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Magnesium in PDB 6ws4: Crystal Structure of Kras-G12D/K104Q Mutant, Gdp-Bound

Protein crystallography data

The structure of Crystal Structure of Kras-G12D/K104Q Mutant, Gdp-Bound, PDB code: 6ws4 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) 44.65 / 1.84
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 84.93, 84.93, 89.3, 90, 90, 120
R / Rfree (%) 13.3 / 15.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Kras-G12D/K104Q Mutant, Gdp-Bound (pdb code 6ws4). 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-G12D/K104Q Mutant, Gdp-Bound, PDB code: 6ws4:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6ws4

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Magnesium binding site 1 out of 4 in the Crystal Structure of Kras-G12D/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-G12D/K104Q Mutant, Gdp-Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:18.3
occ:1.00
 O2B A:GDP201 2.1 13.9 1.0
O A:HOH313 2.1 19.1 1.0
OG A:SER17 2.1 18.5 1.0
O A:HOH318 2.1 19.1 1.0
O A:HOH328 2.1 17.5 1.0
O A:HOH331 2.1 21.3 1.0
CB A:SER17 3.2 21.9 1.0
PB A:GDP201 3.3 18.1 1.0
O3B A:GDP201 3.6 18.1 1.0
N A:SER17 3.9 20.4 1.0
CA A:SER17 4.1 18.9 1.0
OD2 A:ASP57 4.1 25.3 1.0
OD1 A:ASP57 4.2 28.5 1.0
O2A A:GDP201 4.2 21.7 1.0
O A:PRO34 4.3 19.9 1.0
O1B A:GDP201 4.3 17.9 1.0
O3A A:GDP201 4.3 20.9 1.0
O A:ASP33 4.4 20.5 1.0
CD1 A:TYR32 4.4 25.5 1.0
CA A:PRO34 4.5 25.9 1.0
O A:ILE36 4.5 24.3 1.0
CG A:ASP57 4.6 22.7 1.0
O A:THR58 4.6 21.6 1.0
PA A:GDP201 4.7 20.0 1.0
C A:PRO34 4.7 24.2 1.0
CE1 A:TYR32 4.7 27.9 1.0
O1A A:GDP201 4.8 20.5 1.0
CB A:LYS16 4.9 19.6 1.0
O A:TYR32 5.0 22.9 1.0
C A:LYS16 5.0 23.0 1.0

Magnesium binding site 2 out of 4 in 6ws4

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Magnesium binding site 2 out of 4 in the Crystal Structure of Kras-G12D/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-G12D/K104Q Mutant, Gdp-Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:18.9
occ:1.00
 O B:HOH315 2.0 19.3 1.0
O B:HOH336 2.0 19.2 1.0
OG B:SER17 2.1 21.9 1.0
O B:HOH331 2.1 24.8 1.0
O2B B:GDP201 2.2 15.6 1.0
O B:HOH307 2.2 18.4 1.0
CB B:SER17 3.2 22.8 1.0
PB B:GDP201 3.3 20.4 1.0
O3B B:GDP201 3.6 20.5 1.0
N B:SER17 4.0 21.6 1.0
OD2 B:ASP57 4.1 27.7 1.0
CA B:SER17 4.2 20.0 1.0
O2A B:GDP201 4.2 24.1 1.0
O B:PRO34 4.2 22.3 1.0
OD1 B:ASP57 4.3 24.2 1.0
O B:ASP33 4.3 21.5 1.0
O3A B:GDP201 4.4 19.2 1.0
CD1 B:TYR32 4.4 24.2 1.0
CA B:PRO34 4.4 26.5 1.0
O1B B:GDP201 4.4 20.5 1.0
O B:THR58 4.5 21.3 1.0
O B:ILE36 4.5 28.0 1.0
CG B:ASP57 4.6 29.9 1.0
C B:PRO34 4.6 25.4 1.0
PA B:GDP201 4.7 23.5 1.0
CE1 B:TYR32 4.7 27.8 1.0
O1A B:GDP201 4.9 21.5 1.0
CB B:LYS16 4.9 18.8 1.0
O B:TYR32 5.0 28.5 1.0

