Magnesium in PDB 3ab3: Crystal Structure of P115RHOGEF Rgs Domain in Complex with G Alpha 13

The structure of Crystal Structure of P115RHOGEF Rgs Domain in Complex with G Alpha 13, PDB code: 3ab3 was solved by M.Kukimoto-Niino, C.Mishima, M.Shirouzu, T.Kozasa, S.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.88 / 2.40
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	50.481, 70.640, 88.078, 77.77, 84.45, 80.11
R / Rfree (%)	20.5 / 28

The structure of Crystal Structure of P115RHOGEF Rgs Domain in Complex with G Alpha 13 also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the Crystal Structure of P115RHOGEF Rgs Domain in Complex with G Alpha 13 (pdb code 3ab3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of P115RHOGEF Rgs Domain in Complex with G Alpha 13, PDB code: 3ab3:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of P115RHOGEF Rgs Domain in Complex with G Alpha 13


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 P115RHOGEF Rgs Domain in Complex with G Alpha 13 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:30.3 occ:1.00 OG1 A:THR203 2.3 35.7 1.0 OG A:SER62 2.3 4.1 0.5 O3B A:GDP401 2.4 35.2 1.0 O A:HOH408 2.4 19.6 1.0 O A:HOH409 2.4 48.8 1.0 F2 A:ALF601 2.6 51.8 1.0 CB A:THR203 2.9 25.8 1.0 F3 A:ALF601 3.2 41.6 1.0 CB A:SER62 3.4 15.7 1.0 PB A:GDP401 3.5 25.1 1.0 AL A:ALF601 3.7 42.7 1.0 O1B A:GDP401 3.7 40.3 1.0 CG2 A:THR203 3.9 27.8 1.0 N A:SER62 3.9 28.2 1.0 N A:THR203 3.9 32.4 1.0 CA A:THR203 4.0 29.9 1.0 OD2 A:ASP222 4.1 40.8 1.0 CA A:SER62 4.2 25.2 1.0 OD1 A:ASP222 4.2 48.3 1.0 O A:VAL223 4.2 32.5 1.0 O2A A:GDP401 4.4 24.1 1.0 CG A:ASP222 4.5 49.9 1.0 O2B A:GDP401 4.5 31.8 1.0 CB A:LYS61 4.6 23.2 1.0 O3A A:GDP401 4.6 24.2 1.0 CE A:LYS61 4.6 30.5 1.0 F4 A:ALF601 4.6 33.3 1.0 O A:ARG201 4.7 35.5 1.0 O1A A:GDP401 4.8 32.1 1.0 C A:LYS61 4.9 29.8 1.0 PA A:GDP401 4.9 21.6 1.0 NZ A:LYS61 4.9 37.5 1.0 NH1 A:ARG200 5.0 32.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of P115RHOGEF Rgs Domain in Complex with G Alpha 13


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 P115RHOGEF Rgs Domain in Complex with G Alpha 13 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:34.9 occ:1.00 O C:HOH388 2.2 30.0 1.0 OG C:SER62 2.2 15.6 0.5 O C:HOH1 2.3 27.9 1.0 O3B C:GDP402 2.4 37.6 1.0 F2 C:ALF602 2.6 61.2 1.0 OG1 C:THR203 2.7 45.5 1.0 CB C:THR203 2.8 31.4 1.0 CB C:SER62 3.2 23.7 1.0 F3 C:ALF602 3.3 47.7 1.0 OD2 C:ASP222 3.5 59.2 1.0 CG2 C:THR203 3.7 40.6 1.0 PB C:GDP402 3.7 28.9 1.0 AL C:ALF602 3.7 47.4 1.0 N C:SER62 3.8 33.3 1.0 CA C:SER62 4.0 28.8 1.0 O1B C:GDP402 4.0 38.2 1.0 CA C:THR203 4.1 40.4 1.0 N C:THR203 4.1 37.8 1.0 OD1 C:ASP222 4.2 63.3 1.0 CG C:ASP222 4.2 62.1 1.0 O C:VAL223 4.3 41.3 1.0 O2A C:GDP402 4.5 36.6 1.0 O2B C:GDP402 4.6 31.3 1.0 CE C:LYS61 4.6 22.4 1.0 CB C:LYS61 4.7 28.0 1.0 F4 C:ALF602 4.7 49.5 1.0 O1A C:GDP402 4.8 40.3 1.0 C C:LYS61 4.8 28.6 1.0 O3A C:GDP402 4.8 35.2 1.0 O C:ARG201 4.8 35.4 1.0 PA C:GDP402 5.0 31.8 1.0 NH1 C:ARG200 5.0 25.9 1.0

N.Hajicek, M.Kukimoto-Niino, C.Mishima-Tsumagari, C.R.Chow, M.Shirouzu, T.Terada, M.Patel, S.Yokoyama, T.Kozasa. Identification of Critical Residues in G(Alpha)13 For Stimulation of P115RHOGEF Activity and the Structure of the G(Alpha)13-P115RHOGEF Regulator of G Protein Signaling Homology (Rh) Domain Complex. J.Biol.Chem. V. 286 20625 2011.
ISSN: ISSN 0021-9258
PubMed: 21507947
DOI: 10.1074/JBC.M110.201392