Iron in PDB 2z3t: Crystal Structure of Substrate Free Cytochrome P450 Stap (CYP245A1)

The structure of Crystal Structure of Substrate Free Cytochrome P450 Stap (CYP245A1), PDB code: 2z3t was solved by M.Makino, H.Sugimoto, Y.Shiro, S.Asamizu, H.Onaka, S.Nagano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	89.640, 78.718, 145.656, 90.00, 107.92, 90.00
R / Rfree (%)	22.8 / 27.3

The binding sites of Iron atom in the Crystal Structure of Substrate Free Cytochrome P450 Stap (CYP245A1) (pdb code 2z3t). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Substrate Free Cytochrome P450 Stap (CYP245A1), PDB code: 2z3t:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Substrate Free Cytochrome P450 Stap (CYP245A1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Substrate Free Cytochrome P450 Stap (CYP245A1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe500 b:34.5 occ:1.00 FE A:HEM500 0.0 34.5 1.0 ND A:HEM500 2.0 47.0 1.0 NB A:HEM500 2.0 40.1 1.0 NC A:HEM500 2.1 41.2 1.0 NA A:HEM500 2.1 39.5 1.0 N1 A:IMD501 2.4 21.3 1.0 SG A:CYS364 2.5 34.8 1.0 C4D A:HEM500 3.0 46.2 1.0 C1D A:HEM500 3.1 46.0 1.0 C4B A:HEM500 3.1 39.5 1.0 C1C A:HEM500 3.1 41.6 1.0 C1B A:HEM500 3.1 39.1 1.0 C1A A:HEM500 3.1 41.7 1.0 C4C A:HEM500 3.2 43.9 1.0 C4A A:HEM500 3.2 39.5 1.0 C5 A:IMD501 3.3 21.1 1.0 CB A:CYS364 3.4 38.7 1.0 C2 A:IMD501 3.4 20.3 1.0 CHC A:HEM500 3.4 39.1 1.0 CHA A:HEM500 3.4 44.0 1.0 CHD A:HEM500 3.5 43.8 1.0 CHB A:HEM500 3.5 39.8 1.0 CA A:CYS364 4.0 39.0 1.0 C2D A:HEM500 4.3 48.0 1.0 C3D A:HEM500 4.3 48.8 1.0 C2B A:HEM500 4.3 39.2 1.0 C3B A:HEM500 4.3 38.3 1.0 C2C A:HEM500 4.4 41.1 1.0 C3C A:HEM500 4.4 42.9 1.0 C2A A:HEM500 4.4 41.4 1.0 C3A A:HEM500 4.4 40.1 1.0 C4 A:IMD501 4.5 21.4 1.0 N3 A:IMD501 4.5 20.4 1.0 N A:LEU365 4.7 41.1 1.0 C A:CYS364 4.7 39.6 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Substrate Free Cytochrome P450 Stap (CYP245A1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Substrate Free Cytochrome P450 Stap (CYP245A1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe500 b:23.9 occ:1.00 FE B:HEM500 0.0 23.9 1.0 ND B:HEM500 2.0 34.0 1.0 NB B:HEM500 2.1 30.0 1.0 NC B:HEM500 2.1 30.9 1.0 NA B:HEM500 2.2 31.5 1.0 SG B:CYS364 2.4 29.4 1.0 N1 B:IMD501 2.5 29.5 1.0 C4D B:HEM500 3.0 33.5 1.0 C1D B:HEM500 3.0 33.7 1.0 C1C B:HEM500 3.1 33.1 1.0 C4B B:HEM500 3.1 31.7 1.0 C4C B:HEM500 3.1 32.2 1.0 C1A B:HEM500 3.2 32.8 1.0 C1B B:HEM500 3.2 30.1 1.0 C4A B:HEM500 3.3 31.5 1.0 CB B:CYS364 3.3 28.7 1.0 C5 B:IMD501 3.4 29.7 1.0 CHC B:HEM500 3.4 31.8 1.0 C2 B:IMD501 3.4 29.3 1.0 CHA B:HEM500 3.4 32.6 1.0 CHD B:HEM500 3.5 31.0 1.0 CHB B:HEM500 3.6 30.8 1.0 CA B:CYS364 4.0 29.3 1.0 C3D B:HEM500 4.2 34.5 1.0 C2D B:HEM500 4.2 34.6 1.0 C2C B:HEM500 4.4 31.9 1.0 C3B B:HEM500 4.4 30.7 1.0 C2B B:HEM500 4.4 30.3 1.0 C3C B:HEM500 4.4 32.6 1.0 C2A B:HEM500 4.5 