Magnesium binding site 3 out of 4 in 6ws4

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Magnesium binding site 3 out of 4 in the Crystal Structure of Kras-G12D/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-G12D/K104Q Mutant, Gdp-Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg202

b:23.5
occ:1.00
 O C:HOH310 1.8 23.3 1.0
O C:HOH305 1.8 23.9 1.0
O2B C:GDP201 2.1 21.5 1.0
OG C:SER17 2.1 26.1 1.0
O C:HOH320 2.2 26.1 1.0
O C:HOH317 2.2 23.9 1.0
CB C:SER17 3.2 23.7 1.0
PB C:GDP201 3.3 24.6 1.0
O3B C:GDP201 3.6 22.1 1.0
N C:SER17 3.9 21.2 1.0
O2A C:GDP201 4.0 25.3 1.0
CA C:SER17 4.1 19.6 1.0
OD2 C:ASP57 4.2 30.0 1.0
OD1 C:ASP57 4.3 28.7 1.0
O C:ASP33 4.3 30.6 1.0
O C:PRO34 4.3 29.6 1.0
O3A C:GDP201 4.4 23.9 1.0
O1B C:GDP201 4.4 22.9 1.0
CD1 C:TYR32 4.4 43.0 1.0
O C:ILE36 4.4 30.2 1.0
CA C:PRO34 4.4 33.3 1.0
PA C:GDP201 4.5 25.6 1.0
O1A C:GDP201 4.5 24.7 1.0
CG C:ASP57 4.6 33.5 1.0
O C:THR58 4.7 25.3 1.0
C C:PRO34 4.7 35.5 1.0
CE1 C:TYR32 4.8 46.6 1.0
O C:TYR32 4.8 32.9 1.0
O C:HOH309 4.8 38.6 1.0
CB C:LYS16 5.0 24.2 1.0

Magnesium binding site 4 out of 4 in 6ws4

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Magnesium binding site 4 out of 4 in the Crystal Structure of Kras-G12D/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-G12D/K104Q Mutant, Gdp-Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg202

b:23.8
occ:1.00
 O D:HOH325 2.1 23.7 1.0
O2B D:GDP201 2.1 20.4 1.0
O D:HOH335 2.1 21.6 1.0
OG D:SER17 2.1 25.0 1.0
O D:HOH304 2.1 27.2 1.0
O D:HOH317 2.1 23.1 1.0
CB D:SER17 3.2 25.7 1.0
PB D:GDP201 3.3 22.5 1.0
O3B D:GDP201 3.7 22.9 1.0
N D:SER17 3.9 22.6 1.0
OD2 D:ASP57 4.0 25.9 1.0
OD1 D:ASP57 4.1 30.8 1.0
CA D:SER17 4.1 19.7 1.0
O2A D:GDP201 4.2 23.5 1.0
O D:ASP33 4.3 23.2 1.0
CD1 D:TYR32 4.4 27.0 1.0
O D:PRO34 4.4 25.5 1.0
O1B D:GDP201 4.4 21.0 1.0
O3A D:GDP201 4.4 19.6 1.0
CG D:ASP57 4.5 29.9 1.0
O D:THR58 4.5 28.5 1.0
CA D:PRO34 4.5 28.5 1.0
O D:ILE36 4.5 33.0 1.0
O1A D:GDP201 4.7 22.1 1.0
PA D:GDP201 4.7 23.1 1.0
CE1 D:TYR32 4.7 37.0 1.0
C D:PRO34 4.7 29.3 1.0
O D:HOH305 4.9 26.8 1.0
CB D:LYS16 4.9 20.4 1.0
C D:LYS16 5.0 17.8 1.0
O D:TYR32 5.0 28.1 1.0

Reference:

T.H.Tran, D.K.Simanshu. Allosteric Regulation of Switch 2 Controls K-Ras Oncogenicity To Be Published.
Page generated: Tue Oct 1 23:10:54 2024

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