Magnesium in PDB 2b8w: Crystal-Structure of the N-Terminal Large Gtpase Domain of Human Guanylate Binding Protein 1 (HGBP1) in Complex with Gmp/ALF4

The structure of Crystal-Structure of the N-Terminal Large Gtpase Domain of Human Guanylate Binding Protein 1 (HGBP1) in Complex with Gmp/ALF4, PDB code: 2b8w 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)	29.75 / 2.22
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	149.617, 101.927, 54.121, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 23.3

The structure of Crystal-Structure of the N-Terminal Large Gtpase Domain of Human Guanylate Binding Protein 1 (HGBP1) in Complex with Gmp/ALF4 also contains other interesting chemical elements:

Fluorine	(F)	8 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 Gmp/ALF4 (pdb code 2b8w). 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 Gmp/ALF4, PDB code: 2b8w:
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 Gmp/ALF4


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 Gmp/ALF4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg595 b:24.4 occ:1.00 F3 A:ALF594 2.0 23.0 1.0 O A:HOH633 2.2 27.2 1.0 O1P A:5GP593 2.2 24.8 1.0 OG1 A:THR75 2.2 25.9 1.0 OG A:SER52 2.2 23.1 1.0 O A:HOH647 2.2 30.6 1.0 P A:5GP593 3.2 21.5 1.0 CB A:THR75 3.2 26.2 1.0 CB A:SER52 3.3 18.6 1.0 O2P A:5GP593 3.3 20.3 1.0 F2 A:ALF594 3.3 28.2 1.0 AL A:ALF594 3.4 25.6 1.0 OD1 A:ASP97 3.9 25.3 1.0 N A:SER52 3.9 23.1 1.0 CA A:SER52 4.1 21.4 1.0 O A:HOH609 4.2 35.4 1.0 N A:THR75 4.2 23.1 1.0 O3P A:5GP593 4.2 17.8 1.0 CG2 A:THR75 4.2 22.8 1.0 OD2 A:ASP97 4.3 25.5 1.0 F1 A:ALF594 4.3 24.1 1.0 CA A:THR75 4.3 21.9 1.0 O5' A:5GP593 4.4 21.0 1.0 O A:THR98 4.4 24.7 1.0 O A:HOH602 4.5 29.7 1.0 CG A:ASP97 4.5 24.6 1.0 O A:SER66 4.5 21.4 1.0 C5' A:5GP593 4.6 19.1 1.0 CB A:LYS51 4.8 20.9 1.0 O A:LEU67 4.9 24.2 1.0 C A:LYS51 4.9 25.9 1.0 NH2 A:ARG48 5.0 21.6 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 Gmp/ALF4


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 Gmp/ALF4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg595 b:24.7 occ:1.00 F2 B:ALF594 2.0 28.2 1.0 O B:HOH671 2.1 35.6 1.0 O B:HOH649 2.2 29.9 1.0 O1P B:5GP593 2.2 26.5 1.0 OG1 B:THR75 2.2 22.7 1.0 OG B:SER52 2.2 27.4 1.0 CB B:THR75 3.2 20.9 1.0 P B:5GP593 3.2 22.5 1.0 CB B:SER52 3.2 18.6 1.0 O2P B:5GP593 3.3 21.1 1.0 AL B:ALF594 3.4 26.8 1.0 F3 B:ALF594 3.4 23.6 1.0 N B:SER52 3.9 20.3 1.0 OD1 B:ASP97 4.0 25.5 1.0 CA B:SER52 4.0 21.4 1.0 N B:THR75 4.1 23.0 1.0 CG2 B:THR75 4.1 17.1 1.0 F4 B:ALF594 4.2 23.8 1.0 O B:HOH612 4.2 34.8 1.0 O3P B:5GP593 4.2 20.6 1.0 CA B:THR75 4.3 21.6 1.0 OD2 B:ASP97 4.3 24.0 1.0 O5' B:5GP593 4.4 19.1 1.0 O B:THR98 4.4 22.7 1.0 O B:HOH599 4.5 32.4 1.0 CG B:ASP97 4.5 26.5 1.0 O B:SER66 4.5 22.2 1.0 C5' B:5GP593 4.5 22.0 1.0 CB B:LYS51 4.9 21.2 1.0 O B:LEU67 4.9 22.6 1.0 C B:LYS51 5.0 22.1 1.0 NZ B:LYS51 5.0 21.2 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