Magnesium in PDB 5m6x: Crystal Structure of Human Rhogap Mutated in Its Arginine Finger (R85A) in Complex with Rhoa.Gdp.MGF3- Human

The structure of Crystal Structure of Human Rhogap Mutated in Its Arginine Finger (R85A) in Complex with Rhoa.Gdp.MGF3- Human, PDB code: 5m6x was solved by E.Pellegrini, M.W.Bowler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	76.55 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.470, 66.690, 76.890, 90.00, 95.41, 90.00
R / Rfree (%)	22.4 / 27.2

The structure of Crystal Structure of Human Rhogap Mutated in Its Arginine Finger (R85A) in Complex with Rhoa.Gdp.MGF3- Human also contains other interesting chemical elements:

Fluorine

(F)

6 atoms

The binding sites of Magnesium atom in the Crystal Structure of Human Rhogap Mutated in Its Arginine Finger (R85A) in Complex with Rhoa.Gdp.MGF3- Human (pdb code 5m6x). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Human Rhogap Mutated in Its Arginine Finger (R85A) in Complex with Rhoa.Gdp.MGF3- Human, PDB code: 5m6x:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Human Rhogap Mutated in Its Arginine Finger (R85A) in Complex with Rhoa.Gdp.MGF3- Human


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 Rhogap Mutated in Its Arginine Finger (R85A) in Complex with Rhoa.Gdp.MGF3- Human within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:15.4 occ:1.00 F2 B:MGF203 1.9 11.6 1.0 O B:HOH301 2.0 20.4 1.0 O B:HOH306 2.1 10.6 1.0 O2B B:GDP202 2.1 13.3 1.0 OG1 B:THR19 2.1 15.9 1.0 OG1 B:THR37 2.3 17.1 1.0 CB B:THR37 3.2 17.3 1.0 PB B:GDP202 3.2 13.3 1.0 CB B:THR19 3.2 15.9 1.0 O3B B:GDP202 3.4 13.4 1.0 MG B:MGF203 3.5 11.7 1.0 N B:THR37 3.7 17.3 1.0 O2A B:GDP202 3.8 13.4 1.0 OD2 B:ASP59 3.9 17.6 1.0 N B:THR19 3.9 15.6 1.0 CA B:THR37 4.0 17.5 1.0 CA B:THR19 4.1 15.9 1.0 O1B B:GDP202 4.3 13.4 1.0 O3A B:GDP202 4.3 13.4 1.0 CG2 B:THR19 4.3 15.9 1.0 CG2 B:THR37 4.4 17.4 1.0 PA B:GDP202 4.4 13.3 1.0 OD1 B:ASP59 4.4 17.6 1.0 O B:HOH303 4.5 11.5 1.0 O B:HOH309 4.5 12.6 1.0 O B:VAL35 4.5 18.5 1.0 CG B:ASP59 4.5 17.6 1.0 O1A B:GDP202 4.6 13.4 1.0 F1 B:MGF203 4.6 11.8 1.0 C B:PRO36 4.8 17.5 1.0 O B:THR60 4.8 16.5 1.0 CB B:LYS18 4.8 15.0 1.0 F3 B:MGF203 4.8 11.5 1.0 C B:LYS18 5.0 15.4 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Human Rhogap Mutated in Its Arginine Finger (R85A) in Complex with Rhoa.Gdp.MGF3- Human


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 Rhogap Mutated in Its Arginine Finger (R85A) in Complex with Rhoa.Gdp.MGF3- Human within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:11.7 occ:1.00 MG B:MGF203 0.0 11.7 1.0 F3 B:MGF203 1.9 11.5 1.0 F1 B:MGF203 1.9 11.8 1.0 F2 B:MGF203 1.9 11.6 1.0 O B:HOH309 1.9 12.6 1.0 O3B B:GDP202 2.2 13.4 1.0 PB B:GDP202 3.3 13.3 1.0 MG B:MG201 3.5 15.4 1.0 NE2 B:GLN63 3.7 18.1 1.0 O2B B:GDP202 3.8 13.3 1.0 N B:THR37 3.9 17.3 1.0 O B:HOH306 3.9 10.6 1.0 N B:ALA15 4.0 15.6 1.0 O1B B:GDP202 4.0 13.4 1.0 NZ B:LYS18 4.1 14.7 1.0 CA B:PRO36 4.1 17.7 1.0 OE1 B:GLN63 4.1 18.2 1.0 N B:GLY62 4.2 16.8 1.0 OH B:TYR34 4.2 19.9 1.0 CD B:GLN63 4.3 18.1 1.0 O B:HOH301 4.4 20.4 1.0 CA B:GLY14 4.4 16.0 1.0 CB B:PRO36 4.5 17.6 1.0 C B:PRO36 4.5 17.5 1.0 O B:THR37 4.5 17.4 1.0 CE B:LYS18 4.6 14.8 1.0 O3A B:GDP202 4.6 13.4 1.0 C B:GLY14 4.7 15.7 1.0 CE1 B:TYR34 4.8 20.1 1.0 CB B:THR37 4.8 17.3 1.0 OG1 B:THR37 4.8 17.1 1.0 CA B:THR37 4.8 17.5 1.0 CA B:ALA15 4.9 15.7 1.0 CA B:ALA61 4.9 16.5 1.0 CA B:GLY62 5.0 17.2 1.0 O B:THR60 5.0 16.5 1.0 O2A B:GDP202 5.0 13.4 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Human Rhogap Mutated in Its Arginine Finger (R85A) in Complex with Rhoa.Gdp.MGF3- Human


