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Magnesium in PDB 7tlk: Crystal Structure of K-Ras(G12S)

Enzymatic activity of Crystal Structure of K-Ras(G12S)

All present enzymatic activity of Crystal Structure of K-Ras(G12S):
3.6.5.2;

Protein crystallography data

The structure of Crystal Structure of K-Ras(G12S), PDB code: 7tlk was solved by Z.Ziyang, K.Z.Guiley, K.M.Shokat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.80 / 1.71
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 83.609, 83.609, 41.27, 90, 90, 120
R / Rfree (%) 16.9 / 20.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of K-Ras(G12S) (pdb code 7tlk). 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 K-Ras(G12S), PDB code: 7tlk:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7tlk

Go back to Magnesium Binding Sites List in 7tlk
Magnesium binding site 1 out of 2 in the Crystal Structure of K-Ras(G12S)


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 K-Ras(G12S) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:14.8
occ:1.00
O2B A:GDP201 2.3 4.5 1.0
O A:HOH414 2.3 9.0 1.0
O A:HOH332 2.3 8.6 1.0
O A:HOH322 2.4 9.2 1.0
OG A:SER17 2.4 6.8 1.0
O A:HOH366 2.4 7.8 1.0
CB A:SER17 3.4 8.7 1.0
PB A:GDP201 3.5 14.9 1.0
O1B A:GDP201 3.7 9.5 1.0
N A:SER17 4.1 6.4 1.0
O1A A:GDP201 4.2 8.4 1.0
OD2 A:ASP57 4.3 12.0 1.0
CA A:SER17 4.3 6.9 1.0
OD1 A:ASP57 4.4 11.3 1.0
O3B A:GDP201 4.5 5.0 1.0
O3A A:GDP201 4.5 6.1 1.0
O A:THR58 4.5 11.0 1.0
O A:ASP33 4.6 11.2 1.0
CD2 A:TYR32 4.6 14.6 1.0
CA A:PRO34 4.6 14.5 1.0
O A:ILE36 4.7 13.0 1.0
O A:TYR32 4.7 13.4 1.0
PA A:GDP201 4.7 7.5 1.0
CG A:ASP57 4.7 13.2 1.0
O2A A:GDP201 4.8 10.2 1.0
CE A:LYS16 4.8 8.6 1.0
O A:HOH356 4.9 16.2 1.0
CB A:LYS16 4.9 6.8 1.0
CB A:ALA59 4.9 14.0 1.0
O A:PRO34 5.0 20.0 1.0

Magnesium binding site 2 out of 2 in 7tlk

Go back to Magnesium Binding Sites List in 7tlk
Magnesium binding site 2 out of 2 in the Crystal Structure of K-Ras(G12S)


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 K-Ras(G12S) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:14.8
occ:1.00
O3B B:GDP201 2.2 5.1 1.0
O B:HOH439 2.3 10.8 1.0
O B:HOH335 2.3 7.8 1.0
O B:HOH358 2.3 8.1 1.0
O B:HOH345 2.3 7.1 1.0
OG B:SER17 2.4 5.5 1.0
CB B:SER17 3.4 9.6 1.0
PB B:GDP201 3.5 8.6 1.0
O1B B:GDP201 3.7 9.6 1.0
N B:SER17 4.0 5.0 1.0
O1A B:GDP201 4.2 10.0 1.0
CD1 B:TYR32 4.2 10.7 1.0
OD2 B:ASP57 4.2 12.1 1.0
OD1 B:ASP57 4.3 9.5 1.0
CA B:SER17 4.3 7.0 1.0
CA B:PRO34 4.3 12.5 1.0
O B:PRO34 4.4 14.4 1.0
O B:ASP33 4.5 10.2 1.0
O2B B:GDP201 4.5 7.3 1.0
O3A B:GDP201 4.5 7.9 1.0
O B:ILE36 4.5 13.5 1.0
CE1 B:TYR32 4.6 12.2 1.0
O B:THR58 4.6 12.0 1.0
CG B:ASP57 4.7 10.7 1.0
C B:PRO34 4.7 13.3 1.0
PA B:GDP201 4.7 10.1 1.0
CE B:LYS16 4.8 9.5 1.0
O2A B:GDP201 4.8 9.5 1.0
CB B:LYS16 4.9 5.6 1.0
O B:TYR32 4.9 12.4 1.0
CB B:ALA59 5.0 13.6 1.0

Reference:

Z.Zhang, K.Z.Guiley, K.M.Shokat. Chemical Acylation of An Acquired Serine Suppresses Oncogenic Signaling of K-Ras(G12S). Nat.Chem.Biol. V. 18 1177 2022.
ISSN: ESSN 1552-4469
PubMed: 35864332
DOI: 10.1038/S41589-022-01065-9
Page generated: Thu Oct 3 09:20:57 2024

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