Magnesium in PDB 2gj8: Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and K+

The structure of Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and K+, PDB code: 2gj8 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)	20.00 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.540, 70.227, 91.300, 90.00, 95.51, 90.00
R / Rfree (%)	20.5 / 25.6

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

Fluorine	(F)	16 atoms
Aluminium	(Al)	4 atoms
Potassium	(K)	4 atoms

The binding sites of Magnesium atom in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and K+ (pdb code 2gj8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and K+, PDB code: 2gj8:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and K+


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 K+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:11.7 occ:1.00 F3 A:ALF601 1.9 12.5 1.0 O3B A:GDP650 2.0 7.0 1.0 OG A:SER230 2.0 10.3 1.0 OG1 A:THR251 2.2 9.8 1.0 O A:HOH655 2.2 11.0 1.0 O A:HOH654 2.3 10.5 1.0 CB A:SER230 3.1 9.9 1.0 CB A:THR251 3.2 11.9 1.0 PB A:GDP650 3.2 9.8 1.0 O2B A:GDP650 3.4 9.0 1.0 AL A:ALF601 3.5 13.0 1.0 N A:SER230 3.8 8.9 1.0 OD2 A:ASP270 3.9 13.8 1.0 F2 A:ALF601 3.9 12.0 1.0 CA A:SER230 4.0 9.2 1.0 N A:THR251 4.0 11.7 1.0 F1 A:ALF601 4.1 10.5 1.0 O A:HOH653 4.1 13.1 1.0 O2A A:GDP650 4.1 11.1 1.0 OD1 A:ASP270 4.2 14.7 1.0 CA A:THR251 4.2 12.4 1.0 CG2 A:THR251 4.2 11.9 1.0 O1B A:GDP650 4.3 10.1 1.0 O3A A:GDP650 4.3 7.9 1.0 CG A:ASP270 4.5 16.2 1.0 O A:ILE243 4.5 11.7 1.0 PA A:GDP650 4.5 8.4 1.0 O A:HOH652 4.7 11.4 1.0 O1A A:GDP650 4.7 9.1 1.0 O A:THR271 4.7 12.5 1.0 CB A:LYS229 4.8 10.1 1.0 C A:LYS229 4.8 9.4 1.0 K A:K603 5.0 10.8 1.0

Magnesium binding site 2 out of 4 in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and K+


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 K+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg612 b:17.1 occ:1.00 F1 B:ALF611 1.8 17.0 1.0 O3B B:GDP651 2.0 13.7 1.0 O B:HOH655 2.1 11.8 1.0 OG B:SER230 2.1 18.9 1.0 OG1 B:THR251 2.2 12.9 1.0 O B:HOH654 2.2 13.6 1.0 CB B:THR251 3.1 13.7 1.0 PB B:GDP651 3.2 17.3 1.0 CB B:SER230 3.2 15.8 1.0 AL B:ALF611 3.3 15.1 1.0 O2B B:GDP651 3.4 14.7 1.0 F4 B:ALF611 3.6 16.2 1.0 N B:SER230 3.9 15.3 1.0 N B:THR251 3.9 13.5 1.0 F3 B:ALF611 4.0 15.2 1.0 OD1 B:ASP270 4.1 18.6 1.0 CA B:THR251 4.1 13.1 1.0 CA B:SER230 4.1 16.6 1.0 O2A B:GDP651 4.2 18.3 1.0 O A:HOH662 4.2 19.2 1.0 CG2 B:THR251 4.2 13.2 1.0 O1B B:GDP651 4.3 17.5 1.0 O3A B:GDP651 4.3 16.3 1.0 OD2 B:ASP270 4.3 18.4 1.0 O1A B:GDP651 4.5 17.2 1.0 O B:ILE243 4.5 19.6 1.0 O B:HOH653 4.5 9.9 1.0 PA B:GDP651 4.6 16.5 1.0 CG B:ASP270 4.7 17.0 1.0 K B:K613 4.8 16.5 1.0 O B:THR271 4.8 13.3 1.0 CB B:LYS229 4.9 14.9 1.0 CB B:THR250 4.9 14.5 1.0 C B:LYS229 5.0 14.5 1.0

