Magnesium in PDB 5hpy: Crystal Structure of Rhoa.Gdp.MGF3-in Complex with Human Myosin 9B Rhogap Domain

The structure of Crystal Structure of Rhoa.Gdp.MGF3-in Complex with Human Myosin 9B Rhogap Domain, PDB code: 5hpy was solved by F.S.Yi, J.Q.Ren, W.Feng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.70 / 2.40
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	114.055, 90.762, 93.582, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 24.6

The structure of Crystal Structure of Rhoa.Gdp.MGF3-in Complex with Human Myosin 9B Rhogap Domain also contains other interesting chemical elements:

Fluorine

(F)

6 atoms

The binding sites of Magnesium atom in the Crystal Structure of Rhoa.Gdp.MGF3-in Complex with Human Myosin 9B Rhogap Domain (pdb code 5hpy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Rhoa.Gdp.MGF3-in Complex with Human Myosin 9B Rhogap Domain, PDB code: 5hpy:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of Rhoa.Gdp.MGF3-in Complex with Human Myosin 9B Rhogap Domain


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 Rhoa.Gdp.MGF3-in Complex with Human Myosin 9B Rhogap Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:40.7 occ:1.00 MG B:MGF201 0.0 40.7 1.0 F1 B:MGF201 1.8 37.9 1.0 F3 B:MGF201 1.8 38.1 1.0 F2 B:MGF201 1.8 39.0 1.0 O2B B:GDP203 2.4 36.4 1.0 O B:HOH318 2.4 33.0 1.0 PB B:GDP203 3.5 42.7 1.0 MG B:MG202 3.7 38.0 1.0 NH2 A:ARG235 3.8 41.8 1.0 N B:ALA15 3.8 40.8 1.0 O3B B:GDP203 3.9 34.7 1.0 NE2 B:GLN63 3.9 40.3 1.0 NZ B:LYS18 3.9 38.8 1.0 CA B:GLY14 3.9 36.2 1.0 OE1 B:GLN63 4.0 36.5 1.0 O1B B:GDP203 4.0 39.2 1.0 N B:THR37 4.1 39.5 1.0 N B:GLY62 4.2 34.4 1.0 NE A:ARG235 4.2 43.0 1.0 O B:HOH305 4.3 35.7 1.0 CA B:PRO36 4.3 38.9 1.0 O B:HOH319 4.3 37.0 1.0 CB B:PRO36 4.3 40.0 1.0 CD B:GLN63 4.4 39.6 1.0 C B:GLY14 4.4 39.3 1.0 CE B:LYS18 4.5 37.6 1.0 CZ A:ARG235 4.5 43.9 1.0 O B:THR37 4.6 35.7 1.0 O B:THR60 4.7 35.1 1.0 C B:PRO36 4.7 37.9 1.0 O3A B:GDP203 4.8 50.3 1.0 CA B:ALA61 4.8 35.0 1.0 CB B:THR37 4.8 37.0 1.0 CA B:ALA15 4.9 43.7 1.0 CA B:GLY62 4.9 34.7 1.0 CA B:THR37 5.0 39.2 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of Rhoa.Gdp.MGF3-in Complex with Human Myosin 9B Rhogap Domain


