Magnesium in PDB 5n6o: Wild Type Gdp Form RAC1

The structure of Wild Type Gdp Form RAC1, PDB code: 5n6o was solved by J.Cherfils, Y.Ferrandez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.59 / 2.59
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.641, 82.656, 105.898, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 25.2

The binding sites of Magnesium atom in the Wild Type Gdp Form RAC1 (pdb code 5n6o). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Wild Type Gdp Form RAC1, PDB code: 5n6o:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Wild Type Gdp Form RAC1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Wild Type Gdp Form RAC1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:20.1 occ:1.00 O A:HOH305 1.9 24.8 1.0 OG1 A:THR17 1.9 26.8 1.0 O A:HOH313 2.0 19.7 1.0 O A:HOH309 2.0 8.2 1.0 O A:HOH308 2.0 24.4 1.0 O2B A:GDP201 2.2 27.7 1.0 CB A:THR17 3.3 29.5 1.0 PB A:GDP201 3.4 24.6 1.0 O3B A:GDP201 3.5 23.6 1.0 OD2 A:ASP57 3.6 35.0 1.0 N A:THR17 4.0 23.9 1.0 O2A A:GDP201 4.1 25.2 1.0 CG2 A:THR17 4.2 21.8 1.0 CA A:THR17 4.2 24.6 1.0 O3A A:GDP201 4.3 24.9 1.0 O A:HOH307 4.3 10.6 1.0 CE1 A:PHE37 4.4 24.8 1.0 CG A:ASP57 4.5 34.9 1.0 O1B A:GDP201 4.5 24.3 1.0 O1A A:GDP201 4.5 23.1 1.0 OD1 A:ASP57 4.5 35.4 1.0 PA A:GDP201 4.6 24.5 1.0 CD1 A:PHE37 4.6 25.4 1.0 O A:THR58 4.7 28.3 1.0 CB A:LYS16 5.0 25.0 1.0

Magnesium binding site 2 out of 2 in the Wild Type Gdp Form RAC1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Wild Type Gdp Form RAC1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:23.2 occ:1.00 O B:HOH305 2.1 18.1 1.0 O1B B:GDP201 2.1 24.8 1.0 O B:HOH308 2.2 26.8 1.0 OG1 B:THR17 2.2 21.3 1.0 O B:HOH312 2.3 40.4 1.0 O B:HOH302 2.4 19.4 1.0 O2B B:GDP201 3.1 28.0 1.0 PB B:GDP201 3.2 25.9 1.0 CB B:THR17 3.5 26.2 1.0 O B:HOH316 3.9 30.0 1.0 N B:THR17 4.1 25.5 1.0 OD2 B:ASP57 4.1 31.6 1.0 CE1 B:PHE37 4.2 29.9 1.0 O3B B:GDP201 4.2 22.7 1.0 OD1 B:ASP57 4.3 34.0 1.0 O3A B:GDP201 4.3 26.8 1.0 O B:HOH314 4.4 30.0 1.0 CA B:THR17 4.4 25.7 1.0 O1A B:GDP201 4.4 26.0 1.0 O B:THR58 4.5 25.5 1.0 CG2 B:THR17 4.5 20.7 1.0 O B:HOH325 4.6 12.5 1.0 CD1 B:PHE37 4.6 29.7 1.0 O2A B:GDP201 4.6 30.4 1.0 CG B:ASP57 4.6 33.3 1.0 PA B:GDP201 4.7 29.4 1.0 NZ B:LYS16 4.8 24.4 1.0 CB B:LYS16 4.9 22.0 1.0 CE B:LYS16 4.9 24.2 1.0

Y.Ferrandez, W.Zhang, F.Peurois, L.Akendengue, A.Blangy, M.Zeghouf, J.Cherfils. Allosteric Inhibition of the Guanine Nucleotide Exchange Factor DOCK5 By A Small Molecule. Sci Rep V. 7 14409 2017.
ISSN: ESSN 2045-2322
PubMed: 29089502
DOI: 10.1038/S41598-017-13619-2