Magnesium in PDB 8stn: Crystal Structure of Kras-G12D/G75A Mutant, Gdp-Bound

All present enzymatic activity of Crystal Structure of Kras-G12D/G75A Mutant, Gdp-Bound:
3.6.5.2;

The structure of Crystal Structure of Kras-G12D/G75A Mutant, Gdp-Bound, PDB code: 8stn was solved by T.H.Tran, S.Dharmaiah, D.K.Simanshu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	73.73 / 2.03
Space group	P 3
Cell size a, b, c (Å), α, β, γ (°)	85.133, 85.133, 41.929, 90, 90, 120
R / Rfree (%)	16 / 18.3

The structure of Crystal Structure of Kras-G12D/G75A Mutant, Gdp-Bound also contains other interesting chemical elements:

Sodium	(Na)	1 atom
Chlorine	(Cl)	2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Kras-G12D/G75A Mutant, Gdp-Bound (pdb code 8stn). 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 Kras-G12D/G75A Mutant, Gdp-Bound, PDB code: 8stn:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Kras-G12D/G75A Mutant, Gdp-Bound


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 Kras-G12D/G75A Mutant, Gdp-Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:44.3 occ:1.00 O3B A:GDP201 2.2 26.9 1.0 O A:HOH312 2.2 42.9 1.0 O A:HOH302 2.3 28.4 1.0 O A:HOH311 2.3 42.4 1.0 OG A:SER17 2.3 27.1 1.0 CB A:SER17 3.3 29.1 1.0 PB A:GDP201 3.5 27.5 1.0 O2B A:GDP201 3.8 24.4 1.0 N A:SER17 4.0 31.7 1.0 O A:PRO34 4.1 48.8 1.0 OD2 A:ASP57 4.1 36.6 1.0 OD1 A:ASP57 4.2 40.4 1.0 CA A:SER17 4.2 31.7 1.0 O A:HOH303 4.2 28.4 1.0 O A:THR58 4.3 58.3 1.0 CA A:PRO34 4.3 44.6 1.0 O A:ASP33 4.3 42.3 1.0 O2A A:GDP201 4.3 26.4 1.0 O3A A:GDP201 4.4 24.2 1.0 C A:PRO34 4.5 47.0 1.0 CD2 A:TYR32 4.6 40.9 1.0 CG A:ASP57 4.6 39.3 1.0 O1B A:GDP201 4.6 26.2 1.0 PA A:GDP201 4.7 27.1 1.0 O A:ILE36 4.7 54.3 1.0 O1A A:GDP201 4.7 21.9 1.0 CB A:ALA59 4.8 57.5 1.0 NZ A:LYS16 4.8 22.1 1.0 O A:TYR32 5.0 49.8 1.0 C A:ASP33 5.0 44.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Kras-G12D/G75A Mutant, Gdp-Bound


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 Kras-G12D/G75A Mutant, Gdp-Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:26.6 occ:1.00 OG B:SER17 2.1 37.0 1.0 O3B B:GDP201 2.1 22.3 1.0 O B:HOH303 2.2 19.2 1.0 O B:HOH305 2.2 17.6 1.0 O B:HOH304 2.2 21.6 1.0 CB B:SER17 3.1 27.9 1.0 PB B:GDP201 3.4 23.0 1.0 O2B B:GDP201 3.7 19.4 1.0 N B:SER17 4.0 25.1 1.0 OD1 B:ASP57 4.0 41.2 1.0 CA B:SER17 4.1 26.9 1.0 OD2 B:ASP57 4.1 32.4 1.0 O B:ASP33 4.1 34.1 1.0 CA B:PRO34 4.2 34.2 1.0 O3A B:GDP201 4.3 23.4 1.0 O B:PRO34 4.3 29.3 1.0 CG B:ASP57 4.5 34.1 1.0 O2A B:GDP201 4.5 31.9 1.0 O1B B:GDP201 4.5 17.6 1.0 C B:PRO34 4.5 33.8 1.0 CD1 B:TYR32 4.5 30.5 1.0 O B:TYR32 4.6 33.0 1.0 O B:ILE36 4.7 30.3 1.0 O B:THR58 4.7 35.4 1.0 C B:ASP33 4.8 33.2 1.0 PA B:GDP201 4.8 28.7 1.0 N B:PRO34 4.8 36.8 1.0 O1A B:GDP201 4.8 21.5 1.0

M.H.Yang, T.H.Tran, B.Hunt, R.Agnor, C.W.Johnson, B.Shui, T.J.Waybright, J.A.Nowak, A.G.Stephen, D.K.Simanshu, K.M.Haigis. Allosteric Regulation of Switch-II Domain Controls Kras Oncogenicity. Cancer Res. 2023.
ISSN: ESSN 1538-7445
PubMed: 37556505
DOI: 10.1158/0008-5472.CAN-22-3210