Iron in PDB 3a50: Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution with Bound Vitamin D3

The structure of Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution with Bound Vitamin D3, PDB code: 3a50 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)	49.09 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	77.384, 172.266, 189.063, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 24

The structure of Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution with Bound Vitamin D3 also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

The binding sites of Iron atom in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution with Bound Vitamin D3 (pdb code 3a50). 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 Vitamin D3, PDB code: 3a50:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution with Bound Vitamin 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 Vitamin D3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe412 b:13.1 occ:1.00 FE A:HEM412 0.0 13.1 1.0 NB A:HEM412 2.1 13.1 1.0 NA A:HEM412 2.1 12.5 1.0 ND A:HEM412 2.1 13.4 1.0 NC A:HEM412 2.1 13.2 1.0 SG A:CYS347 2.3 12.1 1.0 C1B A:HEM412 3.1 13.2 1.0 C1D A:HEM412 3.1 13.2 1.0 C4C A:HEM412 3.1 14.9 1.0 C4B A:HEM412 3.1 14.6 1.0 C4A A:HEM412 3.1 11.9 1.0 C1A A:HEM412 3.1 12.8 1.0 C1C A:HEM412 3.2 12.9 1.0 C4D A:HEM412 3.2 12.7 1.0 CB A:CYS347 3.3 10.6 1.0 C27 A:VD32001 3.4 47.4 1.0 CHD A:HEM412 3.4 12.2 1.0 CHB A:HEM412 3.5 11.2 1.0 CHC A:HEM412 3.5 12.1 1.0 CHA A:HEM412 3.5 12.2 1.0 CA A:CYS347 3.9 11.2 1.0 C2B A:HEM412 4.3 13.8 1.0 C3B A:HEM412 4.3 12.2 1.0 C3C A:HEM412 4.3 13.8 1.0 C2D A:HEM412 4.4 13.5 1.0 C3A A:HEM412 4.4 12.4 1.0 C2A A:HEM412 4.4 12.7 1.0 C2C A:HEM412 4.4 12.8 1.0 C3D A:HEM412 4.4 11.1 1.0 N A:GLY349 4.5 11.7 1.0 N A:LEU348 4.6 11.2 1.0 C A:CYS347 4.6 11.5 1.0 C25 A:VD32001 4.6 49.2 1.0 C26 A:VD32001 4.7 45.5 1.0

Iron binding site 2 out of 5 in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution with Bound Vitamin 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 Vitamin D3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe412 b:25.7 occ:1.00 FE B:HEM412 0.0 25.7 1.0 NB B:HEM412 2.1 25.4 1.0 NC B:HEM412 2.1 27.0 1.0 NA B:HEM412 2.1 24.8 1.0 ND B:HEM412 2.1 26.3 1.0 SG B:CYS347 2.2 25.7 1.0 C4B B:HEM412 3.0 26.3 1.0 C1C B:HEM412 3.1 26.6 1.0 C1A B:HEM412 3.1 26.0 1.0 C4C B:HEM412 3.1 27.4 1.0 C4D B:HEM412 3.1 25.9 1.0 C1B B:HEM412 3.1 25.4 1.0 C4A B:HEM412 3.1 24.1 1.0 C1D B:HEM412 3.1 28.1 1.0 C27 B:VD32001 3.2 67.9 1.0 CB B:CYS347 3.3 26.6 1.0 CHC B:HEM412 3.4 26.4 1.0 CHA B:HEM412 3.4 25.9 1.0 CHD B:HEM412 3.5 26.8 1.0 CHB B:HEM412 3.5 24.1 1.0 CA B:CYS347 3.9 26.7 1.0 C3B B:HEM412 4.3 24.8 1.0 C2C B:HEM412 4.3 28.1 1.0 C3C B:HEM412 4.3 28.2 1.0 C2B B:HEM412 4.3 23.7 1.0 C2A B:HEM412 4.3 24.2 1.0 C3A B:HEM412 4.4 24.2 1.0 C3D B:HEM412 4.4 26.8 1.0 C2D B:HEM412 4.4 27.9 1.0 N B:LEU348 4.6 28.0 1.0 C B:CYS347 4.6 27.1 1.0 C25 B:VD32001 4.7 68.2 1.0 N B:GLY349 4.7 29.0 1.0