Magnesium binding site 3 out of 4 in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and K+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and K+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg622 b:9.9 occ:1.00 F1 C:ALF621 1.9 11.7 1.0 O1B C:GDP652 2.0 9.2 1.0 OG1 C:THR251 2.0 9.7 1.0 O C:HOH653 2.1 11.7 1.0 OG C:SER230 2.1 8.4 1.0 O C:HOH654 2.2 10.6 1.0 CB C:THR251 3.1 11.4 1.0 CB C:SER230 3.2 10.1 1.0 PB C:GDP652 3.2 11.0 1.0 O3B C:GDP652 3.5 15.8 1.0 AL C:ALF621 3.6 11.4 1.0 N C:SER230 3.8 8.9 1.0 F4 C:ALF621 3.9 12.7 1.0 N C:THR251 3.9 11.3 1.0 OD1 C:ASP270 4.0 14.1 1.0 CA C:SER230 4.0 9.2 1.0 O C:HOH655 4.1 13.1 1.0 CG2 C:THR251 4.1 12.3 1.0 CA C:THR251 4.1 11.1 1.0 F3 C:ALF621 4.1 10.6 1.0 O2A C:GDP652 4.2 11.6 1.0 OD2 C:ASP270 4.2 13.7 1.0 O2B C:GDP652 4.3 11.3 1.0 O3A C:GDP652 4.3 10.4 1.0 O C:HOH656 4.5 10.3 1.0 CG C:ASP270 4.5 14.3 1.0 O C:ILE243 4.6 11.6 1.0 PA C:GDP652 4.6 10.8 1.0 O C:THR271 4.7 11.8 1.0 O1A C:GDP652 4.7 11.2 1.0 C C:LYS229 4.8 9.6 1.0 CB C:LYS229 4.9 10.2 1.0 K C:K623 5.0 11.8 1.0

Magnesium binding site 4 out of 4 in the Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and K+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Mnme G-Domain in Complex with Gdp*ALF4-, MG2+ and K+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg632 b:13.0 occ:1.00 F3 D:ALF631 2.0 12.4 1.0 OG1 D:THR251 2.0 8.5 1.0 OG D:SER230 2.0 12.0 1.0 O D:HOH657 2.1 14.5 1.0 O3B D:GDP653 2.1 12.0 1.0 O D:HOH658 2.1 11.6 1.0 CB D:THR251 3.0 11.8 1.0 CB D:SER230 3.2 13.7 1.0 PB D:GDP653 3.3 12.3 1.0 O2B D:GDP653 3.5 12.4 1.0 AL D:ALF631 3.6 13.6 1.0 N D:SER230 3.8 13.3 1.0 F2 D:ALF631 3.9 13.1 1.0 OD1 D:ASP270 3.9 13.2 1.0 N D:THR251 4.0 12.2 1.0 O D:HOH724 4.0 16.1 1.0 CG2 D:THR251 4.0 14.1 1.0 CA D:SER230 4.1 12.8 1.0 CA D:THR251 4.1 12.0 1.0 F1 D:ALF631 4.2 13.1 1.0 O2A D:GDP653 4.2 12.6 1.0 OD2 D:ASP270 4.3 14.1 1.0 O1B D:GDP653 4.3 13.2 1.0 O3A D:GDP653 4.4 13.1 1.0 CG D:ASP270 4.5 14.6 1.0 O D:ILE243 4.5 12.5 1.0 O D:HOH656 4.6 11.1 1.0 PA D:GDP653 4.6 13.0 1.0 O D:THR271 4.7 13.1 1.0 O1A D:GDP653 4.7 14.2 1.0 C D:LYS229 4.9 13.8 1.0 CB D:LYS229 4.9 13.2 1.0 CB D:THR250 4.9 11.3 1.0 K D:K633 5.0 13.5 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