Magnesium in PDB 2gja: Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and NH4+

The structure of Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and NH4+, PDB code: 2gja was solved by A.Scrima, A.Wittinghofer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.37 / 1.85
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	71.280, 90.650, 138.470, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 22.8

The structure of Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and NH4+ also contains other interesting chemical elements:

Fluorine	(F)	8 atoms
Aluminium	(Al)	2 atoms

The binding sites of Magnesium atom in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and NH4+ (pdb code 2gja). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and NH4+, PDB code: 2gja:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and NH4+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and NH4+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:11.5 occ:1.00 F3 A:ALF401 1.9 15.8 1.0 O3B A:GDP400 2.0 8.6 1.0 OG1 A:THR251 2.1 10.5 1.0 OG A:SER230 2.1 8.7 1.0 O A:HOH101 2.1 11.4 1.0 O A:HOH100 2.1 13.2 1.0 CB A:THR251 3.1 11.6 1.0 CB A:SER230 3.1 10.6 1.0 PB A:GDP400 3.3 10.4 1.0 O2B A:GDP400 3.5 7.8 1.0 AL A:ALF401 3.5 11.2 1.0 F2 A:ALF401 3.8 12.7 1.0 N A:SER230 3.8 10.7 1.0 N A:THR251 4.0 11.3 1.0 O A:HOH7 4.0 15.4 1.0 CA A:SER230 4.0 10.1 1.0 OD2 A:ASP270 4.0 16.3 1.0 CG2 A:THR251 4.1 12.7 1.0 CA A:THR251 4.1 11.8 1.0 F1 A:ALF401 4.1 12.9 1.0 O2A A:GDP400 4.1 10.0 1.0 O1B A:GDP400 4.3 11.4 1.0 OD1 A:ASP270 4.3 19.9 1.0 O3A A:GDP400 4.3 7.8 1.0 O A:ILE243 4.5 11.3 1.0 PA A:GDP400 4.5 9.8 1.0 O A:HOH2 4.6 9.2 1.0 CG A:ASP270 4.6 17.3 1.0 O A:THR271 4.6 13.4 1.0 O1A A:GDP400 4.7 9.3 1.0 C A:LYS229 4.9 10.5 1.0 CB A:LYS229 4.9 9.4 1.0 N A:NH4403 4.9 11.4 1.0

Magnesium binding site 2 out of 2 in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and NH4+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and NH4+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:11.8 occ:1.00 F3 B:ALF501 1.9 14.9 1.0 O3B B:GDP500 2.0 9.6 1.0 OG B:SER230 2.1 11.2 1.0 OG1 B:THR251 2.1 11.3 1.0 O B:HOH113 2.1 11.4 1.0 O B:HOH114 2.2 11.3 1.0 CB B:THR251 3.1 10.6 1.0 PB B:GDP500 3.2 10.1 1.0 CB B:SER230 3.2 11.4 1.0 O2B B:GDP500 3.4 6.6 1.0 AL B:ALF501 3.5 13.4 1.0 F2 B:ALF501 3.8 14.8 1.0 N B:SER230 3.8 11.2 1.0 N B:THR251 4.0 10.6 1.0 OD2 B:ASP270 4.0 19.2 1.0 CA B:SER230 4.1 11.3 1.0 O2A B:GDP500 4.1 10.0 1.0 F1 B:ALF501 4.1 15.4 1.0 CG2 B:THR251 4.1 13.4 1.0 O B:HOH17 4.1 16.0 1.0 CA B:THR251 4.2 11.4 1.0 O1B B:GDP500 4.2 11.8 1.0 O3A B:GDP500 4.2 10.6 1.0 OD1 B:ASP270 4.3 20.1 1.0 O B:ILE243 4.5 10.8 1.0 O B:HOH99 4.5 9.9 1.0 PA B:GDP500 4.5 10.7 1.0 CG B:ASP270 4.6 18.1 1.0 O B:THR271 4.6 14.2 1.0 O1A B:GDP500 4.6 9.0 1.0 CB B:LYS229 4.8 10.0 1.0 C B:LYS229 4.9 10.6 1.0 N B:NH4503 4.9 8.7 1.0 CB B:THR250 5.0 11.9 1.0

A.Scrima, A.Wittinghofer. Dimerisation-Dependent Gtpase Reaction of Mnme: How Potassium Acts As Gtpase-Activating Element. Embo J. V. 25 2940 2006.
ISSN: ISSN 0261-4189
PubMed: 16763562
DOI: 10.1038/SJ.EMBOJ.7601171