33.1 1.0 C3A B:HEM500 4.5 32.2 1.0 N B:LEU365 4.5 30.8 1.0 N3 B:IMD501 4.5 28.0 1.0 C4 B:IMD501 4.6 28.0 1.0 C B:CYS364 4.6 30.4 1.0 N B:GLY366 4.7 30.1 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Substrate Free Cytochrome P450 Stap (CYP245A1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Substrate Free Cytochrome P450 Stap (CYP245A1) within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe500 b:33.0 occ:1.00 FE C:HEM500 0.0 33.0 1.0 ND C:HEM500 1.9 31.4 1.0 NC C:HEM500 2.0 29.9 1.0 NB C:HEM500 2.1 31.0 1.0 NA C:HEM500 2.2 23.2 1.0 SG C:CYS364 2.4 34.8 1.0 N1 C:IMD501 2.4 53.6 1.0 C1D C:HEM500 2.9 31.2 1.0 C4C C:HEM500 3.0 32.4 1.0 C1C C:HEM500 3.0 30.5 1.0 C4D C:HEM500 3.0 29.1 1.0 C4B C:HEM500 3.1 29.3 1.0 C1B C:HEM500 3.2 27.3 1.0 C1A C:HEM500 3.2 26.5 1.0 C2 C:IMD501 3.3 54.4 1.0 C4A C:HEM500 3.3 26.4 1.0 CHD C:HEM500 3.3 30.6 1.0 CHC C:HEM500 3.4 29.6 1.0 CB C:CYS364 3.5 35.5 1.0 C5 C:IMD501 3.5 55.2 1.0 CHA C:HEM500 3.5 27.4 1.0 CHB C:HEM500 3.6 27.4 1.0 CA C:CYS364 4.0 35.0 1.0 C2D C:HEM500 4.2 32.2 1.0 C3D C:HEM500 4.2 31.5 1.0 C2C C:HEM500 4.3 30.1 1.0 C3C C:HEM500 4.3 33.3 1.0 C3B C:HEM500 4.4 27.1 1.0 C2B C:HEM500 4.4 27.2 1.0 N3 C:IMD501 4.5 55.7 1.0 C2A C:HEM500 4.5 25.6 1.0 C3A C:HEM500 4.5 25.7 1.0 C4 C:IMD501 4.6 55.6 1.0 N C:LEU365 4.6 35.1 1.0 C C:CYS364 4.7 34.8 1.0 N C:GLY366 4.7 36.5 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Substrate Free Cytochrome P450 Stap (CYP245A1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Substrate Free Cytochrome P450 Stap (CYP245A1) within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe500 b:25.1 occ:1.00 FE D:HEM500 0.0 25.1 1.0 ND D:HEM500 1.9 31.4 1.0 NB D:HEM500 2.1 20.1 1.0 NC D:HEM500 2.1 22.6 1.0 NA D:HEM500 2.2 22.5 1.0 SG D:CYS364 2.5 32.2 1.0 N1 D:IMD501 2.5 58.1 1.0 C4D D:HEM500 3.0 31.0 1.0 C1D D:HEM500 3.0 31.8 1.0 C1A D:HEM500 3.1 24.9 1.0 C4B D:HEM500 3.1 21.2 1.0 C1C D:HEM500 3.1 24.0 1.0 C1B D:HEM500 3.1 21.9 1.0 C4C D:HEM500 3.2 26.9 1.0 C4A D:HEM500 3.2 21.4 1.0 CHA D:HEM500 3.4 27.4 1.0 CB D:CYS364 3.4 30.0 1.0 C2 D:IMD501 3.4 58.0 1.0 CHD D:HEM500 3.5 28.3 1.0 C5 D:IMD501 3.5 57.2 1.0 CHC D:HEM500 3.5 20.9 1.0 CHB D:HEM500 3.5 21.1 1.0 CA D:CYS364 4.0 29.6 1.0 C2D D:HEM500 4.2 32.7 1.0 C3D D:HEM500 4.2 34.4 1.0 C2B D:HEM500 4.4 22.2 1.0 C3B D:HEM500 4.4 21.4 1.0 C2A D:HEM500 4.4 24.1 1.0 C2C D:HEM500 4.4 23.7 1.0 C3A D:HEM500 4.4 22.6 1.0 C3C D:HEM500 4.4 26.3 1.0 N3 D:IMD501 4.6 56.6 1.0 N D:LEU365 4.6 30.6 1.0 C4 D:IMD501 4.6 56.7 1.0 C D:CYS364 4.7 30.6 1.0 N D:GLY366 4.8 29.4 1.0

M.Makino, H.Sugimoto, Y.Shiro, S.Asamizu, H.Onaka, S.Nagano. Crystal Structures and Catalytic Mechanism of Cytochrome P450 Stap That Produces the Indolocarbazole Skeleton Proc.Natl.Acad.Sci.Usa V. 104 11591 2007.
ISSN: ISSN 0027-8424
PubMed: 17606921
DOI: 10.1073/PNAS.0702946104