.1 20.6 1.0
C1C A:HEM412 3.1 18.6 1.0
C4B A:HEM412 3.1 20.0 1.0
C1D A:HEM412 3.1 20.2 1.0
C1A A:HEM412 3.2 19.2 1.0
C4A A:HEM412 3.2 20.4 1.0
C4D A:HEM412 3.2 20.5 1.0
C1B A:HEM412 3.2 18.5 1.0
CB A:CYS347 3.4 16.6 1.0
CHD A:HEM412 3.4 19.2 1.0
CHC A:HEM412 3.4 18.0 1.0
CHA A:HEM412 3.5 18.9 1.0
CHB A:HEM412 3.5 17.6 1.0
CA A:CYS347 3.9 17.6 1.0
C3C A:HEM412 4.3 19.7 1.0
C2C A:HEM412 4.3 19.8 1.0
C3B A:HEM412 4.3 18.1 1.0
C2A A:HEM412 4.4 19.9 1.0
C2D A:HEM412 4.4 21.4 1.0
C3A A:HEM412 4.4 20.0 1.0
C3D A:HEM412 4.4 17.7 1.0
C2B A:HEM412 4.4 19.1 1.0
N A:LEU348 4.5 17.1 1.0
N A:GLY349 4.5 16.7 1.0
C A:CYS347 4.6 17.4 1.0

Iron binding site 2 out of 5 in 3a4z

Go back to Iron Binding Sites List in 3a4z
Iron binding site 2 out of 5 in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution


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 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe412

b:31.6
occ:1.00
 FE B:HEM412 0.0 31.6 1.0
NC B:HEM412 2.1 33.8 1.0
NA B:HEM412 2.1 32.5 1.0
NB B:HEM412 2.1 32.2 1.0
ND B:HEM412 2.1 33.6 1.0
SG B:CYS347 2.2 30.3 1.0
C1A B:HEM412 3.1 32.8 1.0
C1C B:HEM412 3.1 33.6 1.0
C4C B:HEM412 3.1 33.7 1.0
C4B B:HEM412 3.1 33.3 1.0
C4D B:HEM412 3.1 33.6 1.0
C4A B:HEM412 3.1 31.4 1.0
C1D B:HEM412 3.1 35.5 1.0
C1B B:HEM412 3.2 32.2 1.0
CB B:CYS347 3.3 32.8 1.0
CHA B:HEM412 3.4 32.2 1.0
CHC B:HEM412 3.4 32.6 1.0
CHD B:HEM412 3.5 33.5 1.0
CHB B:HEM412 3.5 30.9 1.0
CA B:CYS347 3.9 32.9 1.0
C3C B:HEM412 4.3 34.5 1.0
C2A B:HEM412 4.3 31.5 1.0
C2C B:HEM412 4.3 34.5 1.0
C3A B:HEM412 4.3 31.5 1.0
C3B B:HEM412 4.3 31.6 1.0
C2B B:HEM412 4.4 30.8 1.0
C3D B:HEM412 4.4 33.9 1.0
C2D B:HEM412 4.4 34.5 1.0
C B:CYS347 4.6 33.2 1.0
N B:LEU348 4.6 34.0 1.0
N B:GLY349 4.6 35.2 1.0

Iron binding site 3 out of 5 in 3a4z

Go back to Iron Binding Sites List in 3a4z
Iron binding site 3 out of 5 in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution


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 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe412

b:22.4
occ:1.00
 FE C:HEM412 0.0 22.4 1.0
NC C:HEM412 2.1 22.4 1.0
NA C:HEM412 2.1 21.6 1.0
NB C:HEM412 2.1 23.3 1.0
ND C:HEM412 2.1 21.7 1.0
SG C:CYS347 2.4 24.0 1.0
C1C C:HEM412 3.1 21.2 1.0
C4B C:HEM412 3.1 24.1 1.0
C1A C:HEM412 3.1 22.5 1.0
C4C C:HEM412 3.1 22.9 1.0
C1D C:HEM412 3.1 21.6 1.0
C4D C:HEM412 3.1 21.1 1.0
C4A C:HEM412 3.1 22.5 1.0
C1B C:HEM412 3.2 22.9 1.0
CB C:CYS347 3.4 22.1 1.0
CHC C:HEM412 3.4 22.6 1.0
CHA C:HEM412 3.5 19.9 1.0
CHD C:HEM412 3.5 20.4 1.0
CHB C:HEM412 3.6 22.2 1.0
CA C:CYS347 3.9 22.8 1.0
C2A C:HEM412 4.3 20.5 1.0
C2C C:HEM412 4.3 20.7 1.0
C3A C:HEM412 4.3 21.6 1.0
C3B C:HEM412 4.3 24.6 1.0
C3C C:HEM412 4.3 22.6 1.0
C2D C:HEM412 4.3 19.3 1.0
C3D C:HEM412 4.4 18.4 1.0
C2B C:HEM412 4.4 23.7 1.0
N C:GLY349 4.5 26.2 1.0
N C:LEU348 4.5 24.6 1.0
C C:CYS347 4.6 23.4 1.0
CA C:GLY349 5.0 27.3 1.0

