Iron in PDB 4x8y: Crystal Structure of Human PGRMC1 Cytochrome B5-Like Domain

The structure of Crystal Structure of Human PGRMC1 Cytochrome B5-Like Domain, PDB code: 4x8y was solved by T.Nakane, T.Yamamoto, T.Shimamura, T.Kobayashi, Y.Kabe, M.Suematsu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.72 / 1.95
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	167.230, 167.230, 63.460, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 21.2

The binding sites of Iron atom in the Crystal Structure of Human PGRMC1 Cytochrome B5-Like Domain (pdb code 4x8y). 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 Human PGRMC1 Cytochrome B5-Like Domain, PDB code: 4x8y:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of Human PGRMC1 Cytochrome B5-Like Domain


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 Human PGRMC1 Cytochrome B5-Like Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe500 b:29.2 occ:1.00 FE A:HEM500 0.0 29.2 1.0 NC A:HEM500 2.0 24.7 1.0 NA A:HEM500 2.1 28.2 1.0 NB A:HEM500 2.1 29.8 1.0 ND A:HEM500 2.1 24.8 1.0 OH A:TYR113 2.2 29.4 1.0 C4C A:HEM500 3.0 26.9 1.0 C1D A:HEM500 3.1 26.7 1.0 C1A A:HEM500 3.1 31.0 1.0 C4B A:HEM500 3.1 29.0 1.0 C1C A:HEM500 3.1 29.5 1.0 C1B A:HEM500 3.1 29.6 1.0 C4A A:HEM500 3.1 32.1 1.0 C4D A:HEM500 3.1 28.9 1.0 CZ A:TYR113 3.1 27.2 1.0 CHD A:HEM500 3.4 27.6 1.0 CHC A:HEM500 3.4 26.7 1.0 CHA A:HEM500 3.4 28.4 1.0 CHB A:HEM500 3.5 33.7 1.0 CE2 A:TYR113 3.8 32.5 1.0 CE1 A:TYR113 3.8 28.9 1.0 O A:HOH618 4.1 43.3 1.0 C3C A:HEM500 4.3 24.2 1.0 C2C A:HEM500 4.3 28.9 1.0 C2A A:HEM500 4.3 31.5 1.0 C3A A:HEM500 4.3 33.0 1.0 C2B A:HEM500 4.3 34.2 1.0 C3B A:HEM500 4.3 33.9 1.0 C2D A:HEM500 4.3 26.4 1.0 C3D A:HEM500 4.3 29.9 1.0

Iron binding site 2 out of 2 in the Crystal Structure of Human PGRMC1 Cytochrome B5-Like Domain


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 Human PGRMC1 Cytochrome B5-Like Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe500 b:48.9 occ:1.00 FE B:HEM500 0.0 48.9 1.0 NA B:HEM500 2.0 49.6 1.0 NC B:HEM500 2.0 48.3 1.0 ND B:HEM500 2.1 48.8 1.0 NB B:HEM500 2.1 52.4 1.0 OH B:TYR113 2.2 53.3 1.0 C1A B:HEM500 3.0 48.0 1.0 C4D B:HEM500 3.1 47.6 1.0 C4C B:HEM500 3.1 47.6 1.0 C4A B:HEM500 3.1 50.6 1.0 C1C B:HEM500 3.1 50.9 1.0 CZ B:TYR113 3.1 56.2 1.0 C4B B:HEM500 3.1 50.2 1.0 C1D B:HEM500 3.1 45.8 1.0 C1B B:HEM500 3.1 51.6 1.0 CHA B:HEM500 3.4 46.1 1.0 CHC B:HEM500 3.4 47.7 1.0 CHD B:HEM500 3.5 46.2 1.0 CHB B:HEM500 3.5 53.1 1.0 CE2 B:TYR113 3.8 49.9 1.0 CE1 B:TYR113 3.8 61.9 1.0 C2A B:HEM500 4.3 50.3 1.0 C3A B:HEM500 4.3 51.4 1.0 C3C B:HEM500 4.3 48.9 1.0 C3D B:HEM500 4.3 47.7 1.0 C2C B:HEM500 4.3 54.0 1.0 C2D B:HEM500 4.3 44.4 1.0 C3B B:HEM500 4.3 51.9 1.0 C2B B:HEM500 4.3 51.8 1.0 CD2 B:TYR113 5.0 47.9 1.0

Y.Kabe, T.Nakane, I.Koike, T.Yamamoto, Y.Sugiura, E.Harada, K.Sugase, T.Shimamura, M.Ohmura, K.Muraoka, A.Yamamoto, T.Uchida, S.Iwata, Y.Yamaguchi, E.Krayukhina, M.Noda, H.Handa, K.Ishimori, S.Uchiyama, T.Kobayashi, M.Suematsu. Haem-Dependent Dimerization of PGRMC1/Sigma-2 Receptor Facilitates Cancer Proliferation and Chemoresistance Nat Commun V. 7 11030 2016.
ISSN: ESSN 2041-1723
PubMed: 26988023
DOI: 10.1038/NCOMMS11030