Magnesium in PDB 7r0q: KRASG12C in Complex with Gdp and Compound 3

The structure of KRASG12C in Complex with Gdp and Compound 3, PDB code: 7r0q was solved by N.Ostermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	17.96 / 1.95
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	33.23, 39.8, 62.81, 76.89, 81.2, 77.32
R / Rfree (%)	23.7 / 29.3

The binding sites of Magnesium atom in the KRASG12C in Complex with Gdp and Compound 3 (pdb code 7r0q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the KRASG12C in Complex with Gdp and Compound 3, PDB code: 7r0q:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the KRASG12C in Complex with Gdp and Compound 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of KRASG12C in Complex with Gdp and Compound 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:12.2 occ:1.00 O2B A:GDP1004 2.1 16.6 1.0 O A:HOH1112 2.1 18.8 1.0 OG A:SER17 2.1 17.5 1.0 O A:HOH1125 2.1 18.1 1.0 O A:HOH1116 2.3 20.2 1.0 O A:HOH1120 2.5 20.3 1.0 CB A:SER17 3.3 15.2 1.0 PB A:GDP1004 3.4 16.8 1.0 O3B A:GDP1004 3.6 15.7 1.0 N A:SER17 3.9 13.4 1.0 CA A:SER17 4.2 14.3 1.0 OD2 A:ASP57 4.3 29.8 1.0 OD1 A:ASP57 4.3 28.7 1.0 O1A A:GDP1004 4.4 18.7 1.0 O A:PRO34 4.4 31.4 1.0 O A:THR58 4.4 20.1 1.0 O3A A:GDP1004 4.5 17.7 1.0 O1B A:GDP1004 4.5 16.5 1.0 CA A:PRO34 4.6 32.7 1.0 O A:ASP33 4.6 32.6 1.0 O A:ILE36 4.6 23.5 1.0 PA A:GDP1004 4.7 18.9 1.0 CG A:ASP57 4.7 27.8 1.0 O2A A:GDP1004 4.7 19.5 1.0 CB A:ALA59 4.7 23.1 1.0 CB A:LYS16 4.7 14.0 1.0 C A:PRO34 4.8 31.5 1.0 CD2 A:TYR32 4.8 31.4 1.0 CE A:LYS16 4.9 17.8 1.0 NZ A:LYS16 4.9 19.9 1.0 C A:LYS16 4.9 12.7 1.0

Magnesium binding site 2 out of 3 in the KRASG12C in Complex with Gdp and Compound 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of KRASG12C in Complex with Gdp and Compound 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:9.2 occ:1.00 O A:HOH1140 2.3 23.6 1.0 O A:GLY138 2.3 17.7 1.0 O A:HOH1123 2.3 25.5 1.0 O A:HOH1106 2.4 19.6 1.0 O A:HOH1162 2.6 20.4 1.0 C A:GLY138 3.4 18.1 1.0 CA A:GLY138 4.0 18.9 1.0 OD1 A:ASP108 4.3 41.5 1.0 N A:ILE139 4.5 17.2 1.0 OE1 A:GLU162 4.5 20.9 1.0 OD2 A:ASP108 4.6 43.5 1.0 O A:HOH1163 4.6 29.8 1.0 O A:HOH1126 4.6 15.1 1.0 O A:HOH1134 4.8 19.3 1.0 CA A:ILE139 4.8 15.9 1.0 CG A:ASP108 4.8 41.0 1.0 O A:TYR137 4.9 19.6 1.0 CG2 A:ILE139 4.9 15.6 1.0

Magnesium binding site 3 out of 3 in the KRASG12C in Complex with Gdp and Compound 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of KRASG12C in Complex with Gdp and Compound 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1001 b:12.4 occ:1.00 O1B B:GDP1003 2.0 20.6 1.0 O B:HOH1115 2.0 21.9 1.0 O B:HOH1113 2.1 26.2 1.0 OG B:SER17 2.1 19.0 1.0 O B:HOH1111 2.1 14.2 1.0 O B:HOH1135 2.2 18.8 1.0 CB B:SER17 3.2 16.9 1.0 PB B:GDP1003 3.2 19.6 1.0 O3B B:GDP1003 3.5 18.4 1.0 N B:SER17 3.9 15.8 1.0 CA B:SER17 4.1 15.9 1.0 OD2 B:ASP57 4.2 31.7 1.0 O2A B:GDP1003 4.2 22.1 1.0 OD1 B:ASP57 4.4 30.3 1.0 O2B B:GDP1003 4.4 19.3 1.0 O3A B:GDP1003 4.4 20.9 1.0 O B:ILE36 4.4 25.3 1.0 O B:ASP33 4.4 23.5 1.0 CA B:PRO34 4.5 25.2 1.0 O B:THR58 4.5 23.9 1.0 O B:PRO34 4.6 25.2 1.0 PA B:GDP1003 4.7 21.9 1.0 CG B:ASP57 4.7 29.9 1.0 CB B:ALA59 4.7 26.8 1.0 O1A B:GDP1003 4.8 23.0 1.0 CD2 B:TYR32 4.8 27.8 1.0 C B:PRO34 4.8 25.2 1.0 O B:HOH1122 4.8 22.9 1.0 CB B:LYS16 4.9 16.1 1.0 CE B:LYS16 4.9 19.8 1.0 C B:LYS16 5.0 15.4 1.0

A.Weiss, E.Lorthiois, L.Barys, K.S.Beyer, C.Bomio-Confaglia, H.Burks, X.Chen, X.Cui, R.De Kanter, L.Dharmarajan, C.Fedele, M.Gerspacher, D.A.Guthy, V.Head, A.Jaeger, E.J.Nunez, J.D.Kearns, C.Leblanc, S.M.Maira, J.Murphy, H.Oakman, N.Ostermann, J.Ottl, P.Rigollier, D.Roman, C.Schnell, R.Sedrani, T.Shimizu, R.Stringer, A.Vaupel, H.Voshol, P.Wessels, T.Widmer, R.Wilcken, K.Xu, F.Zecri, A.F.Farago, S.Cotesta, S.M.Brachmann. Discovery, Preclinical Characterization, and Early Clinical Activity of JDQ443, A Structurally Novel, Potent, and Selective Covalent Oral Inhibitor of KRASG12C. Cancer Discov V. 12 1500 2022.
ISSN: ESSN 2159-8290
PubMed: 35404998
DOI: 10.1158/2159-8290.CD-22-0158