Magnesium in PDB 2dpx: Crystal Structure of Human Rad Gtpase

All present enzymatic activity of Crystal Structure of Human Rad Gtpase:
3.6.5.2;

The structure of Crystal Structure of Human Rad Gtpase, PDB code: 2dpx was solved by A.Yanuar, S.Sakurai, K.Kitano, T.Hakoshima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.64 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.163, 58.608, 53.440, 90.00, 97.98, 90.00
R / Rfree (%)	21.4 / 24

The binding sites of Magnesium atom in the Crystal Structure of Human Rad Gtpase (pdb code 2dpx). 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 Human Rad Gtpase, PDB code: 2dpx:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human Rad Gtpase


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 Human Rad Gtpase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg400 b:24.3 occ:1.00 OG A:SER105 1.9 29.9 1.0 O A:HOH53 2.0 27.2 1.0 O A:HOH52 2.0 28.5 1.0 O A:HOH51 2.1 30.2 1.0 O3B A:GDP500 2.1 21.5 1.0 O A:HOH54 2.2 28.1 1.0 CB A:SER105 3.0 30.5 1.0 PB A:GDP500 3.3 24.8 1.0 O1B A:GDP500 3.5 22.8 1.0 N A:SER105 3.8 22.2 1.0 CA A:SER105 4.0 23.6 1.0 O2A A:GDP500 4.0 26.7 1.0 OD2 A:ASP144 4.1 30.4 1.0 OD1 A:ASP144 4.3 33.3 1.0 O2B A:GDP500 4.3 22.2 1.0 O3A A:GDP500 4.4 27.8 1.0 O A:HOH5 4.6 33.2 1.0 PA A:GDP500 4.6 28.5 1.0 CG A:ASP144 4.6 23.7 1.0 O1A A:GDP500 4.7 23.6 1.0 CB A:LYS104 4.9 19.0 1.0 C A:LYS104 5.0 23.5 1.0 NZ A:LYS104 5.0 25.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human Rad Gtpase


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 Human Rad Gtpase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg400 b:35.3 occ:1.00 O B:HOH57 1.9 31.7 1.0 OG B:SER105 2.0 35.6 1.0 O B:HOH59 2.1 36.0 1.0 O B:HOH58 2.1 35.1 1.0 O3B B:GDP500 2.1 28.3 1.0 O B:HOH56 2.2 32.6 1.0 CB B:SER105 3.1 34.5 1.0 PB B:GDP500 3.4 28.1 1.0 O1B B:GDP500 3.6 29.6 1.0 OD2 B:ASP144 3.8 48.6 1.0 N B:SER105 3.9 26.1 1.0 CA B:SER105 4.1 31.8 1.0 O2A B:GDP500 4.1 27.7 1.0 OD1 B:ASP144 4.1 47.3 1.0 O2B B:GDP500 4.4 29.5 1.0 CG B:ASP144 4.4 50.9 1.0 O3A B:GDP500 4.5 28.2 1.0 PA B:GDP500 4.6 32.5 1.0 O1A B:GDP500 4.7 25.9 1.0 CB B:LYS104 4.9 27.9 1.0 C B:LYS104 5.0 30.8 1.0 O B:HOH68 5.0 44.3 1.0

A.Yanuar, S.Sakurai, K.Kitano, T.Hakoshima. Crystal Structure of Human Rad Gtpase of the Rgk-Family Genes Cells V. 11 961 2006.
ISSN: ISSN 1356-9597
PubMed: 16866878
DOI: 10.1111/J.1365-2443.2006.00994.X