Iron in PDB 5it1: Streptomyces Peucetius CYP105P2 Complex with Biphenyl Compound

All present enzymatic activity of Streptomyces Peucetius CYP105P2 Complex with Biphenyl Compound:
1.14.14.1;

The structure of Streptomyces Peucetius CYP105P2 Complex with Biphenyl Compound, PDB code: 5it1 was solved by C.W.Lee, J.H.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	123.023, 122.941, 193.287, 90.00, 90.03, 90.00
R / Rfree (%)	20 / 24.3

The binding sites of Iron atom in the Streptomyces Peucetius CYP105P2 Complex with Biphenyl Compound (pdb code 5it1). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Streptomyces Peucetius CYP105P2 Complex with Biphenyl Compound, PDB code: 5it1:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Streptomyces Peucetius CYP105P2 Complex with Biphenyl Compound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Streptomyces Peucetius CYP105P2 Complex with Biphenyl Compound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:35.9 occ:1.00 FE A:HEM401 0.0 35.9 1.0 ND A:HEM401 2.0 40.9 1.0 NA A:HEM401 2.0 36.8 1.0 NC A:HEM401 2.0 36.4 1.0 NB A:HEM401 2.1 41.5 1.0 SG A:CYS348 2.5 40.0 1.0 C1D A:HEM401 3.0 38.3 1.0 C4A A:HEM401 3.0 37.5 1.0 C4D A:HEM401 3.0 36.1 1.0 C4C A:HEM401 3.0 41.9 1.0 C1A A:HEM401 3.0 35.6 1.0 C4B A:HEM401 3.0 34.0 1.0 C1B A:HEM401 3.1 41.4 1.0 C1C A:HEM401 3.1 39.3 1.0 CB A:CYS348 3.3 34.3 1.0 CHB A:HEM401 3.4 39.8 1.0 CHC A:HEM401 3.4 36.0 1.0 CHD A:HEM401 3.4 39.3 1.0 CHA A:HEM401 3.5 36.9 1.0 CA A:CYS348 4.0 37.7 1.0 C2A A:HEM401 4.2 37.1 1.0 C3A A:HEM401 4.2 37.5 1.0 C3C A:HEM401 4.2 34.4 1.0 C2C A:HEM401 4.2 36.1 1.0 C2D A:HEM401 4.3 37.7 1.0 C3D A:HEM401 4.3 37.8 1.0 C3B A:HEM401 4.3 38.6 1.0 C2B A:HEM401 4.3 36.9 1.0 O A:ALA237 4.4 36.9 1.0 CB A:ALA237 4.7 31.3 1.0 C A:CYS348 4.8 39.5 1.0 N A:ILE349 4.9 39.4 1.0 C A:ALA237 5.0 38.3 1.0

Iron binding site 2 out of 4 in the Streptomyces Peucetius CYP105P2 Complex with Biphenyl Compound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Streptomyces Peucetius CYP105P2 Complex with Biphenyl Compound within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:36.6 occ:1.00 FE B:HEM401 0.0 36.6 1.0 ND B:HEM401 1.9 37.2 1.0 NB B:HEM401 2.0 37.0 1.0 NA B:HEM401 2.0 41.4 1.0 NC B:HEM401 2.1 38.9 1.0 SG B:CYS348 2.5 40.0 1.0 C1D B:HEM401 2.9 36.1 1.0 C4D B:HEM401 3.0 33.4 1.0 C4B B:HEM401 3.0 36.5 1.0 O B:HOH632 3.0 41.0 1.0 C1B B:HEM401 3.0 38.5 1.0 C4C B:HEM401 3.0 38.5 1.0 C4A B:HEM401 3.1 39.8 1.0 C1A B:HEM401 3.1 36.5 1.0 C1C B:HEM401 3.1 28.5 1.0 CB B:CYS348 3.3 37.5 1.0 CHD B:HEM401 3.3 35.7 1.0 CHB B:HEM401 3.4 37.2 1.0 CHC B:HEM401 3.4 30.9 1.0 CHA B:HEM401 3.5 35.4 1.0 CA B:CYS348 4.0 38.5 1.0 C2D B:HEM401 4.1 34.3 1.0 C3D B:HEM401 4.2 36.1 1.0 C3B B:HEM401 4.2 35.1 1.0 C2B B:HEM401 4.2 35.9 1.0 C3C B:HEM401 4.3 36.1 1.0 C3A B:HEM401 4.3 37.3 1.0 C2C B:HEM401 4.3 34.9 1.0 C2A B:HEM401 4.3 35.6 1.0 O B:ALA237 4.4 38.3 1.0 CB B:ALA237 4.7 33.9 1.0 C B:CYS348 4.8 38.6 1.0 N B:ILE349 4.9 39.3 1.0 C B:ALA237 4.9 40.4 1.0

