Iron in PDB 5gnm: Cytochrome P450 Vdh (CYP107BR1) L348M Mutant

All present enzymatic activity of Cytochrome P450 Vdh (CYP107BR1) L348M Mutant:
1.14.15.15;

The structure of Cytochrome P450 Vdh (CYP107BR1) L348M Mutant, PDB code: 5gnm was solved by Y.Yasutake, T.Tamura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.97 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.220, 107.650, 88.360, 90.00, 90.19, 90.00
R / Rfree (%)	22.3 / 27.5

The binding sites of Iron atom in the Cytochrome P450 Vdh (CYP107BR1) L348M Mutant (pdb code 5gnm). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Cytochrome P450 Vdh (CYP107BR1) L348M Mutant, PDB code: 5gnm:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Cytochrome P450 Vdh (CYP107BR1) L348M Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cytochrome P450 Vdh (CYP107BR1) L348M Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:13.6 occ:1.00 FE A:HEM501 0.0 13.6 1.0 ND A:HEM501 1.9 13.3 1.0 NA A:HEM501 2.0 13.5 1.0 NC A:HEM501 2.1 13.1 1.0 NB A:HEM501 2.1 13.2 1.0 SG A:CYS347 2.7 19.2 1.0 C4D A:HEM501 2.9 13.5 1.0 C1D A:HEM501 2.9 13.3 1.0 C1A A:HEM501 3.0 13.6 1.0 C4A A:HEM501 3.0 13.6 1.0 C4B A:HEM501 3.1 13.2 1.0 C1B A:HEM501 3.1 13.3 1.0 C4C A:HEM501 3.1 13.1 1.0 C1C A:HEM501 3.1 13.1 1.0 CHA A:HEM501 3.4 13.5 1.0 CHD A:HEM501 3.4 13.3 1.0 CHB A:HEM501 3.4 13.4 1.0 CHC A:HEM501 3.5 13.2 1.0 CB A:CYS347 3.6 18.8 1.0 O A:ALA236 3.7 20.5 1.0 CA A:CYS347 4.2 19.0 1.0 C3D A:HEM501 4.2 13.4 1.0 C2D A:HEM501 4.2 13.3 1.0 C2A A:HEM501 4.2 13.8 1.0 C3A A:HEM501 4.2 13.7 1.0 C3C A:HEM501 4.3 12.9 1.0 C2C A:HEM501 4.3 12.9 1.0 C2B A:HEM501 4.3 13.4 1.0 C3B A:HEM501 4.3 13.3 1.0 CB A:ALA236 4.4 21.5 1.0 C A:ALA236 4.5 21.1 1.0 C A:CYS347 4.9 19.4 1.0 N A:MET348 5.0 19.9 1.0

Iron binding site 2 out of 4 in the Cytochrome P450 Vdh (CYP107BR1) L348M Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cytochrome P450 Vdh (CYP107BR1) L348M Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:14.3 occ:1.00 FE B:HEM501 0.0 14.3 1.0 ND B:HEM501 1.9 14.2 1.0 NA B:HEM501 2.0 14.5 1.0 NB B:HEM501 2.1 14.3 1.0 NC B:HEM501 2.1 14.5 1.0 SG B:CYS347 2.4 17.1 1.0 C4D B:HEM501 2.9 14.4 1.0 C1D B:HEM501 2.9 14.3 1.0 C1A B:HEM501 3.0 14.6 1.0 C4A B:HEM501 3.0 14.4 1.0 C4B B:HEM501 3.1 14.4 1.0 C1B B:HEM501 3.1 14.4 1.0 C4C B:HEM501 3.1 14.4 1.0 C1C B:HEM501 3.1 14.3 1.0 CHA B:HEM501 3.4 14.4 1.0 CHD B:HEM501 3.4 14.4 1.0 CHB B:HEM501 3.4 14.4 1.0 CHC B:HEM501 3.5 14.3 1.0 CB B:CYS347 3.5 17.0 1.0 O B:ALA236 3.8 17.5 1.0 CA B:CYS347 4.2 17.1 1.0 C3D B:HEM501 4.2 14.4 1.0 C2D B:HEM501 4.2 14.3 1.0 C2A B:HEM501 4.2 14.7 1.0 C3A B:HEM501 4.2 14.6 1.0 C3C B:HEM501 4.3 14.5 1.0 C2C B:HEM501 4.3 14.5 1.0 C2B B:HEM501 4.3 14.3 1.0 C3B B:HEM501 4.3 14.4 1.0 CB B:ALA236 4.5 17.8 1.0 C B:ALA236 4.7 17.8 1.0 C B:CYS347 4.9 17.5 1.0

