Magnesium in PDB 5zcr: DSM5389 Glycosyltrehalose Synthase

The structure of DSM5389 Glycosyltrehalose Synthase, PDB code: 5zcr was solved by T.Tamada, N.Okazaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	70.04 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	71.132, 84.567, 128.662, 90.00, 103.75, 90.00
R / Rfree (%)	17.1 / 24.8

The binding sites of Magnesium atom in the DSM5389 Glycosyltrehalose Synthase (pdb code 5zcr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the DSM5389 Glycosyltrehalose Synthase, PDB code: 5zcr:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the DSM5389 Glycosyltrehalose Synthase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of DSM5389 Glycosyltrehalose Synthase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:16.0 occ:1.00 OE2 A:GLU269 2.7 24.9 1.0 O2 A:GOL802 2.7 22.3 1.0 OD2 A:ASP460 2.7 20.3 1.0 O A:HOH1066 2.8 26.5 1.0 O1 A:GOL803 3.0 27.3 1.0 O2 A:GOL803 3.1 24.9 1.0 CG A:ASP460 3.4 24.7 1.0 C2 A:GOL802 3.7 24.1 1.0 CD A:GLU269 3.7 24.4 1.0 C1 A:GOL803 3.8 26.0 1.0 O A:HOH952 3.8 14.3 1.0 O3 A:GOL804 3.8 23.2 1.0 OD1 A:ASP460 3.9 27.4 1.0 C2 A:GOL803 3.9 26.0 1.0 OE1 A:GLU269 4.1 23.9 1.0 O A:HOH955 4.2 30.1 1.0 C1 A:GOL802 4.2 25.4 1.0 OD1 A:ASP241 4.3 21.1 1.0 O1 A:GOL802 4.3 24.7 1.0 CB A:ASP460 4.4 24.8 1.0 C3 A:GOL804 4.5 39.1 1.0 NH2 A:ARG239 4.7 22.1 1.0

Magnesium binding site 2 out of 2 in the DSM5389 Glycosyltrehalose Synthase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of DSM5389 Glycosyltrehalose Synthase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg801 b:24.5 occ:1.00 O2 B:GOL803 2.3 30.4 1.0 O3 B:GOL802 2.6 38.5 1.0 O2 B:GOL802 2.6 31.9 1.0 OE2 B:GLU269 2.7 27.1 1.0 OD2 B:ASP460 2.7 27.5 1.0 O B:HOH1005 2.9 28.3 1.0 O B:HOH953 3.0 28.2 1.0 C2 B:GOL803 3.2 32.6 1.0 C3 B:GOL802 3.5 31.7 1.0 CG B:ASP460 3.5 29.8 1.0 C2 B:GOL802 3.5 33.3 1.0 CD B:GLU269 3.6 27.4 1.0 O1 B:GOL804 3.8 26.4 1.0 O B:HOH916 3.8 24.5 1.0 C1 B:GOL803 3.8 30.1 1.0 OE1 B:GLU269 3.8 27.2 1.0 OD1 B:ASP460 3.9 29.8 1.0 O B:HOH945 4.1 32.8 1.0 OD1 B:ASP241 4.1 26.0 1.0 O1 B:GOL803 4.6 30.9 1.0 C1 B:GOL804 4.6 37.4 1.0 NH2 B:ARG239 4.6 27.1 1.0 CB B:ASP460 4.6 26.1 1.0 C3 B:GOL803 4.6 24.6 1.0 C1 B:GOL802 4.8 29.2 1.0

N.Okazaki, M.Blaber, R.Kuroki, T.Tamada. Crystal Structure of Glycosyltrehalose Synthase From Sulfolobus Shibatae DSM5389 Acta Crystallogr F Struct V. 74 741 2018BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 30387780
DOI: 10.1107/S2053230X1801453X