Magnesium in PDB 3g9d: Crystal Structure Glycohydrolase

All present enzymatic activity of Crystal Structure Glycohydrolase:
3.2.2.24;

The structure of Crystal Structure Glycohydrolase, PDB code: 3g9d was solved by X.-D.Li, F.K.Winkler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.50
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	163.866, 163.866, 46.274, 90.00, 90.00, 120.00
R / Rfree (%)	19.9 / 26.6

The binding sites of Magnesium atom in the Crystal Structure Glycohydrolase (pdb code 3g9d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure Glycohydrolase, PDB code: 3g9d:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure Glycohydrolase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure Glycohydrolase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg298 b:41.6 occ:1.00 OD2 A:ASP245 1.9 44.8 1.0 OD1 A:ASP60 1.9 49.3 1.0 O A:HOH335 2.0 39.9 1.0 O A:HOH333 2.0 19.3 1.0 OD1 A:ASP61 2.5 42.3 1.0 OG1 A:THR59 2.5 22.9 1.0 CG A:ASP245 2.9 36.3 1.0 CG A:ASP60 3.1 40.9 1.0 OD1 A:ASP245 3.3 27.4 1.0 CB A:THR59 3.3 31.2 1.0 MG A:MG299 3.5 26.5 1.0 OE2 A:GLU28 3.5 50.3 1.0 OD2 A:ASP60 3.6 48.3 1.0 CG A:ASP61 3.7 35.6 1.0 OD2 A:ASP97 3.7 44.1 1.0 N A:ASP60 3.9 34.3 1.0 O A:HOH336 4.0 35.1 1.0 CG2 A:THR59 4.1 25.8 1.0 OE1 A:GLU28 4.2 52.9 1.0 N A:ASP61 4.2 33.6 1.0 CD A:GLU28 4.2 41.8 1.0 CB A:ASP245 4.2 30.0 1.0 CB A:ASP60 4.3 34.4 1.0 OD2 A:ASP61 4.3 43.4 1.0 OD1 A:ASP21 4.3 36.1 1.0 OG1 A:THR246 4.4 29.4 1.0 CA A:ASP60 4.5 35.0 1.0 CA A:THR59 4.6 31.5 1.0 CG A:ASP97 4.6 42.8 1.0 C A:THR59 4.7 32.2 1.0 O A:HOH334 4.7 34.0 1.0 CB A:ASP97 4.7 37.2 1.0 CB A:ASP61 4.8 34.1 1.0 C A:ASP60 4.9 34.2 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure Glycohydrolase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure Glycohydrolase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg299 b:26.5 occ:1.00 O A:HOH333 2.0 19.3 1.0 OD1 A:ASP243 2.2 38.3 1.0 OD1 A:ASP245 2.2 27.4 1.0 O A:HOH334 2.3 34.0 1.0 O A:HOH338 2.4 49.9 1.0 OE2 A:GLU28 2.4 50.3 1.0 OG1 A:THR246 2.7 29.4 1.0 CG A:ASP245 3.2 36.3 1.0 CG A:ASP243 3.2 38.3 1.0 CD A:GLU28 3.5 41.8 1.0 OD2 A:ASP245 3.5 44.8 1.0 MG A:MG298 3.5 41.6 1.0 OD2 A:ASP243 3.7 39.4 1.0 O A:HOH336 3.7 35.1 1.0 CB A:THR246 3.9 29.1 1.0 O A:HOH335 4.1 39.9 1.0 CG A:GLU28 4.1 41.4 1.0 N A:THR246 4.2 28.0 1.0 OE1 A:GLU28 4.4 52.9 1.0 CB A:ASP243 4.4 34.3 1.0 CA A:ASP243 4.5 34.8 1.0 OD1 A:ASP61 4.6 