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 Apr 7 09:00:56 2023

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy