Magnesium 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:

Zinc

(Zn)

1 atom

The binding sites of Magnesium atom in the Trimeric Heme-Free Cytochrome Variant Apocyt-TRICYT3 (pdb code 8del). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Trimeric Heme-Free Cytochrome Variant Apocyt-TRICYT3, PDB code: 8del:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Trimeric Heme-Free Cytochrome Variant Apocyt-TRICYT3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Trimeric Heme-Free Cytochrome Variant Apocyt-TRICYT3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:55.4 occ:1.00 CD2 A:HIS73 2.6 38.2 1.0 O A:HOH319 2.7 33.8 1.0 O B:HOH234 3.2 49.4 1.0 NE2 A:HIS73 3.4 50.0 1.0 O A:HIS73 3.5 30.0 1.0 CG A:HIS73 3.5 40.6 1.0 CB A:ALA76 3.7 40.0 1.0 CE1 B:HIS73 3.7 46.8 1.0 CD2 A:HIS77 3.7 49.5 1.0 CA A:HIS73 3.7 33.3 1.0 CB A:HIS73 4.0 36.9 1.0 C A:HIS73 4.1 32.2 1.0 CE1 B:HIS77 4.1 57.8 1.0 ND1 B:HIS73 4.2 43.2 1.0 CE1 A:HIS73 4.4 49.1 1.0 N A:HIS77 4.4 37.3 1.0 NE2 A:HIS77 4.4 47.8 1.0 ND1 A:HIS73 4.5 41.7 1.0 O A:HOH327 4.5 46.8 1.0 NH1 A:ARG34 4.6 34.2 1.0 OD1 B:ASP74 4.6 40.4 1.0 ZN A:ZN201 4.7 47.5 1.0 O B:HOH229 4.7 44.9 1.0 C A:ALA76 4.7 34.2 1.0 CA A:ALA76 4.7 28.4 1.0 NE2 B:HIS77 4.7 56.7 1.0 NE2 B:HIS73 4.8 46.4 1.0 CZ3 B:TRP70 4.8 30.6 1.0 CG A:HIS77 4.8 46.2 1.0 ND1 B:HIS77 4.8 52.3 1.0 NZ A:LYS80 5.0 56.5 1.0 N A:HIS73 5.0 32.1 1.0 O A:HOH312 5.0 46.1 1.0

Magnesium binding site 2 out of 2 in the Trimeric Heme-Free Cytochrome Variant Apocyt-TRICYT3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Trimeric Heme-Free Cytochrome Variant Apocyt-TRICYT3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:65.0 occ:1.00 CB A:ALA1 3.1 66.9 1.0 OD2 A:ASP39 3.2 71.0 1.0 O A:HOH316 4.0 59.8 1.0 CG A:ASP39 4.2 64.0 1.0 CA A:ALA1 4.2 74.8 1.0 OD1 A:ASP39 4.4 73.1 1.0 N A:ALA1 4.9 71.9 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