Magnesium in PDB 6ws2: Crystal Structure of Kras-K104Q Mutant, Gdp-Bound

The structure of Crystal Structure of Kras-K104Q Mutant, Gdp-Bound, PDB code: 6ws2 was solved by T.H.Tran, D.K.Simanshu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.18 / 1.59
Space group	P 3
Cell size a, b, c (Å), α, β, γ (°)	84.56, 84.56, 88.36, 90, 90, 120
R / Rfree (%)	18.2 / 19.5

The structure of Crystal Structure of Kras-K104Q Mutant, Gdp-Bound also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of Kras-K104Q Mutant, Gdp-Bound (pdb code 6ws2). 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-K104Q Mutant, Gdp-Bound, PDB code: 6ws2:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Kras-K104Q 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-K104Q Mutant, Gdp-Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:18.9 occ:1.00 O2B A:GDP201 2.0 18.1 1.0 OG A:SER17 2.1 18.2 1.0 O A:HOH331 2.1 17.4 1.0 O A:HOH351 2.1 17.5 1.0 O A:HOH343 2.1 18.4 1.0 O A:HOH359 2.2 18.1 1.0 CB A:SER17 3.1 17.4 1.0 PB A:GDP201 3.2 17.7 1.0 O3B A:GDP201 3.5 18.6 1.0 N A:SER17 3.9 18.3 1.0 CA A:SER17 4.1 17.9 1.0 O2A A:GDP201 4.1 20.8 1.0 OD2 A:ASP57 4.1 21.5 1.0 OD1 A:ASP57 4.2 21.3 1.0 O3A A:GDP201 4.3 18.8 1.0 CD1 A:TYR32 4.3 22.2 1.0 O1B A:GDP201 4.3 17.5 1.0 O A:ASP33 4.3 20.7 1.0 O A:PRO34 4.3 22.0 1.0 CA A:PRO34 4.4 22.0 1.0 PA A:GDP201 4.5 19.1 1.0 O A:ILE36 4.6 23.5 1.0 CG A:ASP57 4.6 20.1 1.0 CE1 A:TYR32 4.6 22.8 1.0 O A:THR58 4.6 18.4 1.0 O1A A:GDP201 4.7 19.7 1.0 C A:PRO34 4.7 22.5 1.0 O A:TYR32 4.8 21.2 1.0 CB A:LYS16 4.9 17.5 1.0 C A:LYS16 5.0 17.9 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Kras-K104Q 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-K104Q Mutant, Gdp-Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:17.3 occ:1.00 O2B B:GDP201 2.0 19.2 1.0 O B:HOH316 2.1 18.7 1.0 OG B:SER17 2.1 19.1 1.0 O B:HOH352 2.1 18.6 1.0 O B:HOH314 2.1 16.8 1.0 O B:HOH304 2.2 16.3 1.0 CB B:SER17 3.2 17.6 1.0 PB B:GDP201 3.3 17.6 1.0 O3B B:GDP201 3.6 19.1 1.0 N B:SER17 4.0 17.2 1.0 O2A B:GDP201 4.1 21.1 1.0 CA B:SER17 4.1 17.7 1.0 OD2 B:ASP57 4.1 22.9 1.0 O B:ASP33 4.2 17.9 1.0 OD1 B:ASP57 4.2 22.0 1.0 O B:PRO34 4.3 20.0 1.0 CD1 B:TYR32 4.3 22.4 1.0 O3A B:GDP201 4.3 18.1 1.0 O1B B:GDP201 4.4 18.1 1.0 CA B:PRO34 4.4 20.2 1.0 O B:ILE36 4.5 20.5 1.0 O B:THR58 4.6 17.5 1.0 PA B:GDP201 4.6 18.5 1.0 CG B:ASP57 4.6 21.6 1.0 C B:PRO34 4.6 21.1 1.0 CE1 B:TYR32 4.6 23.1 1.0 O1A B:GDP201 4.7 18.5 1.0 O B:TYR32 4.7 22.0 1.0 CB B:LYS16 5.0 16.9 1.0 C B:ASP33 5.0 19.9 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Kras-K104Q 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-K104Q Mutant, Gdp-Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:21.5 occ:1.00 O2B C:GDP201 2.1 18.9 1.0 O C:HOH348 2.1 23.5 1.0 O C:HOH312 2.1 22.1 1.0 O C:HOH343 2.1 19.1 1.0 OG C:SER17 2.1 21.9 1.0 O C:HOH320 2.2 22.9 1.0 CB C:SER17 3.2 18.8 1.0 PB C:GDP201 3.3 19.6 1.0 O3B C:GDP201 3.5 21.4 1.0 N C:SER17 4.0 17.4 1.0 CA C:SER17 4.1 18.0 1.0 O2A C:GDP201 4.2 24.9 1.0 OD2 C:ASP57 4.2 25.1 1.0 O C:PRO34 4.2 27.9 1.0 O C:ASP33 4.2 25.2 1.0 OD1 C:ASP57 4.3 23.7 1.0 O C:ILE36 4.3 25.6 1.0 CD2 C:TYR32 4.3 31.8 1.0 CA C:PRO34 4.3 28.9 1.0 O3A C:GDP201 4.4 20.6 1.0 O1B C:GDP201 4.4 19.5 1.0 C C:PRO34 4.6 29.1 1.0 PA C:GDP201 4.6 20.7 1.0 O1A C:GDP201 4.6 22.3 1.0 CG C:ASP57 4.6 23.0 1.0 O C:THR58 4.7 22.0 1.0 O C:TYR32 4.8 28.5 1.0 CE2 C:TYR32 4.9 34.3 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Kras-K104Q 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-K104Q Mutant, Gdp-Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg202 b:20.8 occ:1.00 O2B D:GDP201 2.1 21.2 1.0 O D:HOH333 2.1 20.9 1.0 O D:HOH346 2.1 19.3 1.0 O D:HOH337 2.1 23.0 1.0 O D:HOH311 2.2 24.1 1.0 OG D:SER17 2.2 21.2 1.0 CB D:SER17 3.3 21.3 1.0 PB D:GDP201 3.3 20.7 1.0 O3B D:GDP201 3.5 22.8 1.0 N D:SER17 4.0 21.3 1.0 OD2 D:ASP57 4.1 29.3 1.0 O2A D:GDP201 4.1 24.1 1.0 OD1 D:ASP57 4.1 27.7 1.0 CA D:SER17 4.1 21.6 1.0 O D:ASP33 4.3 25.4 1.0 O1B D:GDP201 4.3 22.0 1.0 O3A D:GDP201 4.3 21.1 1.0 CD1 D:TYR32 4.4 25.6 1.0 CA D:PRO34 4.4 29.1 1.0 O D:PRO34 4.4 28.5 1.0 O D:THR58 4.5 30.1 1.0 CG D:ASP57 4.5 28.6 1.0 O D:ILE36 4.5 31.8 1.0 PA D:GDP201 4.5 22.7 1.0 O1A D:GDP201 4.6 23.5 1.0 C D:PRO34 4.7 29.2 1.0 CE1 D:TYR32 4.7 27.8 1.0 O D:TYR32 4.8 27.9 1.0 CB D:LYS16 4.9 20.3 1.0 CE D:LYS16 5.0 21.7 1.0 C D:LYS16 5.0 20.5 1.0

T.H.Tran, D.K.Simanshu. Allosteric Regulation of Switch 2 Controls K-Ras Oncogenicity To Be Published.