Magnesium in PDB 5jcp: Rhogap Domain of ARAP3 in Complex with Rhoa in the Transition State

The structure of Rhogap Domain of ARAP3 in Complex with Rhoa in the Transition State, PDB code: 5jcp was solved by H.Bao, F.Li, C.Wang, N.Wang, Y.Jiang, Y.Tang, J.Wu, Y.Shi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.71 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.786, 93.208, 164.283, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 22.7

The structure of Rhogap Domain of ARAP3 in Complex with Rhoa in the Transition State also contains other interesting chemical elements:

Fluorine	(F)	8 atoms
Aluminium	(Al)	2 atoms

The binding sites of Magnesium atom in the Rhogap Domain of ARAP3 in Complex with Rhoa in the Transition State (pdb code 5jcp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Rhogap Domain of ARAP3 in Complex with Rhoa in the Transition State, PDB code: 5jcp:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Rhogap Domain of ARAP3 in Complex with Rhoa in the Transition State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rhogap Domain of ARAP3 in Complex with Rhoa in the Transition State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1202 b:26.5 occ:1.00 F1 B:ALF1203 2.0 22.9 1.0 O2B B:GDP1201 2.0 22.1 1.0 O B:HOH1312 2.1 25.5 1.0 O B:HOH1320 2.1 23.0 1.0 OG1 B:THR19 2.2 21.0 1.0 CB B:THR19 3.2 23.8 1.0 PB B:GDP1201 3.3 21.7 1.0 F3 B:ALF1203 3.4 28.8 1.0 O3B B:GDP1201 3.4 22.7 1.0 AL B:ALF1203 3.5 26.7 1.0 N B:THR19 3.9 21.7 1.0 OD2 B:ASP59 3.9 28.1 1.0 CA B:THR19 4.1 23.5 1.0 O2A B:GDP1201 4.2 30.2 1.0 O1B B:GDP1201 4.2 20.9 1.0 CG2 B:THR19 4.3 27.4 1.0 OD1 B:ASP59 4.3 25.1 1.0 F4 B:ALF1203 4.4 26.0 1.0 O3A B:GDP1201 4.4 21.7 1.0 O B:THR60 4.5 21.2 1.0 CG B:ASP59 4.5 25.3 1.0 O B:HOH1304 4.6 19.8 1.0 PA B:GDP1201 4.7 23.1 1.0 NH2 B:ARG942 4.7 23.0 1.0 CE B:LYS18 4.8 16.6 1.0 CB B:LYS18 4.8 17.2 1.0 O1A B:GDP1201 4.9 26.8 1.0 C B:LYS18 5.0 28.4 1.0

Magnesium binding site 2 out of 2 in the Rhogap Domain of ARAP3 in Complex with Rhoa in the Transition State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Rhogap Domain of ARAP3 in Complex with Rhoa in the Transition State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1202 b:28.9 occ:1.00 O2B A:GDP1201 2.0 21.2 1.0 F4 A:ALF1203 2.0 26.2 1.0 O A:HOH1323 2.0 26.0 1.0 O A:HOH1307 2.1 23.2 1.0 OG1 A:THR19 2.1 27.4 1.0 CB A:THR19 3.2 32.4 1.0 PB A:GDP1201 3.2 24.6 1.0 O3B A:GDP1201 3.4 23.8 1.0 F2 A:ALF1203 3.4 29.2 1.0 AL A:ALF1203 3.5 27.2 1.0 N A:THR19 3.9 24.6 1.0 OD2 A:ASP59 3.9 27.3 1.0 CA A:THR19 4.1 30.0 1.0 OD1 A:ASP59 4.2 24.2 1.0 O2A A:GDP1201 4.2 25.9 1.0 O1B A:GDP1201 4.3 22.1 1.0 F1 A:ALF1203 4.3 21.8 1.0 CG2 A:THR19 4.3 28.8 1.0 O3A A:GDP1201 4.4 27.0 1.0 CG A:ASP59 4.4 32.2 1.0 O A:THR60 4.5 21.2 1.0 O A:HOH1305 4.6 25.5 1.0 PA A:GDP1201 4.7 27.4 1.0 CE A:LYS18 4.8 23.4 1.0 O1A A:GDP1201 4.8 25.4 1.0 CB A:LYS18 4.8 20.0 1.0 NH2 A:ARG942 4.8 29.4 1.0 NZ A:LYS18 4.9 20.1 1.0 C A:LYS18 4.9 20.0 1.0

H.Bao, F.Li, C.Wang, N.Wang, Y.Jiang, Y.Tang, J.Wu, Y.Shi. Structural Basis For the Specific Recognition of Rhoa By the Dual Gtpase-Activating Protein ARAP3 J.Biol.Chem. V. 291 16709 2016.
ISSN: ESSN 1083-351X
PubMed: 27311713
DOI: 10.1074/JBC.M116.736140