Iron in PDB 8gtl: Crystal Structure of Cytochrome P450 (CYP101D5)

The structure of Crystal Structure of Cytochrome P450 (CYP101D5), PDB code: 8gtl was solved by H.Do, J.H.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.79 / 3.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.524, 109.573, 113.878, 90, 90, 90
R / Rfree (%)	26.2 / 31.9

The binding sites of Iron atom in the Crystal Structure of Cytochrome P450 (CYP101D5) (pdb code 8gtl). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of Cytochrome P450 (CYP101D5), PDB code: 8gtl:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of Cytochrome P450 (CYP101D5)


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 Cytochrome P450 (CYP101D5) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:62.9 occ:1.00 FE A:HEM501 0.0 62.9 1.0 NA A:HEM501 2.0 60.8 1.0 NB A:HEM501 2.0 62.4 1.0 ND A:HEM501 2.1 65.5 1.0 NC A:HEM501 2.1 63.0 1.0 C1B A:HEM501 3.0 65.7 1.0 SG A:CYS360 3.1 60.7 1.0 C4A A:HEM501 3.1 60.7 1.0 C4B A:HEM501 3.1 65.8 1.0 C1C A:HEM501 3.1 63.0 1.0 C1A A:HEM501 3.1 64.9 1.0 C4D A:HEM501 3.1 61.2 1.0 C1D A:HEM501 3.1 64.3 1.0 C4C A:HEM501 3.1 63.7 1.0 CHB A:HEM501 3.4 63.7 1.0 CHC A:HEM501 3.4 63.4 1.0 CHA A:HEM501 3.4 66.2 1.0 CHD A:HEM501 3.5 62.1 1.0 CB A:CYS360 3.8 66.1 1.0 CB A:ALA251 4.0 65.3 1.0 CA A:CYS360 4.1 65.9 1.0 C2B A:HEM501 4.3 60.3 1.0 C3B A:HEM501 4.3 62.5 1.0 C3A A:HEM501 4.3 56.9 1.0 C2A A:HEM501 4.3 58.8 1.0 C2C A:HEM501 4.3 61.5 1.0 C3D A:HEM501 4.3 62.4 1.0 C2D A:HEM501 4.3 61.5 1.0 C3C A:HEM501 4.3 63.2 1.0 C A:CYS360 4.8 68.1 1.0 OG1 A:THR255 4.9 106.8 1.0 N A:ALA361 4.9 68.1 1.0

Iron binding site 2 out of 2 in the Crystal Structure of Cytochrome P450 (CYP101D5)


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 Cytochrome P450 (CYP101D5) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:60.5 occ:1.00 FE B:HEM501 0.0 60.5 1.0 NA B:HEM501 2.0 70.3 1.0 NB B:HEM501 2.0 72.8 1.0 NC B:HEM501 2.1 77.3 1.0 ND B:HEM501 2.1 74.8 1.0 SG B:CYS360 3.0 101.7 1.0 C1D B:HEM501 3.0 75.5 1.0 C4D B:HEM501 3.0 75.8 1.0 C4A B:HEM501 3.1 67.5 1.0 C1A B:HEM501 3.1 68.0 1.0 C1B B:HEM501 3.1 73.0 1.0 C4B B:HEM501 3.1 73.5 1.0 C1C B:HEM501 3.1 76.8 1.0 C4C B:HEM501 3.1 78.1 1.0 CHD B:HEM501 3.4 74.8 1.0 CHA B:HEM501 3.4 69.2 1.0 CHB B:HEM501 3.4 63.8 1.0 CHC B:HEM501 3.4 73.9 1.0 CB B:CYS360 4.0 63.3 1.0 O B:HOH603 4.1 53.8 1.0 CB B:ALA251 4.2 79.1 1.0 C2D B:HEM501 4.2 71.1 1.0 C3D B:HEM501 4.2 73.7 1.0 C2A B:HEM501 4.3 64.3 1.0 C3A B:HEM501 4.3 61.1 1.0 C2B B:HEM501 4.3 61.0 1.0 C3B B:HEM501 4.3 65.0 1.0 C2C B:HEM501 4.3 69.0 1.0 C3C B:HEM501 4.3 69.5 1.0 CA B:CYS360 4.6 64.2 1.0 OG1 B:THR255 4.7 113.5 1.0

P.Subedi, H.Do, J.H.Lee, T.J.Oh. Crystal Structure and Biochemical Analysis of A Cytochrome P450 CYP101D5 From Sphingomonas Echinoides. Int J Mol Sci V. 23 2022.
ISSN: ESSN 1422-0067
PubMed: 36362105
DOI: 10.3390/IJMS232113317