Magnesium in PDB 3vti: Crystal Structure of Hype-Hypf Complex

The structure of Crystal Structure of Hype-Hypf Complex, PDB code: 3vti was solved by Y.Shomura, Y.Higuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.56
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	118.739, 119.101, 174.631, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 25.1

The structure of Crystal Structure of Hype-Hypf Complex also contains other interesting chemical elements:

Iron	(Fe)	2 atoms
Zinc	(Zn)	4 atoms

The binding sites of Magnesium atom in the Crystal Structure of Hype-Hypf Complex (pdb code 3vti). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Hype-Hypf Complex, PDB code: 3vti:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Hype-Hypf Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Hype-Hypf Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:28.6 occ:1.00 OD1 C:ASP97 2.0 40.1 1.0 OD1 C:ASP59 2.2 46.4 1.0 OD1 C:ASP236 2.4 36.6 1.0 O C:HOH506 2.4 27.3 1.0 CG C:ASP97 3.2 40.7 1.0 CG C:ASP236 3.3 38.5 1.0 CG C:ASP59 3.4 45.0 1.0 OD2 C:ASP236 3.6 39.6 1.0 OD2 C:ASP97 3.8 45.5 1.0 CB C:ASP59 4.2 44.1 1.0 O C:ASP236 4.2 39.8 1.0 O C:HOH509 4.3 24.2 1.0 OD2 C:ASP59 4.4 44.9 1.0 CB C:ASP97 4.4 39.6 1.0 OG1 C:THR238 4.5 43.4 1.0 N C:ASP236 4.7 39.5 1.0 CG C:ARG235 4.7 39.8 1.0 CA C:ASP97 4.7 39.2 1.0 CB C:ASP236 4.7 38.9 1.0 CA C:ASP59 4.7 44.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Hype-Hypf Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Hype-Hypf Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg401 b:34.1 occ:1.00 OD1 D:ASP59 2.2 53.4 1.0 OD1 D:ASP97 2.3 51.0 1.0 O D:HOH514 2.3 16.2 1.0 O D:HOH509 2.4 20.1 1.0 OD1 D:ASP236 2.4 50.5 1.0 CG D:ASP97 2.8 50.6 1.0 OD2 D:ASP97 2.8 51.9 1.0 CG D:ASP236 3.4 51.6 1.0 CG D:ASP59 3.4 54.3 1.0 OD2 D:ASP236 3.7 52.4 1.0 CB D:ASP59 4.0 53.6 1.0 CB D:ASP97 4.2 49.0 1.0 O D:ASP236 4.3 52.0 1.0 OD2 D:ASP59 4.4 55.5 1.0 CA D:ASP59 4.4 53.2 1.0 O D:HOH502 4.5 31.0 1.0 OG1 D:THR238 4.5 51.8 1.0 N D:ASP236 4.6 52.9 1.0 CG D:ARG235 4.7 53.5 1.0 CA D:ASP97 4.7 49.9 1.0 CB D:ASP236 4.8 52.1 1.0 CG D:MET100 4.9 53.7 1.0

Y.Shomura, Y.Higuchi. Structural Basis For the Reaction Mechanism of S-Carbamoylation of Hype By Hypf in the Maturation of [Nife]-Hydrogenases J.Biol.Chem. V. 287 28409 2012.
ISSN: ISSN 0021-9258
PubMed: 22740694
DOI: 10.1074/JBC.M112.387134