Magnesium in PDB 3a06: Crystal Structure of Dxr From Thermooga Maritia, in Complex with Fosmidomycin and Nadph

All present enzymatic activity of Crystal Structure of Dxr From Thermooga Maritia, in Complex with Fosmidomycin and Nadph:
1.1.1.267;

The structure of Crystal Structure of Dxr From Thermooga Maritia, in Complex with Fosmidomycin and Nadph, PDB code: 3a06 was solved by M.Takenoya, A.Ohtaki, K.Noguchi, Y.Sasaki, K.Ohsawa, M.Yohda, S.Yajima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.72 / 2.00
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	108.622, 108.622, 74.662, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 24

The binding sites of Magnesium atom in the Crystal Structure of Dxr From Thermooga Maritia, in Complex with Fosmidomycin and Nadph (pdb code 3a06). 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 Dxr From Thermooga Maritia, in Complex with Fosmidomycin and Nadph, PDB code: 3a06:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Dxr From Thermooga Maritia, in Complex with Fosmidomycin and Nadph


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 Dxr From Thermooga Maritia, in Complex with Fosmidomycin and Nadph within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg500 b:53.2 occ:1.00 OE1 A:GLU144 1.9 45.6 0.5 O A:HOH603 2.1 48.5 0.5 OD1 A:ASP142 2.2 55.5 1.0 OE2 A:GLU209 2.2 56.5 1.0 O A:HOH602 2.3 49.8 0.5 O A:HOH601 2.6 38.8 0.5 CD A:GLU144 2.8 42.9 0.5 OE2 A:GLU144 3.1 45.4 0.5 CG A:ASP142 3.1 49.0 1.0 CD A:GLU209 3.2 51.1 1.0 OD2 A:ASP142 3.5 55.5 1.0 OE1 A:GLU209 3.6 53.8 1.0 OG A:SER143 3.8 42.0 0.5 NZ A:LYS117 4.1 61.5 1.0 CG A:GLU144 4.1 42.1 1.0 ND2 A:ASN205 4.2 41.2 0.5 N A:SER143 4.3 39.8 1.0 CB A:ASP142 4.3 42.7 1.0 C5N A:NDP3001 4.3 57.6 1.0 CG A:GLU209 4.4 45.1 1.0 N A:GLU144 4.4 38.4 1.0 NZ A:LYS206 4.5 51.1 1.0 CB A:GLU144 4.6 39.3 1.0 CA A:ASP142 4.7 41.4 1.0 C4 A:FOM900 4.8 57.5 1.0 C4N A:NDP3001 4.8 58.0 1.0 C A:ASP142 4.8 40.4 1.0 CE A:LYS117 4.9 57.1 1.0 CB A:SER143 4.9 41.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Dxr From Thermooga Maritia, in Complex with Fosmidomycin and Nadph


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 Dxr From Thermooga Maritia, in Complex with Fosmidomycin and Nadph within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:52.1 occ:0.50 OE2 B:GLU209 1.9 51.3 1.0 OE1 B:GLU144 2.0 63.3 1.0 OD1 B:ASP142 2.1 53.5 1.0 O B:HOH380 2.4 58.7 1.0 CG B:ASP142 2.8 50.1 1.0 OD2 B:ASP142 3.0 54.9 1.0 CD B:GLU144 3.1 58.7 1.0 CD B:GLU209 3.1 44.3 1.0 OE2 B:GLU144 3.6 62.0 1.0 OE1 B:GLU209 3.8 49.0 1.0 N B:SER143 4.0 43.2 1.0 CB B:ASP142 4.2 44.9 1.0 N B:GLU144 4.2 43.2 1.0 CG B:GLU209 4.3 41.7 1.0 ND2 B:ASN205 4.3 40.5 0.5 CG B:GLU144 4.4 50.9 1.0 NZ B:LYS117 4.4 58.1 1.0 OG B:SER143 4.4 48.8 1.0 C5N B:NDP3002 4.5 68.1 1.0 CA B:ASP142 4.5 43.5 1.0 C B:ASP142 4.6 43.4 1.0 CB B:GLU144 4.6 44.5 1.0 NZ B:LYS206 4.7 50.1 1.0 CA B:SER143 4.9 44.0 1.0 C4N B:NDP3002 4.9 67.8 1.0 CE B:LYS117 5.0 58.2 1.0

M.Takenoya, A.Ohtaki, K.Noguchi, K.Endo, Y.Sasaki, K.Ohsawa, S.Yajima, M.Yohda. Crystal Structure of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase From the Hyperthermophile Thermotoga Maritima For Insights Into the Coordination of Conformational Changes and An Inhibitor Binding J.Struct.Biol. V. 170 532 2010.
ISSN: ISSN 1047-8477
PubMed: 20353826
DOI: 10.1016/J.JSB.2010.03.015