Magnesium in PDB 7rp4: Crystal Structure of Kras G12C in Complex with Gne-1952

All present enzymatic activity of Crystal Structure of Kras G12C in Complex with Gne-1952:
3.6.5.2;

The structure of Crystal Structure of Kras G12C in Complex with Gne-1952, PDB code: 7rp4 was solved by A.Oh, C.Tam, W.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.01 / 2.15
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	33.586, 43.985, 65.305, 88.97, 84.94, 80.01
R / Rfree (%)	21.3 / 25.3

The structure of Crystal Structure of Kras G12C in Complex with Gne-1952 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Kras G12C in Complex with Gne-1952 (pdb code 7rp4). 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 Kras G12C in Complex with Gne-1952, PDB code: 7rp4:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Kras G12C in Complex with Gne-1952


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 Kras G12C in Complex with Gne-1952 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:31.6 occ:1.00 O A:HOH302 2.1 17.0 1.0 O A:HOH318 2.1 16.4 1.0 O A:HOH333 2.1 16.4 1.0 O A:HOH323 2.1 16.4 1.0 OG A:SER17 2.1 31.8 1.0 O2B A:GDP202 2.1 27.9 1.0 CB A:SER17 3.2 30.1 1.0 PB A:GDP202 3.3 26.2 1.0 O3B A:GDP202 3.3 23.1 1.0 N A:SER17 4.0 28.5 1.0 O1A A:GDP202 4.0 23.9 1.0 OD2 A:ASP57 4.0 27.8 1.0 CA A:SER17 4.2 29.4 1.0 O1B A:GDP202 4.2 29.0 1.0 O A:ASP33 4.2 37.8 1.0 CB A:ALA59 4.3 24.6 1.0 CA A:PRO34 4.3 40.1 1.0 O3A A:GDP202 4.4 27.3 1.0 OD1 A:ASP57 4.4 26.4 1.0 O A:THR58 4.5 21.6 1.0 CD2 A:TYR32 4.5 38.0 1.0 PA A:GDP202 4.6 29.0 1.0 CG A:ASP57 4.6 25.6 1.0 O2A A:GDP202 4.6 27.8 1.0 O A:PRO34 4.7 40.3 1.0 O A:ILE36 4.8 38.4 1.0 C A:PRO34 4.8 40.4 1.0 O A:MKZ201 4.8 35.0 1.0 CB A:LYS16 5.0 19.2 1.0 C A:ASP33 5.0 39.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Kras G12C in Complex with Gne-1952


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 Kras G12C in Complex with Gne-1952 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:41.3 occ:1.00 O B:HOH316 2.1 23.8 1.0 O B:HOH303 2.1 28.0 1.0 O B:HOH311 2.1 23.1 1.0 O B:HOH318 2.1 19.3 1.0 O1B B:GDP202 2.1 42.0 1.0 OG B:SER17 2.1 40.9 1.0 CB B:SER17 3.2 31.1 1.0 PB B:GDP202 3.3 35.5 1.0 O3B B:GDP202 3.3 34.8 1.0 O2A B:GDP202 3.9 31.5 1.0 O B:ASP33 4.0 35.8 1.0 N B:SER17 4.0 26.6 1.0 OD2 B:ASP57 4.1 29.8 1.0 CA B:PRO34 4.1 36.3 1.0 CA B:SER17 4.1 28.9 1.0 O2B B:GDP202 4.2 37.0 1.0 CB B:ALA59 4.2 28.8 1.0 O B:PRO34 4.3 31.3 1.0 O3A B:GDP202 4.4 34.0 1.0 OD1 B:ASP57 4.5 27.8 1.0 PA B:GDP202 4.5 33.5 1.0 C B:PRO34 4.5 36.2 1.0 CD1 B:TYR32 4.6 35.3 1.0 O B:THR58 4.6 29.1 1.0 O1A B:GDP202 4.7 32.8 1.0 CG B:ASP57 4.7 29.2 1.0 O B:ILE36 4.7 29.3 1.0 C B:ASP33 4.8 36.9 1.0 N B:PRO34 4.9 37.4 1.0

C.W.Davies, A.J.Oh, R.Mroue, M.Steffek, J.M.Bruning, Y.Xiao, S.Feng, S.Jayakar, E.Chan, V.Arumugam, S.C.Uribe, J.Drummond, A.Frommlet, C.Lu, Y.Franke, M.Merchant, H.Koeppen, J.G.Quinn, S.Malhotra, S.Do, L.Gazzard, H.E.Purkey, J.Rudolph, M.M.Mulvihill, J.T.Koerber, W.Wang, M.Evangelista. Conformation-Locking Antibodies For the Discovery and Characterization of Kras Inhibitors. Nat.Biotechnol. V. 40 769 2022.
ISSN: ISSN 1087-0156
PubMed: 34992247
DOI: 10.1038/S41587-021-01126-9