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Iron in PDB 3a51: Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution with Bound 25-Hydroxyvitamin D3

Protein crystallography data

The structure of Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution with Bound 25-Hydroxyvitamin D3, PDB code: 3a51 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) 45.60 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 77.173, 171.800, 189.143, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 23.4

Other elements in 3a51:

The structure of Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution with Bound 25-Hydroxyvitamin D3 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 with Bound 25-Hydroxyvitamin D3 (pdb code 3a51). 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 with Bound 25-Hydroxyvitamin D3, PDB code: 3a51:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 3a51

Go back to Iron Binding Sites List in 3a51
Iron binding site 1 out of 5 in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution with Bound 25-Hydroxyvitamin D3


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 with Bound 25-Hydroxyvitamin D3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe412

b:14.7
occ:1.00
 FE A:HEM412 0.0 14.7 1.0
NC A:HEM412 2.1 14.4 1.0
NB A:HEM412 2.1 15.6 1.0
NA A:HEM412 2.1 13.0 1.0
ND A:HEM412 2.1 11.9 1.0
SG A:CYS347 2.3 14.1 1.0
O1 A:VDY6178 2.4 31.3 1.0
C4C A:HEM412 3.1 16.0 1.0
C1D A:HEM412 3.1 13.7 1.0
C4B A:HEM412 3.1 16.2 1.0
C1C A:HEM412 3.1 13.7 1.0
C1B A:HEM412 3.1 14.1 1.0
C1A A:HEM412 3.1 12.8 1.0
C4D A:HEM412 3.1 12.0 1.0
C4A A:HEM412 3.1 14.2 1.0
CB A:CYS347 3.4 12.0 1.0
C3 A:VDY6178 3.4 29.5 1.0
CHD A:HEM412 3.4 13.3 1.0
CHC A:HEM412 3.4 14.1 1.0
CHB A:HEM412 3.5 14.3 1.0
CHA A:HEM412 3.5 13.0 1.0
CA A:CYS347 4.0 12.2 1.0
C2B A:HEM412 4.3 14.2 1.0
C3B A:HEM412 4.3 13.2 1.0
C2 A:VDY6178 4.3 27.9 1.0
C2C A:HEM412 4.3 11.6 1.0
C3C A:HEM412 4.3 14.8 1.0
C2D A:HEM412 4.3 12.8 1.0
C2A A:HEM412 4.3 14.0 1.0
C3D A:HEM412 4.4 9.4 1.0
C3A A:HEM412 4.4 12.9 1.0
N A:GLY349 4.5 12.6 1.0
C4 A:VDY6178 4.5 29.0 1.0
N A:LEU348 4.6 13.2 1.0
C A:CYS347 4.6 13.3 1.0

Iron binding site 2 out of 5 in 3a51

Go back to Iron Binding Sites List in 3a51
Iron binding site 2 out of 5 in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution with Bound 25-Hydroxyvitamin D3


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 with Bound 25-Hydroxyvitamin D3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe412

b:25.8
occ:1.00
 FE B:HEM412 0.0 25.8 1.0
NC B:HEM412 2.1 25.9 1.0
NB B:HEM412 2.1 25.0 1.0
ND B:HEM412 2.1 25.6 1.0
NA B:HEM412 2.1 23.4 1.0
SG B:CYS347 2.1 26.5 1.0
O1 B:VDY6178 2.4 41.2 1.0
C4B B:HEM412 3.0 27.8 1.0
C1C B:HEM412 3.1 27.2 1.0
C4D B:HEM412 3.1 26.0 1.0
C1A B:HEM412 3.1 25.6 1.0
C4C B:HEM412 3.1 27.6 1.0
C1D B:HEM412 3.1 26.6 1.0
C1B B:HEM412 3.1 27.5 1.0
C4A B:HEM412 3.1 23.6 1.0
CHC B:HEM412 3.4 26.3 1.0
CB B:CYS347 3.4 26.8 1.0
CHA B:HEM412 3.4 24.6 1.0
C3 B:VDY6178 3.5 42.5 1.0
CHD B:HEM412 3.5 26.4 1.0
CHB B:HEM412 3.5 24.4 1.0
CA B:CYS347 3.9 26.4 1.0
C3B B:HEM412 4.3 26.4 1.0
C2C B:HEM412 4.3 27.7 1.0
C3C B:HEM412 4.3 27.5 1.0
C2A B:HEM412 4.3 23.4 1.0
C3D B:HEM412 4.3 25.3 1.0
C2B B:HEM412 4.3 26.0 1.0
C3A B:HEM412 4.4 22.2 1.0
C2D B:HEM412 4.4 26.2 1.0
C2 B:VDY6178 4.4 39.4 1.0
C4 B:VDY6178 4.5 42.9 1.0
N B:LEU348 4.6 27.1 1.0
C B:CYS347 4.6 26.6 1.0
N B:GLY349 4.6 27.2 1.0

Iron binding site 3 out of 5 in 3a51

Go back to Iron Binding Sites List in 3a51
Iron binding site 3 out of 5 in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution with Bound 25-Hydroxyvitamin D3