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Human Rhogap Mutated in Its Arginine Finger (R85A) in Complex with Rhoa.Gdp.MGF3- Human within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg201 b:13.3 occ:1.00 F3 I:MGF203 1.8 13.0 1.0 O I:HOH314 1.9 15.3 1.0 O1B I:GDP202 2.0 17.4 1.0 O I:HOH306 2.1 11.0 1.0 OG1 I:THR19 2.3 17.6 1.0 OG1 I:THR37 2.3 17.2 1.0 PB I:GDP202 3.1 17.7 1.0 O3B I:GDP202 3.2 17.7 1.0 CB I:THR37 3.3 17.4 1.0 CB I:THR19 3.3 17.7 1.0 MG I:MGF203 3.3 12.8 1.0 N I:THR37 3.8 17.3 1.0 O2A I:GDP202 3.8 17.5 1.0 N I:THR19 4.0 17.9 1.0 CA I:THR37 4.1 17.4 1.0 O2B I:GDP202 4.2 17.6 1.0 O3A I:GDP202 4.2 17.7 1.0 CA I:THR19 4.2 17.9 1.0 O I:HOH311 4.3 16.0 1.0 OD1 I:ASP59 4.3 15.9 1.0 OD2 I:ASP59 4.3 16.0 1.0 F1 I:MGF203 4.3 12.6 1.0 CG2 I:THR19 4.4 17.7 1.0 CG2 I:THR37 4.4 17.4 1.0 PA I:GDP202 4.4 17.6 1.0 O I:HOH301 4.5 13.4 1.0 O I:VAL35 4.6 17.6 1.0 O I:THR60 4.6 14.1 1.0 CG I:ASP59 4.7 16.0 1.0 F2 I:MGF203 4.7 12.8 1.0 O1A I:GDP202 4.8 17.6 1.0 CB I:LYS18 4.8 17.7 1.0 C I:PRO36 4.8 17.4 1.0 CE I:LYS18 4.9 17.4 1.0 CA I:PRO36 5.0 17.5 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Human Rhogap Mutated in Its Arginine Finger (R85A) in Complex with Rhoa.Gdp.MGF3- Human


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Human Rhogap Mutated in Its Arginine Finger (R85A) in Complex with Rhoa.Gdp.MGF3- Human within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg203 b:12.8 occ:1.00 MG I:MGF203 0.0 12.8 1.0 F2 I:MGF203 1.9 12.8 1.0 F1 I:MGF203 1.9 12.6 1.0 F3 I:MGF203 1.9 13.0 1.0 O I:HOH311 2.0 16.0 1.0 O3B I:GDP202 2.1 17.7 1.0 MG I:MG201 3.3 13.3 1.0 PB I:GDP202 3.4 17.7 1.0 NE2 I:GLN63 3.6 15.3 1.0 O I:HOH314 3.8 15.3 1.0 N I:THR37 3.8 17.3 1.0 O1B I:GDP202 3.8 17.4 1.0 N I:ALA15 3.9 19.2 1.0 CA I:PRO36 4.1 17.5 1.0 O2B I:GDP202 4.1 17.6 1.0 OE1 I:GLN63 4.1 15.4 1.0 NZ I:LYS18 4.1 17.4 1.0 N I:GLY62 4.2 14.3 1.0 CD I:GLN63 4.2 15.2 1.0 CB I:PRO36 4.3 17.4 1.0 O I:HOH306 4.3 11.0 1.0 OH I:TYR34 4.4 19.5 1.0 C I:PRO36 4.4 17.4 1.0 CA I:GLY14 4.4 19.5 1.0 O3A I:GDP202 4.6 17.7 1.0 OG1 I:THR37 4.6 17.2 1.0 O I:THR37 4.7 17.5 1.0 CE I:LYS18 4.7 17.4 1.0 C I:GLY14 4.7 19.3 1.0 CA I:ALA15 4.7 19.1 1.0 CB I:THR37 4.7 17.4 1.0 CE1 I:TYR34 4.7 20.0 1.0 CA I:THR37 4.8 17.4 1.0 CA I:GLY62 4.9 14.5 1.0 CA I:ALA61 5.0 14.1 1.0

Y.Jin, R.W.Molt, E.Pellegrini, M.J.Cliff, M.W.Bowler, N.G.J.Richards, G.M.Blackburn, J.P.Waltho. Assessing the Influence of Mutation on Gtpase Transition States By Using X-Ray Crystallography, (19) F uc(Nmr), and Dft Approaches. Angew. Chem. Int. Ed. Engl. V. 56 9732 2017.
ISSN: ESSN 1521-3773
PubMed: 28498638
DOI: 10.1002/ANIE.201703074