Magnesium in PDB 8qw6: Crystal Structure of Compound 3 in Complex with Kras G12V C118S Gdp and Pvhl:Elonginc:Elonginb

All present enzymatic activity of Crystal Structure of Compound 3 in Complex with Kras G12V C118S Gdp and Pvhl:Elonginc:Elonginb:
3.6.5.2;

The structure of Crystal Structure of Compound 3 in Complex with Kras G12V C118S Gdp and Pvhl:Elonginc:Elonginb, PDB code: 8qw6 was solved by D.Zollman, W.Farnaby, A.Ciulli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.37 / 2.20
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	70.207, 72.298, 80.794, 112.25, 100.61, 100.57
R / Rfree (%)	25.5 / 29.5

The binding sites of Magnesium atom in the Crystal Structure of Compound 3 in Complex with Kras G12V C118S Gdp and Pvhl:Elonginc:Elonginb (pdb code 8qw6). 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 Compound 3 in Complex with Kras G12V C118S Gdp and Pvhl:Elonginc:Elonginb, PDB code: 8qw6:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Compound 3 in Complex with Kras G12V C118S Gdp and Pvhl:Elonginc:Elonginb


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 Compound 3 in Complex with Kras G12V C118S Gdp and Pvhl:Elonginc:Elonginb within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg203 b:57.6 occ:1.00 O E:ASP33 2.3 69.0 1.0 OG E:SER17 2.4 53.2 1.0 CA E:PRO34 2.9 73.2 1.0 CB E:SER17 3.0 61.2 1.0 C E:ASP33 3.1 74.0 1.0 O1B E:GDP201 3.3 52.8 1.0 CD2 E:TYR32 3.4 82.1 1.0 N E:PRO34 3.4 76.2 1.0 C E:PRO34 3.4 60.0 1.0 CE2 E:TYR32 3.7 68.6 1.0 N E:THR35 3.8 64.1 1.0 O1A E:GDP201 3.9 67.1 1.0 O E:PRO34 4.1 63.2 1.0 CB E:PRO34 4.1 69.8 1.0 OD2 E:ASP57 4.2 60.9 1.0 O E:ILE36 4.2 69.7 1.0 CA E:SER17 4.3 59.1 1.0 N E:ILE36 4.5 70.5 1.0 CA E:ASP33 4.5 73.8 1.0 CG E:TYR32 4.6 81.3 1.0 PB E:GDP201 4.7 68.1 1.0 N E:ASP33 4.7 68.9 1.0 CB E:ALA59 4.7 51.3 1.0 CD E:PRO34 4.8 72.5 1.0 C E:TYR32 4.9 79.3 1.0 CA E:THR35 5.0 54.4 1.0 CB E:TYR32 5.0 81.4 1.0 CZ E:TYR32 5.0 54.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Compound 3 in Complex with Kras G12V C118S Gdp and Pvhl:Elonginc:Elonginb


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 Compound 3 in Complex with Kras G12V C118S Gdp and Pvhl:Elonginc:Elonginb within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:62.3 occ:1.00 O2B A:GDP201 3.0 56.9 1.0 OG A:SER17 3.0 47.2 1.0 O1B A:GDP201 3.2 62.4 1.0 O A:ASP33 3.4 83.2 1.0 CA A:PRO34 3.6 83.7 1.0 PB A:GDP201 3.6 58.8 1.0 OD1 A:ASP57 4.1 62.5 1.0 CB A:SER17 4.2 53.7 1.0 O2A A:GDP201 4.2 54.2 1.0 C A:ASP33 4.2 78.6 1.0 C A:PRO34 4.3 81.8 1.0 N A:PRO34 4.3 85.4 1.0 CB A:PRO34 4.6 79.4 1.0 CB A:ALA59 4.6 54.4 1.0 N A:THR35 4.6 81.3 1.0 O3A A:GDP201 4.6 64.1 1.0 O A:ILE36 4.6 48.5 1.0 O3B A:GDP201 4.8 47.4 1.0 O A:TYR32 4.8 74.5 1.0 PA A:GDP201 4.8 64.5 1.0 N A:SER17 4.9 64.0 1.0 N A:ILE36 4.9 67.4 1.0 O A:PRO34 4.9 82.9 1.0

J.Popow, W.Farnaby, A.Gollner, C.Kofink, G.Fischer, M.Wurm, D.Zollman, A.Wijaya, N.Mischerikow, C.Hasenoehrl, P.Prokofeva, H.Arnhof, S.Arce-Solano, S.Bell, G.Boeck, E.Diers, A.Frost, J.Goodwin-Tindall, J.Karolyi-Oezguer, S.Khan, T.Klawatsch, M.Koegl, R.Kousek, B.Kratochvil, K.Kropatsch, A.Lauber, R.Mclennan, S.Olt, D.Peter, O.Petermann, V.Roessler, P.Stolt-Bergner, P.Strack, E.Strauss, N.Trainor, V.Vetma, C.Whitworth, S.Zhong, J.Quant, H.Weinstabl, B.Kuster, P.Ettmayer, A.Ciulli. Targeting Cancer with Small Molecule Pan-Kras Degraders Biorxiv 2023.
ISSN: ISSN 2692-8205
DOI: 10.1101/2023.10.24.563163