Iron binding site 3 out of 4 in the Cytochrome P450 Vdh (CYP107BR1) L348M Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cytochrome P450 Vdh (CYP107BR1) L348M Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:16.9 occ:1.00 FE C:HEM501 0.0 16.9 1.0 ND C:HEM501 1.9 16.7 1.0 NA C:HEM501 2.0 16.6 1.0 NC C:HEM501 2.1 17.1 1.0 NB C:HEM501 2.1 16.9 1.0 SG C:CYS347 2.5 18.1 1.0 C4D C:HEM501 2.9 16.7 1.0 C1D C:HEM501 2.9 16.8 1.0 C1A C:HEM501 3.0 16.6 1.0 C4A C:HEM501 3.0 16.6 1.0 C1B C:HEM501 3.1 16.7 1.0 C4C C:HEM501 3.1 17.3 1.0 C4B C:HEM501 3.1 16.9 1.0 C1C C:HEM501 3.1 17.1 1.0 CHA C:HEM501 3.4 16.6 1.0 CHD C:HEM501 3.4 17.1 1.0 CHB C:HEM501 3.4 16.6 1.0 CHC C:HEM501 3.5 16.9 1.0 CB C:CYS347 3.5 18.0 1.0 O C:ALA236 3.6 18.9 1.0 C3D C:HEM501 4.2 16.5 1.0 C2D C:HEM501 4.2 16.6 1.0 C2A C:HEM501 4.2 16.7 1.0 C3A C:HEM501 4.2 16.4 1.0 CA C:CYS347 4.2 18.2 1.0 C3C C:HEM501 4.3 17.4 1.0 C2C C:HEM501 4.3 17.4 1.0 C2B C:HEM501 4.3 16.9 1.0 C3B C:HEM501 4.3 16.9 1.0 CB C:ALA236 4.4 19.2 1.0 C C:ALA236 4.5 19.1 1.0 CA C:ALA236 5.0 19.3 1.0 C C:CYS347 5.0 18.5 1.0 N C:MET348 5.0 18.8 1.0

Iron binding site 4 out of 4 in the Cytochrome P450 Vdh (CYP107BR1) L348M Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cytochrome P450 Vdh (CYP107BR1) L348M Mutant within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe501 b:14.7 occ:1.00 FE D:HEM501 0.0 14.7 1.0 ND D:HEM501 1.9 14.5 1.0 NA D:HEM501 2.0 14.1 1.0 NC D:HEM501 2.1 14.4 1.0 NB D:HEM501 2.1 14.1 1.0 SG D:CYS347 2.6 24.3 1.0 C1D D:HEM501 2.9 14.5 1.0 C4D D:HEM501 2.9 14.5 1.0 C1A D:HEM501 3.0 14.2 1.0 C4A D:HEM501 3.0 14.0 1.0 C1B D:HEM501 3.1 14.1 1.0 C4B D:HEM501 3.1 14.2 1.0 C4C D:HEM501 3.1 14.5 1.0 C1C D:HEM501 3.1 14.4 1.0 CHA D:HEM501 3.4 14.3 1.0 CHD D:HEM501 3.4 14.6 1.0 CHB D:HEM501 3.4 13.9 1.0 CHC D:HEM501 3.5 14.3 1.0 CB D:CYS347 3.5 23.7 1.0 O D:ALA236 3.8 24.5 1.0 CA D:CYS347 4.1 23.8 1.0 C2D D:HEM501 4.2 14.5 1.0 C3D D:HEM501 4.2 14.6 1.0 C2A D:HEM501 4.2 14.2 1.0 C3A D:HEM501 4.2 14.0 1.0 C3C D:HEM501 4.3 14.4 1.0 C2B D:HEM501 4.3 14.0 1.0 C2C D:HEM501 4.3 14.4 1.0 C3B D:HEM501 4.3 14.1 1.0 CB D:ALA236 4.4 24.9 1.0 C D:ALA236 4.7 24.8 1.0 C D:CYS347 4.9 24.3 1.0 N D:MET348 5.0 24.7 1.0

Y.Yasutake, T.Kameda, T.Tamura. Structural Insights Into the Mechanism of the Drastic Changes in Enzymatic Activity of the Cytochrome P450 Vitamin D3 Hydroxylase (CYP107BR1) Caused By A Mutation Distant From the Active Site Acta Crystallogr F Struct V. 73 266 2017BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 28471358
DOI: 10.1107/S2053230X17004782