Atomistry » Magnesium » PDB 8dh6-8dr5 » 8dnj
Atomistry »
  Magnesium »
    PDB 8dh6-8dr5 »
      8dnj »

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

Last articles

Ca in 2OXE
Ca in 2OXS
Ca in 2OX8
Ca in 2OW2
Ca in 2OWL
Ca in 2OVZ
Ca in 2OVX
Ca in 2OW4
Ca in 2OW0
Ca in 2OW1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy