Magnesium in PDB 5irc: P190A Gap Domain Complex with Rhoa

The structure of P190A Gap Domain Complex with Rhoa, PDB code: 5irc was solved by U.Derewenda, Z.Derewenda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.54 / 1.72
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.026, 112.322, 147.611, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 21.3

The structure of P190A Gap Domain Complex with Rhoa also contains other interesting chemical elements:

Fluorine	(F)	6 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Magnesium atom in the P190A Gap Domain Complex with Rhoa (pdb code 5irc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the P190A Gap Domain Complex with Rhoa, PDB code: 5irc:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the P190A Gap Domain Complex with Rhoa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of P190A Gap Domain Complex with Rhoa within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg202 b:15.9 occ:1.00 O2B F:GDP201 2.0 12.4 1.0 F2 F:MGF203 2.1 13.4 1.0 O F:HOH318 2.1 12.3 1.0 O F:HOH338 2.1 15.5 1.0 OG1 F:THR19 2.1 14.7 1.0 OG1 F:THR37 2.1 15.0 1.0 CB F:THR37 3.1 16.2 1.0 CB F:THR19 3.1 16.4 1.0 PB F:GDP201 3.3 13.3 1.0 O1B F:GDP201 3.6 15.0 1.0 MG F:MGF203 3.7 13.6 1.0 N F:THR37 3.7 14.6 1.0 N F:THR19 3.9 15.6 1.0 OD2 F:ASP59 4.0 20.1 1.0 CA F:THR37 4.0 14.5 1.0 CA F:THR19 4.1 14.9 1.0 O1A F:GDP201 4.1 16.1 1.0 OD1 F:ASP59 4.2 18.9 1.0 CG2 F:THR19 4.2 16.6 1.0 CG2 F:THR37 4.2 18.3 1.0 O F:HOH319 4.2 17.6 1.0 O3A F:GDP201 4.3 11.1 1.0 O3B F:GDP201 4.4 11.0 1.0 NH2 A:ARG1284 4.4 15.6 1.0 CG F:ASP59 4.5 21.7 1.0 O F:THR60 4.6 17.6 1.0 F1 F:MGF203 4.6 11.7 1.0 PA F:GDP201 4.6 13.6 1.0 O F:VAL35 4.8 21.2 1.0 O2A F:GDP201 4.8 15.8 1.0 O F:HOH308 4.8 13.9 1.0 C F:PRO36 4.8 13.3 1.0 O F:HOH390 4.9 31.0 1.0 CB F:LYS18 4.9 15.0 1.0 O F:HOH312 4.9 23.9 1.0

Magnesium binding site 2 out of 4 in the P190A Gap Domain Complex with Rhoa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of P190A Gap Domain Complex with Rhoa within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg203 b:13.6 occ:1.00 MG F:MGF203 0.0 13.6 1.0 F1 F:MGF203 1.8 11.7 1.0 F3 F:MGF203 1.8 12.1 1.0 F2 F:MGF203 1.8 13.4 1.0 O1B F:GDP201 2.3 15.0 1.0 O F:HOH308 2.4 13.9 1.0 PB F:GDP201 3.5 13.3 1.0 MG F:MG202 3.7 15.9 1.0 O2B F:GDP201 3.7 12.4 1.0 NH2 A:ARG1284 3.8 15.6 1.0 N F:ALA15 3.9 10.0 1.0 NE2 F:GLN63 3.9 8.6 1.0 N F:THR37 4.0 14.6 1.0 NZ F:LYS18 4.0 15.9 1.0 O F:HOH318 4.1 12.3 1.0 N F:GLY62 4.1 14.0 1.0 CA F:GLY14 4.1 12.5 1.0 OE1 F:GLN63 4.1 12.2 1.0 NE A:ARG1284 4.2 13.2 1.0 O3B F:GDP201 4.2 11.0 1.0 CA F:PRO36 4.3 14.1 1.0 CB F:PRO36 4.4 13.1 1.0 O F:HOH338 4.4 15.5 1.0 CD F:GLN63 4.5 15.3 1.0 CZ A:ARG1284 4.5 14.5 1.0 O F:THR37 4.5 17.1 1.0 C F:GLY14 4.6 11.8 1.0 O3A F:GDP201 4.6 11.1 1.0 C F:PRO36 4.6 13.3 1.0 CE F:LYS18 4.7 15.1 1.0 O F:THR60 4.7 17.6 1.0 CB F:THR37 4.7 16.2 1.0 CA F:ALA61 4.7 14.0 1.0 OG1 F:THR37 4.8 15.0 1.0 CA F:THR37 4.8 14.5 1.0 CA F:ALA15 4.8 14.5 1.0 CA F:GLY62 4.9 15.9 1.0 C F:ALA61 4.9 16.8 1.0

