Iron in PDB 5zle: Human Duodenal Cytochrome B (Dcytb) in Substrate Free Form

The structure of Human Duodenal Cytochrome B (Dcytb) in Substrate Free Form, PDB code: 5zle was solved by M.Ganasen, H.Togashi, G.A.Mauk, Y.Shiro, H.Sawai, H.Sugimoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.94 / 2.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	64.450, 115.940, 48.430, 90.00, 118.45, 90.00
R / Rfree (%)	19.7 / 24.6

The binding sites of Iron atom in the Human Duodenal Cytochrome B (Dcytb) in Substrate Free Form (pdb code 5zle). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Human Duodenal Cytochrome B (Dcytb) in Substrate Free Form, PDB code: 5zle:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Human Duodenal Cytochrome B (Dcytb) in Substrate Free Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Human Duodenal Cytochrome B (Dcytb) in Substrate Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:18.9 occ:1.00 FE A:HEM401 0.0 18.9 1.0 ND A:HEM401 1.9 21.1 1.0 NE2 A:HIS50 2.0 15.4 1.0 NE2 A:HIS120 2.0 17.7 1.0 NA A:HEM401 2.0 16.9 1.0 NC A:HEM401 2.1 13.7 1.0 NB A:HEM401 2.1 15.0 1.0 C4D A:HEM401 2.9 17.1 1.0 C1D A:HEM401 2.9 17.4 1.0 CE1 A:HIS50 2.9 17.4 1.0 C1A A:HEM401 3.0 19.3 1.0 CE1 A:HIS120 3.0 13.3 1.0 CD2 A:HIS120 3.0 16.9 1.0 CD2 A:HIS50 3.0 10.1 1.0 C4C A:HEM401 3.0 27.6 1.0 C4A A:HEM401 3.1 18.3 1.0 C4B A:HEM401 3.1 13.9 1.0 C1B A:HEM401 3.1 11.9 1.0 C1C A:HEM401 3.1 14.7 1.0 CHA A:HEM401 3.3 21.8 1.0 CHD A:HEM401 3.4 18.7 1.0 CHB A:HEM401 3.5 10.7 1.0 CHC A:HEM401 3.5 12.4 1.0 ND1 A:HIS50 4.1 16.8 1.0 ND1 A:HIS120 4.1 18.2 1.0 CG A:HIS120 4.1 17.4 1.0 CG A:HIS50 4.1 17.2 1.0 C3D A:HEM401 4.1 16.1 1.0 C2D A:HEM401 4.2 20.2 1.0 C2A A:HEM401 4.2 15.1 1.0 C3A A:HEM401 4.2 15.1 1.0 C3C A:HEM401 4.3 25.1 1.0 C2C A:HEM401 4.3 19.2 1.0 C3B A:HEM401 4.3 15.9 1.0 C2B A:HEM401 4.3 13.9 1.0 CA A:GLY177 4.9 10.5 1.0

Iron binding site 2 out of 2 in the Human Duodenal Cytochrome B (Dcytb) in Substrate Free Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Human Duodenal Cytochrome B (Dcytb) in Substrate Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:29.7 occ:1.00 FE A:HEM402 0.0 29.7 1.0 ND A:HEM402 1.9 26.2 1.0 NA A:HEM402 2.0 20.9 1.0 NE2 A:HIS159 2.1 37.4 1.0 NE2 A:HIS86 2.1 36.9 1.0 NC A:HEM402 2.1 25.7 1.0 NB A:HEM402 2.1 26.6 1.0 CE1 A:HIS159 2.9 30.7 1.0 C4D A:HEM402 2.9 26.4 1.0 C1D A:HEM402 2.9 28.8 1.0 CD2 A:HIS86 2.9 25.9 1.0 C1A A:HEM402 3.0 21.8 1.0 C4C A:HEM402 3.0 33.2 1.0 C4A A:HEM402 3.1 20.1 1.0 C1B A:HEM402 3.1 19.1 1.0 C4B A:HEM402 3.1 20.6 1.0 CE1 A:HIS86 3.1 23.7 1.0 C1C A:HEM402 3.2 25.2 1.0 CD2 A:HIS159 3.2 24.6 1.0 CHA A:HEM402 3.3 27.0 1.0 CHD A:HEM402 3.4 30.8 1.0 CHB A:HEM402 3.5 17.1 1.0 CHC A:HEM402 3.6 22.9 1.0 ND1 A:HIS159 4.1 26.0 1.0 CG A:HIS86 4.1 33.7 1.0 ND1 A:HIS86 4.1 27.1 1.0 C2D A:HEM402 4.2 30.8 1.0 C3D A:HEM402 4.2 29.3 1.0 C2A A:HEM402 4.2 19.9 1.0 C3A A:HEM402 4.2 19.5 1.0 CG A:HIS159 4.2 27.8 1.0 C3C A:HEM402 4.3 29.8 1.0 C2C A:HEM402 4.3 27.8 1.0 C2B A:HEM402 4.3 24.4 1.0 C3B A:HEM402 4.4 23.0 1.0 CE2 A:TYR69 4.8 30.1 1.0 ND2 A:ASN90 4.8 21.3 1.0

M.Ganasen, H.Togashi, H.Takeda, H.Asakura, T.Tosha, K.Yamashita, K.Hirata, Y.Nariai, T.Urano, X.Yuan, I.Hamza, A.G.Mauk, Y.Shiro, H.Sugimoto, H.Sawai. Structural Basis For Promotion of Duodenal Iron Absorption By Enteric Ferric Reductase with Ascorbate. Commun Biol V. 1 120 2018.
ISSN: ESSN 2399-3642
PubMed: 30272000
DOI: 10.1038/S42003-018-0121-8