Magnesium in PDB 5aun: Crystal Structure of the Hypab-Ni Complex

The structure of Crystal Structure of the Hypab-Ni Complex, PDB code: 5aun was solved by S.Watanabe, T.Kawashima, Y.Nishitani, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.36 / 1.63
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	74.720, 82.744, 65.128, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 21.3

The structure of Crystal Structure of the Hypab-Ni Complex also contains other interesting chemical elements:

Nickel	(Ni)	1 atom
Zinc	(Zn)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the Crystal Structure of the Hypab-Ni Complex (pdb code 5aun). 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 the Hypab-Ni Complex, PDB code: 5aun:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Hypab-Ni 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 the Hypab-Ni Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:22.2 occ:1.00 O B:HOH422 2.1 24.0 1.0 O1B B:ADP301 2.1 21.9 1.0 O B:HOH423 2.1 22.6 1.0 O B:HOH519 2.1 24.8 1.0 OG B:SER34 2.1 21.8 1.0 O B:HOH421 2.2 22.8 1.0 CB B:SER34 3.2 24.1 1.0 PB B:ADP301 3.3 22.9 1.0 O3B B:ADP301 3.5 25.3 1.0 N B:SER34 3.9 20.6 1.0 OD2 B:ASP57 3.9 27.4 1.0 CA B:SER34 4.1 23.4 1.0 O B:HOH415 4.1 23.4 1.0 O1A B:ADP301 4.2 24.9 1.0 OD2 B:ASP132 4.2 22.5 1.0 O B:HOH521 4.2 43.2 1.0 OD1 B:ASP132 4.3 21.5 1.0 O2B B:ADP301 4.3 23.7 1.0 OG B:SER62 4.3 25.3 1.0 O3A B:ADP301 4.3 24.6 1.0 CB B:LYS33 4.5 22.5 1.0 PA B:ADP301 4.6 25.2 1.0 CE B:LYS33 4.6 25.0 1.0 CB B:SER62 4.6 24.3 1.0 CG B:ASP132 4.7 21.1 1.0 O B:MET133 4.7 22.2 1.0 O2A B:ADP301 4.7 25.6 1.0 O B:HOH538 4.8 27.1 1.0 O B:GLY60 4.8 27.6 1.0 C B:LYS33 4.8 20.9 1.0 CG B:ASP57 4.9 28.4 1.0 NZ B:LYS33 5.0 24.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Hypab-Ni 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 the Hypab-Ni Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:32.2 occ:1.00 O B:LYS149 2.1 24.9 1.0 O B:HOH473 2.1 30.3 1.0 O B:HOH416 2.1 30.1 1.0 O B:HOH550 2.3 37.5 1.0 C B:LYS149 3.3 24.5 1.0 O B:HOH465 3.9 35.9 1.0 CA B:LYS149 4.1 25.9 1.0 O B:HOH492 4.3 37.5 1.0 O B:GLY151 4.3 25.7 1.0 N B:ARG150 4.3 24.5 1.0 N B:LYS180 4.4 25.2 1.0 O B:HOH587 4.4 48.8 1.0 O B:GLY178 4.4 28.3 1.0 CB B:LYS149 4.4 29.0 1.0 CA B:ARG150 4.5 24.3 1.0 ND1 B:HIS179 4.6 31.9 1.0 CA B:HIS179 4.6 22.6 1.0 C B:ARG150 4.7 24.2 1.0 N B:GLY151 4.7 23.4 1.0 CB B:LYS180 4.9 23.0 1.0

S.Watanabe, T.Kawashima, Y.Nishitani, T.Kanai, T.Wada, K.Inaba, H.Atomi, T.Imanaka, K.Miki. Structural Basis of A Ni Acquisition Cycle For [Nife] Hydrogenase By Ni-Metallochaperone Hypa and Its Enhancer Proc.Natl.Acad.Sci.Usa V. 112 7701 2015.
ISSN: ESSN 1091-6490
PubMed: 26056269
DOI: 10.1073/PNAS.1503102112