Magnesium in PDB 8qw7: Crystal Structure of Compound 4 in Complex with Kras G12V C118S Gdp and Pvhl:Elonginc:Elonginb

All present enzymatic activity of Crystal Structure of Compound 4 in Complex with Kras G12V C118S Gdp and Pvhl:Elonginc:Elonginb:
3.6.5.2;

The structure of Crystal Structure of Compound 4 in Complex with Kras G12V C118S Gdp and Pvhl:Elonginc:Elonginb, PDB code: 8qw7 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)	67.42 / 2.36
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	72.52, 125.929, 81.056, 90, 111.61, 90
R / Rfree (%)	24.6 / 27.3

The binding sites of Magnesium atom in the Crystal Structure of Compound 4 in Complex with Kras G12V C118S Gdp and Pvhl:Elonginc:Elonginb (pdb code 8qw7). 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 4 in Complex with Kras G12V C118S Gdp and Pvhl:Elonginc:Elonginb, PDB code: 8qw7:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Compound 4 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 4 in Complex with Kras G12V C118S Gdp and Pvhl:Elonginc:Elonginb within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:55.3 occ:1.00 OG A:SER17 2.2 76.5 1.0 O1B A:GDP201 2.2 71.9 1.0 O A:ASP33 3.2 77.7 1.0 CA A:PRO34 3.4 70.1 1.0 CB A:SER17 3.5 75.0 1.0 PB A:GDP201 3.6 80.6 1.0 O1A A:GDP201 3.6 86.9 1.0 C A:PRO34 3.8 66.8 1.0 O A:PRO34 3.8 73.0 1.0 CB A:ALA59 4.0 58.8 1.0 C A:ASP33 4.0 73.5 1.0 O3B A:GDP201 4.1 77.2 1.0 O A:ILE36 4.1 64.7 1.0 N A:PRO34 4.2 74.7 1.0 OD2 A:ASP57 4.3 74.6 1.0 N A:SER17 4.5 78.7 1.0 CB A:PRO34 4.5 61.7 1.0 CA A:SER17 4.6 74.6 1.0 PA A:GDP201 4.6 86.7 1.0 O3A A:GDP201 4.6 86.2 1.0 O2B A:GDP201 4.6 72.1 1.0 N A:THR35 4.7 63.6 1.0 O A:THR58 4.7 59.7 1.0 OD1 A:ASP57 4.9 77.7 1.0 O A:TYR32 4.9 83.8 1.0 CG A:ASP57 5.0 74.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Compound 4 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 4 in Complex with Kras G12V C118S Gdp and Pvhl:Elonginc:Elonginb within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg202 b:88.8 occ:1.00 O2B E:GDP201 2.3 96.1 1.0 OG E:SER17 2.4 83.3 1.0 O E:PRO34 2.7 93.2 1.0 O E:ASP33 3.1 98.1 1.0 C E:PRO34 3.3 97.1 1.0 PB E:GDP201 3.4 109.7 1.0 CA E:PRO34 3.5 100.3 1.0 CB E:SER17 3.5 88.5 1.0 O3B E:GDP201 3.5 95.0 1.0 CB E:ALA59 3.9 82.1 1.0 O E:ILE36 3.9 82.9 1.0 C E:ASP33 4.0 98.5 1.0 O E:TYR32 4.0 96.8 1.0 N E:ILE36 4.1 82.6 1.0 N E:PRO34 4.2 98.8 1.0 O3A E:GDP201 4.3 112.3 1.0 N E:THR35 4.3 90.2 1.0 OD2 E:ASP57 4.3 81.4 1.0 N E:SER17 4.6 92.2 1.0 CA E:SER17 4.6 90.5 1.0 CD1 E:TYR32 4.7 89.6 1.0 O1B E:GDP201 4.7 91.8 1.0 C E:ILE36 4.8 81.3 1.0 CB E:PRO34 4.8 93.9 1.0 CA E:ILE36 4.9 85.6 1.0 C E:TYR32 4.9 94.2 1.0 OD1 E:ASP57 4.9 82.2 1.0 O2A E:GDP201 4.9 105.4 1.0 C E:THR35 4.9 88.1 1.0 CA E:THR35 5.0 84.4 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