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 Rhoa.Gdp.MGF3-in Complex with Human Myosin 9B Rhogap Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:38.0 occ:1.00 O B:HOH319 2.0 37.0 1.0 F2 B:MGF201 2.0 39.0 1.0 O B:HOH305 2.1 35.7 1.0 O3B B:GDP203 2.1 34.7 1.0 OG1 B:THR19 2.2 38.5 1.0 OG1 B:THR37 2.2 37.2 1.0 CB B:THR37 2.8 37.0 1.0 CB B:THR19 3.2 42.4 1.0 PB B:GDP203 3.3 42.7 1.0 O2B B:GDP203 3.4 36.4 1.0 N B:THR37 3.7 39.5 1.0 MG B:MGF201 3.7 40.7 1.0 OD2 B:ASP59 3.7 38.6 1.0 CA B:THR37 3.9 39.2 1.0 CG2 B:THR37 3.9 35.7 1.0 OD1 B:ASP59 4.0 36.3 1.0 N B:THR19 4.0 40.6 1.0 CA B:THR19 4.2 42.2 1.0 CG B:ASP59 4.2 37.1 1.0 O2A B:GDP203 4.3 34.9 1.0 O B:THR60 4.3 35.1 1.0 CG2 B:THR19 4.3 40.8 1.0 O1B B:GDP203 4.3 39.2 1.0 F3 B:MGF201 4.5 38.1 1.0 O3A B:GDP203 4.5 50.3 1.0 NH2 A:ARG235 4.6 41.8 1.0 O B:HOH318 4.7 33.0 1.0 O1A B:GDP203 4.8 36.6 1.0 PA B:GDP203 4.8 42.7 1.0 CE B:LYS18 4.8 37.6 1.0 C B:PRO36 4.8 37.9 1.0 CB B:LYS18 4.9 40.4 1.0 O B:VAL35 4.9 42.7 1.0 C B:THR37 4.9 39.1 1.0 O B:HOH317 5.0 43.6 1.0 F1 B:MGF201 5.0 37.9 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of Rhoa.Gdp.MGF3-in Complex with Human Myosin 9B Rhogap Domain


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 Rhoa.Gdp.MGF3-in Complex with Human Myosin 9B Rhogap Domain within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg201 b:41.9 occ:1.00 MG F:MGF201 0.0 41.9 1.0 F3 F:MGF201 1.8 47.1 1.0 F1 F:MGF201 1.8 40.6 1.0 F2 F:MGF201 1.8 36.9 1.0 O F:HOH314 2.5 38.4 1.0 O3B F:GDP202 2.7 39.8 1.0 PB F:GDP202 3.6 43.6 1.0 MG F:MG203 3.6 42.7 1.0 O2B F:GDP202 3.8 41.0 1.0 O1B F:GDP202 3.8 52.8 1.0 NZ F:LYS18 3.8 44.5 1.0 N F:ALA15 3.9 45.1 1.0 NE2 F:GLN63 3.9 42.4 1.0 NH2 D:ARG235 3.9 47.7 1.0 CA F:GLY14 3.9 44.7 1.0 N F:GLY62 4.1 39.7 1.0 N F:THR37 4.1 43.0 1.0 OE1 F:GLN63 4.1 40.3 1.0 CA F:PRO36 4.1 41.8 1.0 O F:HOH307 4.2 39.3 1.0 CB F:PRO36 4.3 40.0 1.0 NE D:ARG235 4.3 47.5 1.0 CD F:GLN63 4.5 42.7 1.0 CE F:LYS18 4.5 42.7 1.0 C F:GLY14 4.5 47.6 1.0 O F:HOH315 4.6 38.9 1.0 CZ D:ARG235 4.6 49.8 1.0 O F:THR37 4.6 36.4 1.0 C F:PRO36 4.6 43.7 1.0 CA F:ALA61 4.7 40.0 1.0 O F:THR60 4.8 39.5 1.0 CB F:THR37 4.8 39.8 1.0 CA F:GLY62 4.8 39.4 1.0 OG1 F:THR37 4.9 42.8 1.0 CA F:ALA15 4.9 48.9 1.0 C F:ALA61 4.9 42.0 1.0 CA F:THR37 5.0 42.9 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of Rhoa.Gdp.MGF3-in Complex with Human Myosin 9B Rhogap Domain


