Magnesium in PDB 5uk9: Wild-Type K-Ras(Gcp) pH 6.5

The structure of Wild-Type K-Ras(Gcp) pH 6.5, PDB code: 5uk9 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)	43.78 / 1.89
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.107, 87.553, 93.692, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 20.6

The binding sites of Magnesium atom in the Wild-Type K-Ras(Gcp) pH 6.5 (pdb code 5uk9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Wild-Type K-Ras(Gcp) pH 6.5, PDB code: 5uk9:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Wild-Type K-Ras(Gcp) pH 6.5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Wild-Type K-Ras(Gcp) pH 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:14.1 occ:1.00 O A:HOH345 2.0 15.3 1.0 O1B A:GDP201 2.0 11.3 1.0 O A:HOH308 2.1 14.2 1.0 O A:HOH310 2.1 13.6 1.0 O A:HOH322 2.1 12.9 1.0 OG A:SER17 2.1 13.2 1.0 CB A:SER17 3.2 15.4 1.0 PB A:GDP201 3.3 13.5 1.0 O3B A:GDP201 3.5 15.2 1.0 N A:SER17 3.9 13.0 1.0 OD2 A:ASP57 4.0 16.7 1.0 O2A A:GDP201 4.1 13.5 1.0 CA A:SER17 4.1 14.4 1.0 OD1 A:ASP57 4.2 15.4 1.0 CD1 A:TYR32 4.2 16.5 1.0 O A:ASP33 4.2 17.8 1.0 O2B A:GDP201 4.3 12.0 1.0 O A:PRO34 4.4 19.8 1.0 O3A A:GDP201 4.4 13.5 1.0 O A:ILE36 4.5 19.5 1.0 CE1 A:TYR32 4.5 15.0 1.0 CG A:ASP57 4.5 16.6 1.0 CA A:PRO34 4.5 20.0 1.0 PA A:GDP201 4.6 14.6 1.0 O A:THR58 4.6 14.8 1.0 CB A:ALA59 4.6 19.8 1.0 O1A A:GDP201 4.7 13.7 1.0 C A:PRO34 4.7 19.8 1.0 O A:TYR32 4.8 15.6 1.0 CB A:LYS16 4.9 12.5 1.0 C A:LYS16 5.0 13.4 1.0 CE A:LYS16 5.0 17.7 1.0

Magnesium binding site 2 out of 2 in the Wild-Type K-Ras(Gcp) pH 6.5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Wild-Type K-Ras(Gcp) pH 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:15.2 occ:1.00 O2B B:GCP201 1.9 13.4 1.0 O B:HOH309 2.1 17.1 1.0 OG B:SER17 2.1 14.4 1.0 O B:HOH323 2.1 15.9 1.0 O1G B:GCP201 2.1 18.2 1.0 O B:HOH348 2.1 15.7 1.0 CB B:SER17 3.1 14.2 1.0 PG B:GCP201 3.2 26.6 1.0 PB B:GCP201 3.3 14.1 1.0 C3B B:GCP201 3.6 11.8 1.0 O B:HOH387 3.7 28.6 1.0 N B:SER17 3.8 13.7 1.0 O B:HOH395 3.8 40.5 1.0 OD2 B:ASP57 4.0 16.7 1.0 CA B:SER17 4.0 14.1 1.0 O2A B:GCP201 4.0 12.6 1.0 OD1 B:ASP57 4.1 17.5 1.0 O1B B:GCP201 4.3 14.3 1.0 O2G B:GCP201 4.3 27.1 1.0 O3A B:GCP201 4.4 14.6 1.0 O3G B:GCP201 4.4 26.3 1.0 CG B:ASP57 4.5 19.4 1.0 O B:THR58 4.5 26.3 1.0 PA B:GCP201 4.6 17.3 1.0 O B:HOH398 4.6 35.9 1.0 O1A B:GCP201 4.6 15.4 1.0 CB B:LYS16 4.7 14.5 1.0 C B:LYS16 4.8 15.0 1.0 CE B:LYS16 4.8 17.5 1.0

J.A.Parker, A.Y.Volmar, S.Pavlopoulos, C.Mattos. K-Ras Populates Conformational States Differently From Its Isoform H-Ras and Oncogenic Mutant K-RASG12D. Structure V. 26 810 2018.
ISSN: ISSN 1878-4186
PubMed: 29706533
DOI: 10.1016/J.STR.2018.03.018