Iron binding site 3 out of 5 in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution with Bound Vitamin 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 Vitamin D3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe412 b:17.4 occ:1.00 FE C:HEM412 0.0 17.4 1.0 NC C:HEM412 2.0 16.8 1.0 NA C:HEM412 2.1 15.6 1.0 NB C:HEM412 2.1 18.3 1.0 ND C:HEM412 2.1 15.2 1.0 SG C:CYS347 2.4 20.4 1.0 C4A C:HEM412 3.1 15.6 1.0 C1A C:HEM412 3.1 15.8 1.0 C4C C:HEM412 3.1 19.4 1.0 C1C C:HEM412 3.1 17.2 1.0 C1D C:HEM412 3.1 16.2 1.0 C4D C:HEM412 3.1 15.7 1.0 C1B C:HEM412 3.1 16.7 1.0 C4B C:HEM412 3.1 19.6 1.0 C27 C:VD32001 3.2 48.2 1.0 CB C:CYS347 3.4 16.8 1.0 CHD C:HEM412 3.5 17.2 1.0 CHC C:HEM412 3.5 17.5 1.0 CHA C:HEM412 3.5 13.8 1.0 CHB C:HEM412 3.5 16.7 1.0 CA C:CYS347 3.9 18.1 1.0 C3A C:HEM412 4.3 16.4 1.0 C2A C:HEM412 4.3 14.8 1.0 C2C C:HEM412 4.3 17.7 1.0 C3C C:HEM412 4.3 19.0 1.0 C2B C:HEM412 4.3 18.6 1.0 C3B C:HEM412 4.4 19.3 1.0 C2D C:HEM412 4.4 15.2 1.0 C3D C:HEM412 4.4 14.1 1.0 C25 C:VD32001 4.5 49.8 1.0 N C:LEU348 4.5 18.5 1.0 N C:GLY349 4.5 19.9 1.0 C C:CYS347 4.6 18.1 1.0 C26 C:VD32001 4.7 45.9 1.0

Iron binding site 4 out of 5 in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution with Bound Vitamin 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 Vitamin D3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe412 b:16.6 occ:1.00 FE D:HEM412 0.0 16.6 1.0 NB D:HEM412 2.1 18.4 1.0 NC D:HEM412 2.1 18.4 1.0 NA D:HEM412 2.1 15.8 1.0 ND D:HEM412 2.1 16.5 1.0 SG D:CYS347 2.4 16.6 1.0 C4B D:HEM412 3.1 17.9 1.0 C4C D:HEM412 3.1 16.3 1.0 C1C D:HEM412 3.1 16.6 1.0 C4A D:HEM412 3.1 16.6 1.0 C1A D:HEM412 3.1 16.3 1.0 C1D D:HEM412 3.1 16.1 1.0 C1B D:HEM412 3.1 17.3 1.0 C4D D:HEM412 3.1 17.9 1.0 C27 D:VD32001 3.1 58.2 1.0 CB D:CYS347 3.4 14.1 1.0 CHC D:HEM412 3.4 17.3 1.0 CHD D:HEM412 3.5 17.0 1.0 CHA D:HEM412 3.5 15.2 1.0 CHB D:HEM412 3.5 16.0 1.0 CA D:CYS347 3.9 14.8 1.0 C3C D:HEM412 4.3 18.2 1.0 C3B D:HEM412 4.3 17.0 1.0 C2C D:HEM412 4.3 17.7 1.0 C2B D:HEM412 4.3 16.5 1.0 C3A D:HEM412 4.3 16.4 1.0 C2A D:HEM412 4.3 15.2 1.0 C3D D:HEM412 4.3 15.6 1.0 C2D D:HEM412 4.3 17.0 1.0 C25 D:VD32001 4.4 58.6 1.0 N D:GLY349 4.5 15.9 1.0 C26 D:VD32001 4.5 56.8 1.0 N D:LEU348 4.6 14.7 1.0 C D:CYS347 4.6 14.8 1.0

Iron binding site 5 out of 5 in the Structure of Cytochrome P450 Vdh Mutant (Vdh-K1) Obtained By Directed Evolution with Bound Vitamin 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 Vitamin D3 within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe412 b:19.7 occ:1.00 FE E:HEM412 0.0 19.7 1.0 NC E:HEM412 2.0 19.3 1.0 ND E:HEM412 2.1 18.9 1.0 NA E:HEM412 2.1 19.6 1.0 NB E:HEM412 2.2 19.5 1.0 SG E:CYS347 2.4 19.5 1.0 C4C E:HEM412 3.0 19.1 1.0 C1D E:HEM412 3.0 17.1 1.0 C1C E:HEM412 3.1 18.0 1.0 C4A E:HEM412 3.1 19.7 1.0 C4D E:HEM412 3.1 17.3 1.0 C1A E:HEM412 3.1 17.9 1.0 C1B E:HEM412 3.2 19.4 1.0 C4B E:HEM412 3.2 19.3 1.0 C27 E:VD32001 3.3 64.2 1.0 CHD E:HEM412 3.4 17.3 1.0 CB E:CYS347 3.4 17.7 1.0 CHB E:HEM412 3.5 19.8 1.0 CHA E:HEM412 3.5 16.7 1.0 CHC E:HEM412 3.5 18.0 1.0 CA E:CYS347 3.9 18.2 1.0 C3C E:HEM412 4.2 18.1 1.0 C2C E:HEM412 4.3 17.5 1.0 C2D E:HEM412 4.3 17.6 1.0 C3A E:HEM412 4.3 20.0 1.0 C3D E:HEM412 4.3 17.0 1.0 C2A E:HEM412 4.3 18.9 1.0 C2B E:HEM412 4.4 18.8 1.0 C3B E:HEM412 4.4 18.7 1.0 N E:LEU348 4.5 17.8 1.0 N E:GLY349 4.5 18.1 1.0 C E:CYS347 4.6 18.3 1.0 C25 E:VD32001 4.7 64.0 1.0

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