Magnesium in PDB 5aup: Crystal Structure of the Hypab Complex

The structure of Crystal Structure of the Hypab Complex, PDB code: 5aup 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)	46.54 / 3.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	121.945, 123.931, 55.099, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 23.9

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

Zinc

(Zn)

2 atoms

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

Magnesium binding site 1 out of 2 in the Crystal Structure of the Hypab 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 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:59.9 occ:1.00 O3G B:ACP301 1.9 63.0 1.0 O B:HOH402 2.1 60.2 1.0 O B:HOH403 2.1 66.5 1.0 O B:HOH401 2.1 70.7 1.0 OG B:SER34 2.1 66.7 1.0 O2B B:ACP301 2.1 60.9 1.0 PG B:ACP301 3.1 57.4 1.0 PB B:ACP301 3.3 61.4 1.0 CB B:SER34 3.3 63.9 1.0 C3B B:ACP301 3.4 68.7 1.0 O B:HOH404 3.5 69.3 1.0 OD2 B:ASP57 3.8 64.7 1.0 O1G B:ACP301 4.0 63.6 1.0 N B:SER34 4.1 62.9 1.0 OD2 B:ASP132 4.1 61.5 1.0 O2A B:ACP301 4.1 66.8 1.0 O1B B:ACP301 4.1 63.8 1.0 CA B:SER34 4.2 59.9 1.0 O2G B:ACP301 4.2 59.3 1.0 NZ I:LYS28 4.2 72.4 1.0 O B:GLY60 4.4 70.3 1.0 O3A B:ACP301 4.4 66.5 1.0 OG B:SER62 4.7 68.2 1.0 PA B:ACP301 4.7 65.5 1.0 OD1 B:ASP132 4.7 74.0 1.0 CG B:ASP57 4.8 69.3 1.0 CG B:ASP132 4.8 69.0 1.0 CB B:LYS33 4.8 63.8 1.0 O B:MET133 4.8 62.5 1.0 CB B:SER62 4.9 75.1 1.0 O1A B:ACP301 4.9 56.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Hypab 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 Complex within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg302 b:57.1 occ:1.00 O3G I:ACP301 2.0 54.8 1.0 O I:HOH401 2.1 58.1 1.0 O I:HOH402 2.1 62.1 1.0 O I:HOH403 2.1 52.5 1.0 OG I:SER34 2.1 61.3 1.0 O1B I:ACP301 2.2 60.2 1.0 PG I:ACP301 3.2 54.1 1.0 PB I:ACP301 3.3 52.3 1.0 CB I:SER34 3.3 56.5 1.0 C3B I:ACP301 3.5 55.4 1.0 OD2 I:ASP57 3.6 67.9 1.0 OD2 I:ASP132 4.0 61.2 1.0 O2B I:ACP301 4.1 49.8 1.0 N I:SER34 4.1 55.2 1.0 O2G I:ACP301 4.1 54.1 1.0 CA I:SER34 4.2 52.9 1.0 O1G I:ACP301 4.3 67.7 1.0 O1A I:ACP301 4.3 51.4 1.0 OD1 I:ASP132 4.3 63.4 1.0 O I:GLY60 4.5 71.7 1.0 CE B:LYS28 4.5 68.6 1.0 O3A I:ACP301 4.5 60.5 1.0 CG I:ASP132 4.6 58.9 1.0 CG I:ASP57 4.6 66.9 1.0 O I:MET133 4.7 59.9 1.0 NZ B:LYS28 4.8 62.7 1.0 PA I:ACP301 4.8 59.4 1.0 CB I:ASP57 4.8 65.4 1.0 CB I:LYS33 4.9 55.2 1.0 O2A I:ACP301 4.9 55.1 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