Zinc in PDB 5zlg: Human Duodenal Cytochrome B (Dcytb) in Zinc Ion and Ascorbate Bound Form

The structure of Human Duodenal Cytochrome B (Dcytb) in Zinc Ion and Ascorbate Bound Form, PDB code: 5zlg 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)	43.11 / 2.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	65.180, 115.570, 48.600, 90.00, 118.44, 90.00
R / Rfree (%)	20.6 / 25.3

The structure of Human Duodenal Cytochrome B (Dcytb) in Zinc Ion and Ascorbate Bound Form also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Zinc atom in the Human Duodenal Cytochrome B (Dcytb) in Zinc Ion and Ascorbate Bound Form (pdb code 5zlg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Human Duodenal Cytochrome B (Dcytb) in Zinc Ion and Ascorbate Bound Form, PDB code: 5zlg:

Zinc binding site 1 out of 1 in the Human Duodenal Cytochrome B (Dcytb) in Zinc Ion and Ascorbate Bound Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Duodenal Cytochrome B (Dcytb) in Zinc Ion and Ascorbate Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:43.2 occ:1.00 NE2 A:HIS108 2.0 28.1 1.0 O2 A:ASC404 2.2 42.0 1.0 CD2 A:HIS108 2.7 29.5 1.0 O1 A:ASC404 2.8 42.0 1.0 C2 A:ASC404 2.8 43.1 1.0 C1 A:ASC404 3.1 44.3 1.0 CE1 A:HIS108 3.1 36.5 1.0 ND2 A:ASN107 3.3 54.7 1.0 CE1 A:PHE47 3.6 46.4 1.0 CD1 A:PHE47 3.8 39.7 1.0 CG A:HIS108 4.0 35.4 1.0 C3 A:ASC404 4.0 52.9 1.0 CD1 A:ILE113 4.1 36.4 1.0 CAD A:HEM401 4.1 17.3 1.0 ND1 A:HIS108 4.1 36.3 1.0 CZ A:PHE47 4.5 48.8 1.0 O4 A:ASC404 4.5 44.8 1.0 CG A:ASN107 4.6 56.9 1.0 O3 A:ASC404 4.6 59.3 1.0 O5 A:ASC404 4.7 60.4 1.0 CG A:PHE47 4.8 50.1 1.0 CG1 A:VAL104 4.8 19.9 1.0 C4 A:ASC404 4.9 46.2 1.0 CG2 A:ILE113 5.0 25.6 1.0 CBD A:HEM401 5.0 17.5 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