Magnesium in PDB 5ufq: K-RASG12D(Gnp)/R11.1.6 Complex

The structure of K-RASG12D(Gnp)/R11.1.6 Complex, PDB code: 5ufq was solved by J.A.Parker, C.Mattos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.17 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	119.717, 42.707, 100.235, 90.00, 113.33, 90.00
R / Rfree (%)	20 / 26.3

The structure of K-RASG12D(Gnp)/R11.1.6 Complex also contains other interesting chemical elements:

Cadmium	(Cd)	2 atoms
Calcium	(Ca)	2 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Magnesium atom in the K-RASG12D(Gnp)/R11.1.6 Complex (pdb code 5ufq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the K-RASG12D(Gnp)/R11.1.6 Complex, PDB code: 5ufq:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the K-RASG12D(Gnp)/R11.1.6 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of K-RASG12D(Gnp)/R11.1.6 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:21.6 occ:1.00 O1G A:GNP201 1.9 27.6 1.0 OG1 A:THR35 2.0 29.2 1.0 O2B A:GNP201 2.0 26.3 1.0 O A:THR35 2.2 36.9 1.0 O A:HOH308 2.2 24.4 1.0 OG A:SER17 2.3 24.8 1.0 PG A:GNP201 3.1 30.2 1.0 C A:THR35 3.2 41.1 1.0 CB A:THR35 3.2 32.2 1.0 PB A:GNP201 3.2 27.7 1.0 CB A:SER17 3.3 23.2 1.0 N3B A:GNP201 3.4 29.1 1.0 CA A:THR35 3.5 35.3 1.0 N A:SER17 3.9 25.9 1.0 CG2 A:THR35 4.0 30.2 1.0 O A:HOH329 4.1 37.8 1.0 O2G A:GNP201 4.1 32.1 1.0 OD2 A:ASP57 4.1 32.0 1.0 CA A:SER17 4.2 27.1 1.0 O2A A:GNP201 4.2 28.1 1.0 O1B A:GNP201 4.2 28.8 1.0 O3G A:GNP201 4.2 28.9 1.0 O3A A:GNP201 4.3 23.4 1.0 OD1 A:ASP57 4.4 29.1 1.0 N A:ILE36 4.4 32.9 1.0 PA A:GNP201 4.6 27.9 1.0 O A:THR58 4.6 29.5 1.0 CG A:ASP57 4.7 29.4 1.0 O1A A:GNP201 4.7 29.8 1.0 CB A:LYS16 4.7 26.7 1.0 C A:LYS16 4.9 27.7 1.0 CA A:ILE36 5.0 41.2 1.0 N A:THR35 5.0 37.2 1.0

Magnesium binding site 2 out of 2 in the K-RASG12D(Gnp)/R11.1.6 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of K-RASG12D(Gnp)/R11.1.6 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:18.9 occ:1.00 O1G B:GNP201 1.8 28.9 1.0 OG1 B:THR35 1.9 32.1 1.0 O2B B:GNP201 2.1 27.7 1.0 O B:HOH309 2.2 24.8 1.0 O B:THR35 2.2 30.5 1.0 OG B:SER17 2.3 24.5 1.0 PG B:GNP201 3.1 28.6 1.0 CB B:THR35 3.2 34.7 1.0 PB B:GNP201 3.2 27.0 1.0 C B:THR35 3.2 38.1 1.0 CB B:SER17 3.3 24.5 1.0 N3B B:GNP201 3.4 29.4 1.0 CA B:THR35 3.5 35.9 1.0 CG2 B:THR35 3.9 33.7 1.0 O B:HOH328 4.0 35.3 1.0 N B:SER17 4.0 23.6 1.0 O2G B:GNP201 4.1 32.2 1.0 O3G B:GNP201 4.2 32.2 1.0 O2A B:GNP201 4.2 26.7 1.0 OD2 B:ASP57 4.2 28.2 1.0 O1B B:GNP201 4.2 25.8 1.0 O3A B:GNP201 4.2 26.4 1.0 CA B:SER17 4.3 26.8 1.0 OD1 B:ASP57 4.3 23.8 1.0 N B:ILE36 4.4 28.2 1.0 PA B:GNP201 4.5 28.9 1.0 O B:THR58 4.6 30.2 1.0 CG B:ASP57 4.7 28.1 1.0 O1A B:GNP201 4.8 28.5 1.0 CB B:LYS16 4.8 21.1 1.0 CE B:LYS16 4.9 23.9 1.0 NZ B:LYS16 4.9 25.9 1.0 N B:THR35 5.0 29.5 1.0

M.J.Kauke, M.W.Traxlmayr, J.A.Parker, J.D.Kiefer, R.Knihtila, J.Mcgee, G.Verdine, C.Mattos, K.D.Wittrup. An Engineered Protein Antagonist of K-Ras/B-Raf Interaction. Sci Rep V. 7 5831 2017.
ISSN: ESSN 2045-2322
PubMed: 28724936
DOI: 10.1038/S41598-017-05889-7