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 Rhoa.Gdp.MGF3-in Complex with Human Myosin 9B Rhogap Domain within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg203 b:42.7 occ:1.00 F3 F:MGF201 2.0 47.1 1.0 OG1 F:THR37 2.0 42.8 1.0 OG1 F:THR19 2.1 41.3 1.0 O F:HOH307 2.1 39.3 1.0 O2B F:GDP202 2.2 41.0 1.0 O F:HOH315 2.3 38.9 1.0 CB F:THR37 2.8 39.8 1.0 CB F:THR19 3.3 45.1 1.0 PB F:GDP202 3.4 43.6 1.0 N F:THR37 3.5 43.0 1.0 MG F:MGF201 3.6 41.9 1.0 O3B F:GDP202 3.7 39.8 1.0 CA F:THR37 3.8 42.9 1.0 OD2 F:ASP59 3.9 40.2 1.0 CG2 F:THR37 4.0 39.9 1.0 O2A F:GDP202 4.1 45.0 1.0 OD1 F:ASP59 4.1 40.4 1.0 N F:THR19 4.2 43.2 1.0 O F:HOH312 4.2 38.3 1.0 O1B F:GDP202 4.2 52.8 1.0 CA F:THR19 4.3 45.6 1.0 CG2 F:THR19 4.3 43.6 1.0 O F:THR60 4.4 39.5 1.0 CG F:ASP59 4.4 40.6 1.0 F1 F:MGF201 4.5 40.6 1.0 O F:HOH305 4.5 49.0 1.0 O3A F:GDP202 4.5 57.0 1.0 C F:PRO36 4.6 43.7 1.0 NH2 D:ARG235 4.7 47.7 1.0 O F:HOH314 4.7 38.4 1.0 PA F:GDP202 4.8 49.7 1.0 O F:VAL35 4.8 44.9 1.0 C F:THR37 4.9 40.7 1.0 CA F:PRO36 4.9 41.8 1.0 MG F:MG204 4.9 49.3 1.0 F2 F:MGF201 4.9 36.9 1.0 O1A F:GDP202 5.0 40.6 1.0 O F:THR37 5.0 36.4 1.0 CB F:LYS18 5.0 44.9 1.0 CE F:LYS18 5.0 42.7 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of Rhoa.Gdp.MGF3-in Complex with Human Myosin 9B Rhogap Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Rhoa.Gdp.MGF3-in Complex with Human Myosin 9B Rhogap Domain within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg204 b:49.3 occ:1.00 OH F:TYR42 2.7 49.7 1.0 O F:HOH312 2.7 38.3 1.0 OD2 F:ASP59 2.8 40.2 1.0 CG F:GLU40 3.2 45.0 1.0 CG2 F:THR19 3.3 43.6 1.0 CB F:GLU40 3.3 43.4 1.0 CZ F:TYR42 3.6 46.8 1.0 OG1 F:THR37 3.6 42.8 1.0 CE2 F:TYR42 3.6 44.1 1.0 CG F:ASP59 3.8 40.6 1.0 OG1 F:THR19 3.8 41.3 1.0 CG2 F:THR37 3.9 39.9 1.0 CB F:ASP59 4.1 39.1 1.0 CB F:THR19 4.2 45.1 1.0 CB F:THR37 4.3 39.8 1.0 CD F:GLU40 4.5 50.4 1.0 O F:HOH339 4.5 40.9 1.0 CA F:GLU40 4.8 41.3 1.0 OD1 F:ASP59 4.9 40.4 1.0 CE1 F:TYR42 4.9 50.0 1.0 MG F:MG203 4.9 42.7 1.0 CD1 F:ILE23 5.0 52.2 1.0 CD2 F:TYR42 5.0 44.2 1.0

F.Yi, R.Kong, J.Ren, L.Zhu, J.Lou, J.Y.Wu, W.Feng. Noncanonical MYO9B-Rhogap Accelerates Rhoa Gtp Hydrolysis By A Dual-Arginine-Finger Mechanism J.Mol.Biol. V. 428 3043 2016.
ISSN: ESSN 1089-8638
PubMed: 27363609
DOI: 10.1016/J.JMB.2016.06.014