Iron binding site 4 out of 5 in 3a4z

Go back to Iron Binding Sites List in 3a4z
Iron binding site 4 out of 5 in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution


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 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe412

b:22.0
occ:1.00
 FE D:HEM412 0.0 22.0 1.0
NA D:HEM412 2.1 23.1 1.0
ND D:HEM412 2.1 23.1 1.0
NB D:HEM412 2.1 22.9 1.0
NC D:HEM412 2.1 24.7 1.0
SG D:CYS347 2.4 22.1 1.0
C4D D:HEM412 3.1 23.6 1.0
C1A D:HEM412 3.1 21.2 1.0
C4B D:HEM412 3.1 21.1 1.0
C1C D:HEM412 3.1 23.1 1.0
C1D D:HEM412 3.1 23.4 1.0
C1B D:HEM412 3.1 22.2 1.0
C4A D:HEM412 3.1 23.0 1.0
C4C D:HEM412 3.2 22.7 1.0
CHA D:HEM412 3.4 20.7 1.0
CB D:CYS347 3.4 20.1 1.0
CHC D:HEM412 3.4 21.2 1.0
CHD D:HEM412 3.5 23.1 1.0
CHB D:HEM412 3.5 22.6 1.0
CA D:CYS347 3.9 20.9 1.0
C2A D:HEM412 4.3 21.1 1.0
C3B D:HEM412 4.3 21.2 1.0
C3D D:HEM412 4.3 21.8 1.0
C2B D:HEM412 4.3 21.6 1.0
C2C D:HEM412 4.3 22.8 1.0
C3A D:HEM412 4.3 23.0 1.0
C2D D:HEM412 4.4 22.8 1.0
C3C D:HEM412 4.4 22.7 1.0
N D:LEU348 4.5 21.4 1.0
C D:CYS347 4.5 21.2 1.0
N D:GLY349 4.6 21.3 1.0

Iron binding site 5 out of 5 in 3a4z

Go back to Iron Binding Sites List in 3a4z
Iron binding site 5 out of 5 in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution


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 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe412

b:24.3
occ:1.00
 FE E:HEM412 0.0 24.3 1.0
NC E:HEM412 2.0 22.5 1.0
NB E:HEM412 2.1 22.7 1.0
ND E:HEM412 2.1 23.4 1.0
NA E:HEM412 2.2 23.6 1.0
SG E:CYS347 2.4 23.1 1.0
C4C E:HEM412 3.0 23.1 1.0
C1C E:HEM412 3.1 22.4 1.0
C1D E:HEM412 3.1 22.1 1.0
C4B E:HEM412 3.1 22.9 1.0
C1B E:HEM412 3.2 24.4 1.0
C4A E:HEM412 3.2 23.3 1.0
C1A E:HEM412 3.2 23.7 1.0
C4D E:HEM412 3.2 22.7 1.0
CHD E:HEM412 3.4 22.4 1.0
CB E:CYS347 3.4 22.5 1.0
CHC E:HEM412 3.4 22.9 1.0
CHA E:HEM412 3.5 21.7 1.0
CHB E:HEM412 3.5 23.6 1.0
CA E:CYS347 4.0 23.2 1.0
C3C E:HEM412 4.2 22.5 1.0
C2C E:HEM412 4.3 22.4 1.0
C2D E:HEM412 4.3 22.7 1.0
C3B E:HEM412 4.4 24.8 1.0
C2B E:HEM412 4.4 23.8 1.0
C3D E:HEM412 4.4 21.3 1.0
C3A E:HEM412 4.4 23.8 1.0
C2A E:HEM412 4.4 22.7 1.0
N E:GLY349 4.5 22.6 1.0
N E:LEU348 4.5 23.0 1.0
C E:CYS347 4.6 23.2 1.0

Reference:

Y.Yasutake, Y.Fujii, T.Nishioka, W.K.Cheon, A.Arisawa, T.Tamura. Structural Evidence For Enhancement of Sequential Vitamin D3 Hydroxylation Activities By Directed Evolution of Cytochrome P450 Vitamin D3 Hydroxylase J.Biol.Chem. V. 285 31193 2010.
ISSN: ISSN 0021-9258
PubMed: 20667833
DOI: 10.1074/JBC.M110.147009
Page generated: Sun Aug 4 06:40:29 2024

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