Magnesium in PDB 8stm: Crystal Structure of Kras-G75A Mutant, Gdp-Bound

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

The structure of Crystal Structure of Kras-G75A Mutant, Gdp-Bound, PDB code: 8stm 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)	43.83 / 2.00
Space group	P 3
Cell size a, b, c (Å), α, β, γ (°)	84.93, 84.93, 87.65, 90, 90, 120
R / Rfree (%)	16.3 / 19.2

The binding sites of Magnesium atom in the Crystal Structure of Kras-G75A Mutant, Gdp-Bound (pdb code 8stm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Kras-G75A Mutant, Gdp-Bound, PDB code: 8stm:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Kras-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-G75A Mutant, Gdp-Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:26.2 occ:1.00 OG A:SER17 2.1 26.6 1.0 O A:HOH304 2.1 29.0 1.0 O A:HOH313 2.2 23.4 1.0 O A:HOH310 2.2 25.6 1.0 O2B A:GDP201 2.3 36.2 1.0 O A:HOH309 2.3 40.7 1.0 O3B A:GDP201 3.2 37.6 1.0 PB A:GDP201 3.2 38.5 1.0 CB A:SER17 3.3 26.5 1.0 O A:PRO34 4.0 27.2 1.0 O2A A:GDP201 4.1 38.8 1.0 N A:SER17 4.1 28.4 1.0 OD1 A:ASP57 4.2 31.5 1.0 OD2 A:ASP57 4.2 32.4 1.0 O3A A:GDP201 4.2 35.5 1.0 O A:ASP33 4.3 28.4 1.0 CA A:SER17 4.3 25.6 1.0 CA A:PRO34 4.3 29.6 1.0 CD1 A:TYR32 4.4 27.4 1.0 O1B A:GDP201 4.4 41.5 1.0 O1A A:GDP201 4.4 30.2 1.0 PA A:GDP201 4.5 36.6 1.0 O A:ILE36 4.5 31.5 1.0 C A:PRO34 4.5 28.3 1.0 O A:THR58 4.5 33.1 1.0 CG A:ASP57 4.6 29.9 1.0 O A:TYR32 4.8 29.5 1.0 CE1 A:TYR32 4.8 28.2 1.0 O A:HOH330 5.0 41.4 1.0 CB A:LYS16 5.0 25.9 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Kras-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-G75A Mutant, Gdp-Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:21.3 occ:1.00 O B:HOH301 2.2 30.6 1.0 O B:HOH316 2.2 35.3 1.0 OG B:SER17 2.3 24.6 1.0 O B:HOH302 2.3 25.1 1.0 O2B B:GDP201 2.3 24.4 1.0 O B:HOH317 2.4 29.5 1.0 O3B B:GDP201 3.0 30.2 1.0 PB B:GDP201 3.1 32.9 1.0 CB B:SER17 3.5 25.9 1.0 O B:PRO34 4.0 24.6 1.0 N B:SER17 4.1 27.7 1.0 OD1 B:ASP57 4.1 27.9 1.0 O3A B:GDP201 4.1 29.8 1.0 O2A B:GDP201 4.2 34.0 1.0 O1B B:GDP201 4.3 30.8 1.0 OD2 B:ASP57 4.3 25.1 1.0 CA B:SER17 4.4 27.4 1.0 O B:THR58 4.4 35.5 1.0 CA B:PRO34 4.4 26.4 1.0 PA B:GDP201 4.5 35.7 1.0 O B:ASP33 4.5 29.0 1.0 O1A B:GDP201 4.5 30.5 1.0 C B:PRO34 4.6 27.1 1.0 CG B:ASP57 4.6 28.6 1.0 O B:ILE36 4.6 32.1 1.0 O B:HOH327 4.7 42.8 1.0 CD1 B:TYR32 4.7 26.0 1.0 CB B:LYS16 4.8 23.8 1.0 CE B:LYS16 4.8 20.2 1.0 O B:TYR32 4.9 27.8 1.0 NZ B:LYS16 4.9 20.1 1.0 C B:LYS16 5.0 28.6 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Kras-G75A Mutant, Gdp-Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Kras-G75A Mutant, Gdp-Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:40.4 occ:1.00 O C:HOH315 2.1 27.5 1.0 O C:HOH301 2.2 30.1 1.0 O C:HOH314 2.2 39.9 1.0 O C:HOH309 2.6 34.7 1.0 O2B C:GDP201 2.7 41.9 1.0 OG C:SER17 2.7 41.3 1.0 O3B C:GDP201 3.0 35.9 1.0 PB C:GDP201 3.4 40.0 1.0 CB C:SER17 3.5 40.0 1.0 O C:PRO34 4.0 41.1 1.0 CD2 C:TYR32 4.2 49.1 1.0 O2A C:GDP201 4.2 35.1 1.0 N C:SER17 4.3 40.7 1.0 O3A C:GDP201 4.3 39.2 1.0 CA C:PRO34 4.4 39.0 1.0 OD2 C:ASP57 4.4 57.0 1.0 OD1 C:ASP57 4.4 58.7 1.0 O C:ILE36 4.5 51.0 1.0 O C:TYR32 4.5 38.4 1.0 CA C:SER17 4.5 36.9 1.0 PA C:GDP201 4.5 41.7 1.0 O C:ASP33 4.5 37.8 1.0 O1A C:GDP201 4.5 40.4 1.0 C C:PRO34 4.5 44.1 1.0 O1B C:GDP201 4.7 36.2 1.0 O C:THR58 4.7 50.6 1.0 CE2 C:TYR32 4.7 50.5 1.0 CG C:ASP57 4.8 55.5 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Kras-G75A Mutant, Gdp-Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Kras-G75A Mutant, Gdp-Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg202 b:33.3 occ:1.00 OG D:SER17 2.1 31.8 1.0 O D:HOH303 2.1 31.9 1.0 O D:HOH302 2.2 39.9 1.0 O2B D:GDP201 2.2 34.7 1.0 O D:HOH309 2.2 30.2 1.0 O D:HOH327 2.2 38.6 1.0 PB D:GDP201 3.3 35.8 1.0 CB D:SER17 3.3 31.6 1.0 O3B D:GDP201 3.4 34.8 1.0 N D:SER17 4.0 31.3 1.0 OD1 D:ASP57 4.0 37.4 1.0 OD2 D:ASP57 4.1 37.5 1.0 CA D:SER17 4.2 31.4 1.0 O D:PRO34 4.2 32.4 1.0 O D:THR58 4.2 43.2 1.0 O2A D:GDP201 4.2 35.3 1.0 O3A D:GDP201 4.3 34.0 1.0 O1B D:GDP201 4.4 34.9 1.0 O D:ASP33 4.4 31.9 1.0 CG D:ASP57 4.4 38.5 1.0 O D:ILE36 4.5 46.4 1.0 O1A D:GDP201 4.5 37.2 1.0 CD1 D:TYR32 4.5 30.4 1.0 PA D:GDP201 4.5 37.9 1.0 CA D:PRO34 4.5 32.2 1.0 C D:PRO34 4.7 33.2 1.0 O D:TYR32 4.8 36.6 1.0 CE1 D:TYR32 4.9 30.8 1.0 CB D:LYS16 4.9 28.7 1.0 C D:LYS16 4.9 29.9 1.0 NZ D:LYS16 5.0 23.9 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