Iron binding site 3 out of 4 in the Streptomyces Peucetius CYP105P2 Complex with Biphenyl Compound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Streptomyces Peucetius CYP105P2 Complex with Biphenyl Compound within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:35.9 occ:1.00 FE C:HEM401 0.0 35.9 1.0 ND C:HEM401 1.9 42.4 1.0 NA C:HEM401 2.0 34.4 1.0 NC C:HEM401 2.0 34.4 1.0 NB C:HEM401 2.1 38.4 1.0 SG C:CYS348 2.4 40.9 1.0 C1D C:HEM401 3.0 39.3 1.0 C4D C:HEM401 3.0 34.7 1.0 C4C C:HEM401 3.0 38.4 1.0 C1A C:HEM401 3.0 34.6 1.0 C4A C:HEM401 3.0 36.7 1.0 C4B C:HEM401 3.0 30.6 1.0 C1B C:HEM401 3.1 40.2 1.0 C1C C:HEM401 3.1 37.1 1.0 CB C:CYS348 3.3 34.9 1.0 CHD C:HEM401 3.4 37.4 1.0 CHB C:HEM401 3.4 39.4 1.0 CHC C:HEM401 3.4 33.2 1.0 CHA C:HEM401 3.4 37.3 1.0 CA C:CYS348 4.0 36.6 1.0 C3A C:HEM401 4.2 34.6 1.0 C2A C:HEM401 4.2 36.8 1.0 C3C C:HEM401 4.2 37.5 1.0 C2D C:HEM401 4.2 36.9 1.0 C3D C:HEM401 4.2 38.9 1.0 C2C C:HEM401 4.3 36.0 1.0 O C:ALA237 4.3 38.3 1.0 C3B C:HEM401 4.3 38.6 1.0 C2B C:HEM401 4.3 37.8 1.0 CB C:ALA237 4.7 32.0 1.0 C C:CYS348 4.8 38.7 1.0 N C:ILE349 4.9 40.8 1.0 C C:ALA237 4.9 41.5 1.0

Iron binding site 4 out of 4 in the Streptomyces Peucetius CYP105P2 Complex with Biphenyl Compound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Streptomyces Peucetius CYP105P2 Complex with Biphenyl Compound within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:35.8 occ:1.00 FE D:HEM401 0.0 35.8 1.0 ND D:HEM401 1.9 35.4 1.0 NB D:HEM401 2.0 36.5 1.0 NA D:HEM401 2.0 40.8 1.0 NC D:HEM401 2.1 36.6 1.0 SG D:CYS348 2.4 40.2 1.0 C1D D:HEM401 2.9 34.9 1.0 C4D D:HEM401 3.0 34.7 1.0 C4B D:HEM401 3.0 38.0 1.0 C1B D:HEM401 3.0 39.8 1.0 C4A D:HEM401 3.0 38.8 1.0 C4C D:HEM401 3.1 37.7 1.0 C1A D:HEM401 3.1 34.6 1.0 C1C D:HEM401 3.1 31.9 1.0 CB D:CYS348 3.3 32.7 1.0 CHD D:HEM401 3.4 36.8 1.0 CHB D:HEM401 3.4 36.6 1.0 CHC D:HEM401 3.4 34.4 1.0 CHA D:HEM401 3.5 37.2 1.0 CA D:CYS348 3.9 35.2 1.0 C2D D:HEM401 4.2 38.1 1.0 C3D D:HEM401 4.2 35.0 1.0 C3B D:HEM401 4.2 34.9 1.0 C3A D:HEM401 4.2 36.7 1.0 C2A D:HEM401 4.3 36.0 1.0 C2B D:HEM401 4.3 34.3 1.0 C3C D:HEM401 4.3 33.6 1.0 C2C D:HEM401 4.3 33.8 1.0 O D:ALA237 4.4 39.7 1.0 CB D:ALA237 4.7 33.5 1.0 C D:CYS348 4.7 41.7 1.0 N D:ILE349 4.8 40.0 1.0 C D:ALA237 5.0 41.2 1.0

C.W.Lee, J.H.Lee, H.Rimal, H.Park, J.H.Lee, T.J.Oh. Crystal Structure of Cytochrome P450 (CYP105P2) From Streptomyces Peucetius and Its Conformational Changes in Response to Substrate Binding Int J Mol Sci V. 17 2016.
ISSN: ESSN 1422-0067
PubMed: 27231902
DOI: 10.3390/IJMS17060813