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 with Bound 25-Hydroxyvitamin D3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe412

b:19.2
occ:1.00
 FE C:HEM412 0.0 19.2 1.0
NC C:HEM412 2.0 17.8 1.0
NA C:HEM412 2.0 18.4 1.0
NB C:HEM412 2.1 19.7 1.0
ND C:HEM412 2.1 17.2 1.0
SG C:CYS347 2.4 22.4 1.0
O1 C:VDY6178 2.7 31.0 1.0
C4C C:HEM412 3.0 21.1 1.0
C1C C:HEM412 3.0 19.1 1.0
C1A C:HEM412 3.1 18.1 1.0
C1D C:HEM412 3.1 17.4 1.0
C4A C:HEM412 3.1 18.6 1.0
C4B C:HEM412 3.1 20.4 1.0
C1B C:HEM412 3.1 18.3 1.0
C4D C:HEM412 3.1 17.6 1.0
CB C:CYS347 3.4 20.2 1.0
CHD C:HEM412 3.4 18.8 1.0
CHC C:HEM412 3.4 19.8 1.0
CHA C:HEM412 3.5 17.5 1.0
C3 C:VDY6178 3.5 30.9 1.0
CHB C:HEM412 3.5 18.8 1.0
CA C:CYS347 4.0 20.5 1.0
C3C C:HEM412 4.2 21.4 1.0
C2C C:HEM412 4.3 20.1 1.0
C2A C:HEM412 4.3 17.7 1.0
C3A C:HEM412 4.3 18.3 1.0
C2 C:VDY6178 4.3 28.6 1.0
C2D C:HEM412 4.3 16.4 1.0
C3B C:HEM412 4.3 19.5 1.0
C2B C:HEM412 4.3 19.6 1.0
C3D C:HEM412 4.4 15.3 1.0
N C:GLY349 4.5 21.6 1.0
N C:LEU348 4.5 20.7 1.0
C C:CYS347 4.6 21.3 1.0
C4 C:VDY6178 4.7 31.7 1.0

Iron binding site 4 out of 5 in 3a51

Go back to Iron Binding Sites List in 3a51
Iron binding site 4 out of 5 in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution with Bound 25-Hydroxyvitamin D3


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 with Bound 25-Hydroxyvitamin D3 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe412

b:18.0
occ:1.00
 FE D:HEM412 0.0 18.0 1.0
ND D:HEM412 2.0 16.7 1.0
NA D:HEM412 2.1 15.1 1.0
NB D:HEM412 2.1 18.0 1.0
NC D:HEM412 2.1 19.8 1.0
SG D:CYS347 2.4 17.8 1.0
O1 D:VDY6178 2.6 45.5 1.0
C4C D:HEM412 3.1 17.8 1.0
C1D D:HEM412 3.1 17.3 1.0
C4D D:HEM412 3.1 17.6 1.0
C1A D:HEM412 3.1 15.6 1.0
C4A D:HEM412 3.1 17.6 1.0
C1B D:HEM412 3.1 17.0 1.0
C4B D:HEM412 3.1 18.6 1.0
C1C D:HEM412 3.1 17.6 1.0
CB D:CYS347 3.4 15.6 1.0
CHD D:HEM412 3.4 18.1 1.0
CHA D:HEM412 3.5 15.3 1.0
CHB D:HEM412 3.5 16.0 1.0
CHC D:HEM412 3.5 18.4 1.0
C3 D:VDY6178 3.6 45.4 1.0
CA D:CYS347 3.9 15.9 1.0
C3C D:HEM412 4.3 19.2 1.0
C3A D:HEM412 4.3 16.0 1.0
C2B D:HEM412 4.3 16.1 1.0
C2A D:HEM412 4.3 14.7 1.0
C2D D:HEM412 4.3 16.0 1.0
C3D D:HEM412 4.3 15.2 1.0
C3B D:HEM412 4.3 18.2 1.0
C2C D:HEM412 4.3 18.2 1.0
C2 D:VDY6178 4.5 43.9 1.0
N D:LEU348 4.5 16.5 1.0
C D:CYS347 4.5 16.1 1.0
N D:GLY349 4.5 17.3 1.0
C4 D:VDY6178 4.7 45.8 1.0

Iron binding site 5 out of 5 in 3a51

Go back to Iron Binding Sites List in 3a51
Iron binding site 5 out of 5 in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution with Bound 25-Hydroxyvitamin D3


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 with Bound 25-Hydroxyvitamin D3 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe412

b:21.6
occ:1.00
 FE E:HEM412 0.0 21.6 1.0
NC E:HEM412 2.0 20.9 1.0
NB E:HEM412 2.1 21.3 1.0
NA E:HEM412 2.1 20.2 1.0
ND E:HEM412 2.1 19.7 1.0
SG E:CYS347 2.4 21.7 1.0
O1 E:VDY6178 2.4 40.0 1.0
C1C E:HEM412 3.0 20.1 1.0
C4C E:HEM412 3.0 20.9 1.0
C1D E:HEM412 3.1 17.9 1.0
C4B E:HEM412 3.1 20.6 1.0
C4A E:HEM412 3.1 20.3 1.0
C1B E:HEM412 3.1 19.6 1.0
C4D E:HEM412 3.1 18.6 1.0
C1A E:HEM412 3.2 19.6 1.0
CHD E:HEM412 3.4 19.9 1.0
CB E:CYS347 3.4 18.5 1.0
CHC E:HEM412 3.4 19.8 1.0
C3 E:VDY6178 3.5 40.2 1.0
CHB E:HEM412 3.5 19.5 1.0
CHA E:HEM412 3.5 17.6 1.0
CA E:CYS347 4.0 19.4 1.0
C2C E:HEM412 4.2 18.5 1.0
C3C E:HEM412 4.2 21.0 1.0
C3B E:HEM412 4.3 20.6 1.0
C2B E:HEM412 4.3 17.8 1.0
C2D E:HEM412 4.3 18.8 1.0
C3A E:HEM412 4.3 19.0 1.0
C2 E:VDY6178 4.3 37.8 1.0
C3D E:HEM412 4.4 17.4 1.0
C2A E:HEM412 4.4 19.7 1.0
N E:GLY349 4.5 20.3 1.0
C4 E:VDY6178 4.6 39.0 1.0
N E:LEU348 4.6 19.2 1.0
C E:CYS347 4.6 19.8 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 06:41:13 2024

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