Magnesium in PDB 5fr1: Double Acetylated Rhogdi-Alpha in Complex with Rhoa-Gdp

The structure of Double Acetylated Rhogdi-Alpha in Complex with Rhoa-Gdp, PDB code: 5fr1 was solved by N.Kuhlmann, S.Wroblowski, M.Lammers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.11 / 2.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.100, 67.640, 120.230, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 25.6

The binding sites of Magnesium atom in the Double Acetylated Rhogdi-Alpha in Complex with Rhoa-Gdp (pdb code 5fr1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Double Acetylated Rhogdi-Alpha in Complex with Rhoa-Gdp, PDB code: 5fr1:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Double Acetylated Rhogdi-Alpha in Complex with Rhoa-Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Double Acetylated Rhogdi-Alpha in Complex with Rhoa-Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1195 b:56.5 occ:1.00 HG1 A:THR19 1.9 42.1 1.0 O A:HOH2005 1.9 48.0 1.0 O A:HOH2004 2.0 44.0 1.0 O1B A:GDP1194 2.3 55.4 1.0 OG1 A:THR19 2.3 42.1 1.0 O A:THR37 2.4 48.1 1.0 O3B A:GDP1194 2.9 50.8 1.0 PB A:GDP1194 3.0 51.2 1.0 C A:THR37 3.5 46.9 1.0 CB A:THR19 3.6 43.2 1.0 HB A:THR19 3.7 43.2 1.0 HA A:THR37 3.7 47.8 1.0 H A:THR19 3.8 43.2 1.0 HE2 A:LYS18 3.8 40.0 1.0 HB2 A:LYS18 3.9 40.6 1.0 O2B A:GDP1194 4.1 50.8 1.0 HA A:VAL38 4.1 46.8 1.0 HG23 A:THR37 4.1 49.7 1.0 O3A A:GDP1194 4.1 54.3 1.0 O1A A:GDP1194 4.1 54.1 1.0 HZ3 A:LYS18 4.1 39.9 1.0 CA A:THR37 4.2 47.8 1.0 HG21 A:THR37 4.2 49.7 1.0 HZ2 A:LYS18 4.2 39.9 1.0 N A:THR19 4.3 43.2 1.0 O A:THR60 4.4 39.8 1.0 OD2 A:ASP59 4.4 42.9 1.0 HG22 A:THR19 4.4 42.6 1.0 O A:PRO36 4.4 47.2 1.0 PA A:GDP1194 4.5 57.1 1.0 OD1 A:ASP59 4.5 41.2 1.0 NZ A:LYS18 4.5 39.9 1.0 N A:VAL38 4.5 47.4 1.0 CA A:THR19 4.5 43.2 1.0 CG2 A:THR37 4.6 49.7 1.0 CE A:LYS18 4.6 40.0 1.0 CG2 A:THR19 4.6 42.6 1.0 H A:ALA15 4.6 45.9 1.0 HG23 A:VAL38 4.7 45.3 1.0 CA A:VAL38 4.8 46.8 1.0 HA A:THR19 4.8 43.2 1.0 CG A:ASP59 4.9 42.5 1.0 CB A:LYS18 4.9 40.6 1.0 HG21 A:THR19 4.9 42.6 1.0 O2A A:GDP1194 4.9 60.9 1.0 HG21 A:VAL38 5.0 45.3 1.0 HE22 A:GLN63 5.0 69.5 1.0

Magnesium binding site 2 out of 3 in the Double Acetylated Rhogdi-Alpha in Complex with Rhoa-Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Double Acetylated Rhogdi-Alpha in Complex with Rhoa-Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1196 b:86.8 occ:1.00 OD2 A:ASP45 3.1 89.8 1.0 O A:VAL43 3.1 56.9 1.0 HG13 A:VAL43 3.4 53.0 1.0 HB A:VAL43 3.7 51.6 1.0 CG A:ASP45 4.0 87.6 1.0 CG1 A:VAL43 4.1 53.0 1.0 HG12 A:VAL43 4.1 53.0 1.0 C A:VAL43 4.1 54.6 1.0 OD1 A:ASP45 4.2 89.7 1.0 CB A:VAL43 4.3 51.6 1.0 HA A:ALA44 4.6 63.5 1.0 H A:ASP45 4.8 78.3 1.0 CA A:VAL43 4.8 52.3 1.0 H A:VAL43 4.9 52.1 1.0 HG11 A:VAL43 4.9 53.0 1.0