42.3 1.0 CB A:ASP245 4.6 30.0 1.0 O A:ASP243 4.6 37.7 1.0 CA A:THR246 4.6 27.8 1.0 C A:ASP243 4.7 35.8 1.0 OD1 A:ASP60 4.9 49.3 1.0 C A:ASP245 4.9 30.8 1.0 OD2 A:ASP97 4.9 44.1 1.0 OD2 A:ASP61 4.9 43.4 1.0 N A:ASP245 4.9 31.2 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure Glycohydrolase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure Glycohydrolase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg298 b:37.0 occ:1.00 OD1 B:ASP243 2.2 43.3 1.0 O B:HOH327 2.2 21.2 1.0 O B:HOH330 2.4 46.8 1.0 OD1 B:ASP245 2.6 29.7 1.0 OE2 B:GLU28 2.6 41.0 1.0 OG1 B:THR246 2.7 31.0 1.0 OD2 B:ASP245 3.0 50.8 1.0 CG B:ASP243 3.1 38.1 1.0 CG B:ASP245 3.2 36.9 1.0 O B:HOH329 3.4 53.2 1.0 OD2 B:ASP243 3.4 46.7 1.0 MG B:MG299 3.4 55.4 1.0 CD B:GLU28 3.6 36.4 1.0 CB B:THR246 4.0 29.0 1.0 OE1 B:GLU28 4.1 41.4 1.0 OD1 B:ASP61 4.2 40.1 1.0 OD2 B:ASP61 4.4 42.6 1.0 N B:THR246 4.4 30.6 1.0 CB B:ASP243 4.5 33.4 1.0 CG B:GLU28 4.5 35.0 1.0 CB B:ASP245 4.7 34.5 1.0 CG B:ASP61 4.8 42.2 1.0 CA B:THR246 4.8 29.0 1.0 CA B:ASP243 4.9 33.6 1.0 CG2 B:THR246 5.0 23.8 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure Glycohydrolase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure Glycohydrolase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg299 b:55.4 occ:1.00 OD2 B:ASP245 2.1 50.8 1.0 OD1 B:ASP60 2.1 41.2 1.0 OD1 B:ASP61 2.3 40.1 1.0 OG1 B:THR59 2.6 37.3 1.0 O B:HOH330 3.0 46.8 1.0 CG B:ASP60 3.2 37.2 1.0 CG B:ASP245 3.3 36.9 1.0 MG B:MG298 3.4 37.0 1.0 CB B:THR59 3.5 40.4 1.0 CG B:ASP61 3.5 42.2 1.0 OD2 B:ASP60 3.5 48.2 1.0 OD1 B:ASP97 3.6 59.3 1.0 OD1 B:ASP245 4.0 29.7 1.0 N B:ASP60 4.1 38.4 1.0 OD2 B:ASP61 4.1 42.6 1.0 OD2 B:ASP97 4.2 50.4 1.0 OE1 B:GLU28 4.3 41.4 1.0 N B:ASP61 4.3 34.6 1.0 CG2 B:THR59 4.3 40.4 1.0 CG B:ASP97 4.3 52.5 1.0 CB B:ASP245 4.4 34.5 1.0 OE2 B:GLU28 4.4 41.0 1.0 OD1 B:ASP21 4.4 49.6 1.0 CB B:ASP60 4.5 38.3 1.0 OG1 B:THR246 4.6 31.0 1.0 CB B:ASP61 4.7 35.5 1.0 CD B:GLU28 4.7 36.4 1.0 CA B:ASP60 4.7 37.6 1.0 CA B:THR59 4.8 40.5 1.0 C B:THR59 4.8 39.9 1.0 O B:HOH329 4.8 53.2 1.0

X.-D.Li, L.F.Huergo, A.Gasperina, F.O.Pedrosa, M.Merrick, F.K.Winkler. Crystal Structure of Dinitrogenase Reductase-Activating Glycohydrolase (Drag) Reveals Conservation in the Adp-Ribosylhydrolase Fold and Specific Features in the Adp-Ribose-Binding Pocket J.Mol.Biol. V. 390 737 2009.
ISSN: ISSN 0022-2836
PubMed: 19477184
DOI: 10.1016/J.JMB.2009.05.031