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Magnesium in PDB 8dnk: Crystal Structure of Human Kras G12C Covalently Bound with Taiho WO2020/085493A1 Compound 6

Enzymatic activity of Crystal Structure of Human Kras G12C Covalently Bound with Taiho WO2020/085493A1 Compound 6

All present enzymatic activity of Crystal Structure of Human Kras G12C Covalently Bound with Taiho WO2020/085493A1 Compound 6:
3.6.5.2;

Protein crystallography data

The structure of Crystal Structure of Human Kras G12C Covalently Bound with Taiho WO2020/085493A1 Compound 6, PDB code: 8dnk was solved by C.Mohr, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.23
Space group P 2 3
Cell size a, b, c (Å), α, β, γ (°) 91.181, 91.181, 91.181, 90, 90, 90
R / Rfree (%) 18.1 / 23.5

Other elements in 8dnk:

The structure of Crystal Structure of Human Kras G12C Covalently Bound with Taiho WO2020/085493A1 Compound 6 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Kras G12C Covalently Bound with Taiho WO2020/085493A1 Compound 6 (pdb code 8dnk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of Human Kras G12C Covalently Bound with Taiho WO2020/085493A1 Compound 6, PDB code: 8dnk:

Magnesium binding site 1 out of 1 in 8dnk

Go back to Magnesium Binding Sites List in 8dnk
Magnesium binding site 1 out of 1 in the Crystal Structure of Human Kras G12C Covalently Bound with Taiho WO2020/085493A1 Compound 6


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 Human Kras G12C Covalently Bound with Taiho WO2020/085493A1 Compound 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:31.0
occ:1.00
 O2B A:GDP302 2.1 27.9 1.0
OG A:SER17 2.1 32.4 1.0
O A:HOH401 2.1 31.1 1.0
O A:HOH407 2.1 32.6 1.0
O A:HOH405 2.2 23.6 1.0
O A:HOH406 2.2 36.5 1.0
CB A:SER17 3.1 32.3 1.0
PB A:GDP302 3.3 27.4 1.0
O1B A:GDP302 3.5 32.0 1.0
N A:SER17 3.9 30.4 1.0
OD2 A:ASP57 4.0 54.2 1.0
CA A:SER17 4.1 30.6 1.0
O1A A:GDP302 4.1 28.1 1.0
OD1 A:ASP57 4.2 47.4 1.0
O A:ASP33 4.3 44.3 1.0
CA A:PRO34 4.3 47.1 1.0
O3A A:GDP302 4.4 28.4 1.0
O A:PRO34 4.4 45.5 1.0
O3B A:GDP302 4.4 24.1 1.0
CD1 A:TYR32 4.4 42.3 1.0
CG A:ASP57 4.5 46.0 1.0
CB A:ALA59 4.5 39.4 1.0
O A:THR58 4.5 36.8 1.0
PA A:GDP302 4.6 31.7 1.0
O A:ILE36 4.6 47.8 1.0
C A:PRO34 4.6 48.6 1.0
O2A A:GDP302 4.8 30.9 1.0
CE A:LYS16 4.8 28.1 1.0
O A:HOH410 4.8 31.9 1.0
CE1 A:TYR32 4.8 44.6 1.0
O A:TYR32 4.8 40.6 1.0
O2 A:U50303 4.8 42.8 1.0
CB A:LYS16 4.9 26.9 1.0

Reference:

K.Zhu, C.Li, K.Y.Wu, C.Mohr, X.Li, B.Lanman. Modeling Receptor Flexibility in the Structure-Based Design of Kras G12C Inhibitors. J.Comput.Aided Mol.Des. V. 36 591 2022.
ISSN: ESSN 1573-4951
PubMed: 35930206
DOI: 10.1007/S10822-022-00467-0
Page generated: Fri Aug 15 03:25:48 2025

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