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Magnesium in PDB 8dnj: Crystal Structure of Human Kras G12C Covalently Bound with Astrazeneca WO2020/178282A1 Compound 76

Enzymatic activity of Crystal Structure of Human Kras G12C Covalently Bound with Astrazeneca WO2020/178282A1 Compound 76

All present enzymatic activity of Crystal Structure of Human Kras G12C Covalently Bound with Astrazeneca WO2020/178282A1 Compound 76:
3.6.5.2;

Protein crystallography data

The structure of Crystal Structure of Human Kras G12C Covalently Bound with Astrazeneca WO2020/178282A1 Compound 76, PDB code: 8dnj 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 / 1.81
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 37.594, 112.162, 57.821, 90, 96.8, 90
R / Rfree (%) 23.9 / 28.9

Other elements in 8dnj:

The structure of Crystal Structure of Human Kras G12C Covalently Bound with Astrazeneca WO2020/178282A1 Compound 76 also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Fluorine (F) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Kras G12C Covalently Bound with Astrazeneca WO2020/178282A1 Compound 76 (pdb code 8dnj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Human Kras G12C Covalently Bound with Astrazeneca WO2020/178282A1 Compound 76, PDB code: 8dnj:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 8dnj

Go back to Magnesium Binding Sites List in 8dnj
Magnesium binding site 1 out of 3 in the Crystal Structure of Human Kras G12C Covalently Bound with Astrazeneca WO2020/178282A1 Compound 76


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 Astrazeneca WO2020/178282A1 Compound 76 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:13.8
occ:1.00
 O A:HOH405 2.2 13.2 1.0
O A:HOH431 2.2 13.0 1.0
O A:HOH414 2.2 14.5 1.0
O A:HOH401 2.2 13.0 1.0
O2B A:GDP302 2.2 14.1 1.0
OG A:SER17 2.2 14.0 1.0
CB A:SER17 3.3 13.9 1.0
PB A:GDP302 3.4 13.8 1.0
O1B A:GDP302 3.6 13.5 1.0
OD2 A:ASP57 4.0 21.6 1.0
O1A A:GDP302 4.0 14.9 1.0
N A:SER17 4.1 13.7 1.0
OD1 A:ASP57 4.1 21.5 1.0
CD1 A:TYR32 4.2 20.5 1.0
CA A:SER17 4.3 13.9 1.0
CA A:PRO34 4.4 20.9 1.0
O3A A:GDP302 4.4 14.3 1.0
O A:ASP33 4.5 20.0 1.0
CG A:ASP57 4.5 21.0 1.0
O A:THR58 4.5 17.4 1.0
O3B A:GDP302 4.5 13.9 1.0
O A:PRO34 4.6 20.0 1.0
CB A:ALA59 4.6 17.4 1.0
O3 A:U4U303 4.6 19.2 1.0
PA A:GDP302 4.6 14.4 1.0
CE1 A:TYR32 4.6 20.3 1.0
O A:ILE36 4.7 17.9 1.0
O A:TYR32 4.7 20.2 1.0
C A:PRO34 4.8 20.4 1.0
O2A A:GDP302 4.8 14.0 1.0
NZ A:LYS16 4.9 13.2 1.0
CB A:LYS16 5.0 13.4 1.0
O A:HOH439 5.0 24.4 1.0

Magnesium binding site 2 out of 3 in 8dnj

Go back to Magnesium Binding Sites List in 8dnj
Magnesium binding site 2 out of 3 in the Crystal Structure of Human Kras G12C Covalently Bound with Astrazeneca WO2020/178282A1 Compound 76


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 Human Kras G12C Covalently Bound with Astrazeneca WO2020/178282A1 Compound 76 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:13.4
occ:1.00
 O2B B:GDP302 2.2 14.3 1.0
O B:HOH413 2.2 12.5 1.0
O B:HOH425 2.2 13.6 1.0
O B:HOH401 2.2 12.9 1.0
O B:HOH417 2.2 13.5 1.0
OG B:SER17 2.2 14.3 1.0
CB B:SER17 3.3 14.4 1.0
PB B:GDP302 3.4 14.4 1.0
O3B B:GDP302 3.6 14.3 1.0
OD2 B:ASP57 4.0 20.1 1.0
OD1 B:ASP57 4.1 21.0 1.0
N B:SER17 4.1 14.3 1.0
O2A B:GDP302 4.2 15.7 1.0
CA B:SER17 4.3 14.3 1.0
CD1 B:TYR32 4.3 19.3 1.0
O B:ASP33 4.4 18.5 1.0
CA B:PRO34 4.4 19.3 1.0
O1B B:GDP302 4.4 14.4 1.0
O3A B:GDP302 4.4 15.5 1.0
CG B:ASP57 4.4 19.6 1.0
O B:THR58 4.5 15.7 1.0
O3 B:U4U303 4.6 19.2 1.0
O B:TYR32 4.6 19.8 1.0
O B:PRO34 4.6 18.8 1.0
CB B:ALA59 4.6 15.4 1.0
PA B:GDP302 4.6 16.0 1.0
O B:ILE36 4.7 17.2 1.0
CE1 B:TYR32 4.8 18.8 1.0
O1A B:GDP302 4.8 15.9 1.0
C B:PRO34 4.8 19.2 1.0
CB B:LYS16 5.0 14.4 1.0

Magnesium binding site 3 out of 3 in 8dnj

Go back to Magnesium Binding Sites List in 8dnj
Magnesium binding site 3 out of 3 in the Crystal Structure of Human Kras G12C Covalently Bound with Astrazeneca WO2020/178282A1 Compound 76


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 Human Kras G12C Covalently Bound with Astrazeneca WO2020/178282A1 Compound 76 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:17.2
occ:1.00
 O C:HOH407 2.2 16.7 1.0
O2B C:GDP302 2.2 16.6 1.0
O C:HOH427 2.2 17.0 1.0
O C:HOH402 2.2 18.2 1.0
O C:HOH414 2.2 16.4 1.0
OG C:SER17 2.2 17.5 1.0
CB C:SER17 3.3 17.2 1.0
PB C:GDP302 3.4 16.8 1.0
O1B C:GDP302 3.6 17.2 1.0
O1A C:GDP302 4.0 18.5 1.0
OD2 C:ASP57 4.0 28.2 1.0
N C:SER17 4.1 17.6 1.0
O C:ASP33 4.1 21.7 1.0
OD1 C:ASP57 4.2 28.5 1.0
CA C:SER17 4.2 17.1 1.0
CA C:PRO34 4.3 24.5 1.0
O3A C:GDP302 4.4 17.4 1.0
O C:PRO34 4.4 26.4 1.0
O3B C:GDP302 4.5 16.8 1.0
PA C:GDP302 4.5 17.7 1.0
O3 C:U4U303 4.5 31.6 1.0
CG C:ASP57 4.5 27.5 1.0
CD2 C:TYR32 4.6 24.6 1.0
C C:PRO34 4.6 24.8 1.0
O C:ILE36 4.6 24.1 1.0
O C:THR58 4.6 24.7 1.0
O2A C:GDP302 4.7 16.9 1.0
O C:TYR32 4.9 22.3 1.0
CB C:ALA59 4.9 30.7 1.0
C C:ASP33 4.9 22.6 1.0
O C:HOH409 5.0 19.6 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 Oct 4 00:47:08 2024

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