Magnesium binding site 3 out of 4 in the P190A Gap Domain Complex with Rhoa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of P190A Gap Domain Complex with Rhoa within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg202 b:17.7 occ:1.00 F2 D:MGF203 2.0 16.2 1.0 O3B D:GDP201 2.0 18.2 1.0 O D:HOH339 2.0 17.7 1.0 OG1 D:THR19 2.1 20.1 1.0 OG1 D:THR37 2.2 22.0 1.0 O D:HOH302 2.2 19.9 1.0 CB D:THR37 3.1 20.2 1.0 CB D:THR19 3.2 22.7 1.0 PB D:GDP201 3.3 16.0 1.0 O2B D:GDP201 3.6 18.5 1.0 MG D:MGF203 3.6 15.8 1.0 N D:THR37 3.7 17.4 1.0 N D:THR19 3.9 23.8 1.0 OD2 D:ASP59 4.0 26.1 1.0 CA D:THR37 4.0 18.4 1.0 O2A D:GDP201 4.1 20.5 1.0 CA D:THR19 4.1 22.6 1.0 OD1 D:ASP59 4.2 22.2 1.0 O D:HOH314 4.2 21.1 1.0 CG2 D:THR37 4.2 22.6 1.0 CG2 D:THR19 4.2 25.4 1.0 O1B D:GDP201 4.3 15.7 1.0 O3A D:GDP201 4.3 16.4 1.0 NH2 B:ARG1284 4.4 19.6 1.0 CG D:ASP59 4.4 23.1 1.0 O D:THR60 4.5 19.0 1.0 F1 D:MGF203 4.5 14.2 1.0 PA D:GDP201 4.6 17.4 1.0 O D:VAL35 4.6 24.1 1.0 O1A D:GDP201 4.7 19.7 1.0 O D:HOH301 4.7 18.3 1.0 C D:PRO36 4.8 20.9 1.0 O D:HOH328 4.9 38.8 1.0 CB D:LYS18 4.9 17.0 1.0 F3 D:MGF203 4.9 16.5 1.0 O D:HOH315 5.0 29.3 1.0

Magnesium binding site 4 out of 4 in the P190A Gap Domain Complex with Rhoa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of P190A Gap Domain Complex with Rhoa within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg203 b:15.8 occ:1.00 MG D:MGF203 0.0 15.8 1.0 F3 D:MGF203 1.8 16.5 1.0 F1 D:MGF203 1.8 14.2 1.0 F2 D:MGF203 1.8 16.2 1.0 O2B D:GDP201 2.4 18.5 1.0 O D:HOH301 2.4 18.3 1.0 PB D:GDP201 3.5 16.0 1.0 MG D:MG202 3.6 17.7 1.0 O3B D:GDP201 3.7 18.2 1.0 N D:ALA15 3.9 13.5 1.0 NH2 B:ARG1284 3.9 19.6 1.0 NE2 D:GLN63 3.9 12.6 1.0 NZ D:LYS18 3.9 16.4 1.0 O D:HOH339 4.0 17.7 1.0 N D:THR37 4.0 17.4 1.0 N D:GLY62 4.0 14.1 1.0 CA D:GLY14 4.1 12.1 1.0 O1B D:GDP201 4.1 15.7 1.0 OE1 D:GLN63 4.1 16.3 1.0 NE B:ARG1284 4.1 16.6 1.0 CA D:PRO36 4.3 16.7 1.0 CD D:GLN63 4.5 14.2 1.0 CB D:PRO36 4.5 19.8 1.0 CZ B:ARG1284 4.5 18.8 1.0 O D:HOH302 4.5 19.9 1.0 O D:THR37 4.5 20.8 1.0 C D:GLY14 4.5 12.6 1.0 CE D:LYS18 4.6 14.7 1.0 C D:PRO36 4.6 20.9 1.0 O D:THR60 4.6 19.0 1.0 CA D:ALA61 4.7 14.7 1.0 O3A D:GDP201 4.7 16.4 1.0 CB D:THR37 4.7 20.2 1.0 OG1 D:THR37 4.7 22.0 1.0 CA D:ALA15 4.8 18.4 1.0 CA D:THR37 4.8 18.4 1.0 CA D:GLY62 4.9 13.6 1.0 C D:ALA61 4.9 14.3 1.0

E.Amin, M.Jaiswal, U.Derewenda, K.Reis, K.Nouri, K.T.Koessmeier, P.Aspenstrom, A.V.Somlyo, R.Dvorsky, M.R.Ahmadian. Deciphering the Molecular and Functional Basis of Rhogap Family Proteins: A Systematic Approach Toward Selective Inactivation of Rho Family Proteins. J.Biol.Chem. V. 291 20353 2016.
ISSN: ESSN 1083-351X
PubMed: 27481945
DOI: 10.1074/JBC.M116.736967