Magnesium binding site 3 out of 3 in the Double Acetylated Rhogdi-Alpha in Complex with Rhoa-Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Double Acetylated Rhogdi-Alpha in Complex with Rhoa-Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1203 b:67.3 occ:1.00 H B:VAL118 2.1 49.9 1.0 O B:ARG152 2.6 48.6 1.0 HA B:ARG117 2.7 51.4 1.0 N B:VAL118 2.9 49.9 1.0 HG3 B:ARG117 2.9 59.6 1.0 H B:ARG152 2.9 44.8 1.0 HG2 B:ARG152 3.0 46.4 1.0 O B:GLU154 3.1 48.5 1.0 O B:VAL118 3.2 48.5 1.0 HD3 B:ARG117 3.3 62.7 1.0 HA B:GLU155 3.4 50.5 1.0 CA B:ARG117 3.5 51.4 1.0 HE2 B:TYR156 3.5 42.0 1.0 C B:ARG152 3.5 48.1 1.0 HG3 B:ARG152 3.6 46.4 1.0 C B:ARG117 3.7 50.6 1.0 CG B:ARG117 3.7 59.6 1.0 N B:ARG152 3.7 44.8 1.0 HB B:VAL118 3.7 49.0 1.0 CG B:ARG152 3.7 46.4 1.0 HD2 B:TYR156 3.8 42.6 1.0 CA B:VAL118 3.9 48.6 1.0 C B:VAL118 3.9 50.3 1.0 CD B:ARG117 3.9 62.7 1.0 CE2 B:TYR156 3.9 42.0 1.0 C B:GLU154 4.0 52.2 1.0 CA B:ARG152 4.0 46.4 1.0 CB B:ARG117 4.1 55.6 1.0 CD2 B:TYR156 4.1 42.6 1.0 HD2 B:ARG117 4.2 62.7 1.0 HG21 B:VAL118 4.2 47.9 1.0 CB B:VAL118 4.2 49.0 1.0 O B:ALA153 4.3 55.9 1.0 CA B:GLU155 4.3 50.5 1.0 HE B:ARG152 4.3 46.4 1.0 CB B:ARG152 4.4 46.2 1.0 HA B:PRO151 4.5 43.0 1.0 HG2 B:ARG117 4.5 59.6 1.0 C B:ALA153 4.5 54.9 1.0 O B:PHE116 4.5 43.2 1.0 HB2 B:ARG117 4.5 55.6 1.0 N B:GLU155 4.6 52.0 1.0 N B:ALA153 4.6 51.0 1.0 H B:TYR156 4.6 47.3 1.0 N B:ARG117 4.7 48.5 1.0 HA B:VAL118 4.7 48.6 1.0 CG2 B:VAL118 4.8 47.9 1.0 C B:PRO151 4.8 43.5 1.0 N B:GLU154 4.8 55.8 1.0 HB3 B:ARG152 4.9 46.2 1.0 CZ B:TYR156 4.9 42.1 1.0 O B:ARG117 4.9 52.4 1.0 NE B:ARG152 4.9 46.4 1.0 CD B:ARG152 4.9 46.2 1.0 HB3 B:ARG117 4.9 55.6 1.0 C B:GLU155 4.9 48.8 1.0 HA B:ARG152 4.9 46.4 1.0 N B:TYR156 5.0 47.3 1.0 HH B:TYR156 5.0 42.8 1.0

N.Kuhlmann, S.Wroblowski, L.Scislowski, M.Lammers. Rhogdi Alpha Acetylation at K127 and K141 Affects Binding Towards Non-Prenylated Rhoa. Biochemistry V. 55 304 2016.
ISSN: ISSN 0006-2960
PubMed: 26695096
DOI: 10.1021/ACS.BIOCHEM.5B01242