Magnesium in PDB 2b92: Crystal-Structure of the N-Terminal Large Gtpase Domain of Human Guanylate Binding Protein 1 (HGBP1) in Complex with Gdp/ALF3

The structure of Crystal-Structure of the N-Terminal Large Gtpase Domain of Human Guanylate Binding Protein 1 (HGBP1) in Complex with Gdp/ALF3, PDB code: 2b92 was solved by A.Ghosh, G.J.K.Praefcke, L.Renault, A.Wittinghofer, C.Herrmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 3.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	148.820, 103.921, 55.485, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 25

The structure of Crystal-Structure of the N-Terminal Large Gtpase Domain of Human Guanylate Binding Protein 1 (HGBP1) in Complex with Gdp/ALF3 also contains other interesting chemical elements:

Fluorine	(F)	6 atoms
Aluminium	(Al)	2 atoms

The binding sites of Magnesium atom in the Crystal-Structure of the N-Terminal Large Gtpase Domain of Human Guanylate Binding Protein 1 (HGBP1) in Complex with Gdp/ALF3 (pdb code 2b92). 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 N-Terminal Large Gtpase Domain of Human Guanylate Binding Protein 1 (HGBP1) in Complex with Gdp/ALF3, PDB code: 2b92:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal-Structure of the N-Terminal Large Gtpase Domain of Human Guanylate Binding Protein 1 (HGBP1) in Complex with Gdp/ALF3


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 N-Terminal Large Gtpase Domain of Human Guanylate Binding Protein 1 (HGBP1) in Complex with Gdp/ALF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg595 b:40.1 occ:1.00 F1 A:AF3594 1.9 39.0 1.0 O2B A:GDP593 1.9 56.8 1.0 OG A:SER52 2.1 37.5 1.0 OG1 A:THR75 2.3 51.7 1.0 CB A:THR75 3.1 52.2 1.0 PB A:GDP593 3.2 48.0 1.0 CB A:SER52 3.2 36.9 1.0 O3B A:GDP593 3.4 46.7 1.0 AL A:AF3594 3.4 32.3 1.0 O2A A:GDP593 3.5 52.3 1.0 N A:SER52 4.0 36.3 1.0 OD1 A:ASP97 4.1 63.8 1.0 O1B A:GDP593 4.1 51.9 1.0 N A:THR75 4.1 53.5 1.0 OD2 A:ASP97 4.1 59.8 1.0 PA A:GDP593 4.1 55.1 1.0 O3A A:GDP593 4.1 53.7 1.0 F2 A:AF3594 4.1 37.8 1.0 CG2 A:THR75 4.1 50.4 1.0 CA A:SER52 4.2 37.4 1.0 O1A A:GDP593 4.2 59.1 1.0 CA A:THR75 4.2 52.3 1.0 O A:SER66 4.4 53.6 1.0 O A:THR98 4.4 42.3 1.0 CG A:ASP97 4.5 52.8 1.0 F3 A:AF3594 4.7 38.5 1.0 CB A:LYS51 4.9 33.8 1.0 O A:LEU67 5.0 55.4 1.0

Magnesium binding site 2 out of 2 in the Crystal-Structure of the N-Terminal Large Gtpase Domain of Human Guanylate Binding Protein 1 (HGBP1) in Complex with Gdp/ALF3


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 N-Terminal Large Gtpase Domain of Human Guanylate Binding Protein 1 (HGBP1) in Complex with Gdp/ALF3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg595 b:43.6 occ:1.00 O2B B:GDP593 1.9 48.8 1.0 OG B:SER52 2.0 36.9 1.0 F3 B:AF3594 2.1 34.6 1.0 OG1 B:THR75 2.3 52.4 1.0 CB B:THR75 3.1 53.0 1.0 PB B:GDP593 3.1 47.9 1.0 AL B:AF3594 3.3 30.4 1.0 O3B B:GDP593 3.4 47.3 1.0 CB B:SER52 3.4 36.6 1.0 OD1 B:ASP97 3.6 61.9 1.0 F2 B:AF3594 3.7 36.5 1.0 O2A B:GDP593 3.8 55.8 1.0 N B:SER52 3.9 35.7 1.0 OD2 B:ASP97 3.9 60.7 1.0 O1B B:GDP593 3.9 53.2 1.0 CG2 B:THR75 4.0 51.4 1.0 N B:THR75 4.1 54.4 1.0 CG B:ASP97 4.2 53.2 1.0 CA B:SER52 4.2 37.1 1.0 O B:THR98 4.2 42.9 1.0 CA B:THR75 4.2 53.3 1.0 O3A B:GDP593 4.2 55.8 1.0 PA B:GDP593 4.4 55.4 1.0 O1A B:GDP593 4.4 56.7 1.0 CB B:LYS51 4.6 32.6 1.0 CE B:LYS51 4.7 29.4 1.0 O B:HOH599 4.7 64.2 1.0 O B:SER66 4.8 53.8 1.0 F1 B:AF3594 4.9 37.5 1.0 C B:LYS51 5.0 34.4 1.0

A.Ghosh, G.J.Praefcke, L.Renault, A.Wittinghofer, C.Herrmann. How Guanylate-Binding Proteins Achieve Assembly-Stimulated Processive Cleavage of Gtp to Gmp. Nature V. 440 101 2006.
ISSN: ISSN 0028-0836
PubMed: 16511497
DOI: 10.1038/NATURE04510