Zinc in PDB 8del: Trimeric Heme-Free Cytochrome Variant Apocyt-TRICYT3

The structure of Trimeric Heme-Free Cytochrome Variant Apocyt-TRICYT3, PDB code: 8del was solved by A.M.Hoffnagle, V.H.Eng, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.80 / 2.56
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	43.778, 77.076, 92.653, 90, 98.69, 90
R / Rfree (%)	20.3 / 27.9

The structure of Trimeric Heme-Free Cytochrome Variant Apocyt-TRICYT3 also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Trimeric Heme-Free Cytochrome Variant Apocyt-TRICYT3 (pdb code 8del). 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 Trimeric Heme-Free Cytochrome Variant Apocyt-TRICYT3, PDB code: 8del:

Zinc binding site 1 out of 1 in the Trimeric Heme-Free Cytochrome Variant Apocyt-TRICYT3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Trimeric Heme-Free Cytochrome Variant Apocyt-TRICYT3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:47.5 occ:1.00 NE2 B:HIS73 2.1 46.4 1.0 NE2 A:HIS73 2.2 50.0 1.0 NE2 C:HIS73 2.2 46.7 1.0 NE2 A:HIS77 2.3 47.8 1.0 NE2 B:HIS77 2.4 56.7 1.0 CE1 C:HIS73 2.6 52.1 1.0 CE1 B:HIS73 2.7 46.8 1.0 NE2 C:HIS77 2.8 51.0 1.0 CE1 A:HIS73 2.8 49.1 1.0 CD2 C:HIS77 3.2 55.4 1.0 CE1 A:HIS77 3.2 55.9 1.0 CE1 B:HIS77 3.2 57.8 1.0 CD2 A:HIS77 3.3 49.5 1.0 CD2 A:HIS73 3.4 38.2 1.0 CD2 B:HIS73 3.4 38.6 1.0 CD2 B:HIS77 3.4 56.8 1.0 CD2 C:HIS73 3.5 39.5 1.0 ND1 C:HIS73 3.9 44.3 1.0 ND1 B:HIS73 3.9 43.2 1.0 CE1 C:HIS77 4.0 50.1 1.0 ND1 A:HIS73 4.1 41.7 1.0 CG B:HIS73 4.3 38.9 1.0 CG C:HIS73 4.3 36.2 1.0 ND1 A:HIS77 4.3 62.5 1.0 CG A:HIS73 4.4 40.6 1.0 ND1 B:HIS77 4.4 52.3 1.0 CG A:HIS77 4.4 46.2 1.0 CG C:HIS77 4.5 53.1 1.0 CG B:HIS77 4.5 48.0 1.0 MG A:MG202 4.7 55.4 1.0 ND1 C:HIS77 4.8 48.0 1.0

A.M.Hoffnagle, V.H.Eng, U.Markel, F.A.Tezcan. Computationally Guided Redesign of A Heme-Free Cytochrome with Native-Like Structure and Stability. Biochemistry V. 61 2063 2022.
ISSN: ISSN 0006-2960
PubMed: 36106943
DOI: 10.1021/ACS.BIOCHEM.2C00369