Magnesium in PDB 8qvu: Crystal Structure of Ligand ACBI3 in Complex with Kras G12D C118S Gdp and Pvhl:Elonginc:Elonginb Complex

The structure of Crystal Structure of Ligand ACBI3 in Complex with Kras G12D C118S Gdp and Pvhl:Elonginc:Elonginb Complex, PDB code: 8qvu was solved by A.J.Wijaya, 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)	55.86 / 2.24
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	72.253, 120.9, 81.016, 90, 111.67, 90
R / Rfree (%)	24.8 / 28.7

The binding sites of Magnesium atom in the Crystal Structure of Ligand ACBI3 in Complex with Kras G12D C118S Gdp and Pvhl:Elonginc:Elonginb Complex (pdb code 8qvu). 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 Ligand ACBI3 in Complex with Kras G12D C118S Gdp and Pvhl:Elonginc:Elonginb Complex, PDB code: 8qvu:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Ligand ACBI3 in Complex with Kras G12D C118S Gdp and Pvhl:Elonginc:Elonginb Complex


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 Ligand ACBI3 in Complex with Kras G12D C118S Gdp and Pvhl:Elonginc:Elonginb Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg203 b:59.7 occ:1.00 OG E:SER17 2.0 80.8 1.0 O2B E:GDP202 2.7 84.6 1.0 OD2 E:ASP57 2.7 90.6 1.0 OD1 E:ASP57 2.7 82.6 1.0 CG E:ASP57 3.1 84.4 1.0 O E:THR58 3.1 70.5 1.0 CB E:SER17 3.4 69.5 1.0 N E:SER17 3.8 73.8 1.0 PB E:GDP202 3.8 94.3 1.0 O3B E:GDP202 3.8 78.9 1.0 CB E:ALA59 3.9 93.4 1.0 CA E:SER17 4.0 58.9 1.0 O2A E:GDP202 4.1 75.7 1.0 C E:THR58 4.2 77.3 1.0 O E:ILE36 4.3 80.5 1.0 O E:PRO34 4.4 117.4 1.0 CE E:LYS16 4.5 53.5 1.0 CB E:ASP57 4.6 76.0 1.0 O E:ASP33 4.6 105.7 1.0 CB E:LYS16 4.6 57.9 1.0 CA E:ALA59 4.7 87.8 1.0 C E:LYS16 4.8 69.5 1.0 PA E:GDP202 4.8 80.9 1.0 O3A E:GDP202 4.8 83.8 1.0 N E:ALA59 4.8 87.5 1.0 N E:THR58 4.9 72.3 1.0 O1B E:GDP202 4.9 78.9 1.0 NZ E:LYS16 4.9 59.4 1.0 O1A E:GDP202 5.0 63.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Ligand ACBI3 in Complex with Kras G12D C118S Gdp and Pvhl:Elonginc:Elonginb Complex


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 Ligand ACBI3 in Complex with Kras G12D C118S Gdp and Pvhl:Elonginc:Elonginb Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:65.8 occ:1.00 OG A:SER17 1.8 86.6 1.0 O1B A:GDP201 2.2 96.7 1.0 CB A:SER17 3.1 96.7 1.0 OD1 A:ASP57 3.4 106.8 1.0 PB A:GDP201 3.6 102.6 1.0 OD2 A:ASP57 3.7 86.2 1.0 O A:PRO34 3.7 125.6 1.0 NZ A:LYS16 3.7 87.2 1.0 CB A:ALA59 3.8 92.0 1.0 O A:ASP33 3.9 96.9 1.0 CA A:SER17 3.9 92.4 1.0 O2B A:GDP201 3.9 97.8 1.0 CG A:ASP57 3.9 102.9 1.0 N A:SER17 4.0 80.8 1.0 O1A A:GDP201 4.0 103.5 1.0 CE A:LYS16 4.1 76.2 1.0 CA A:PRO34 4.1 111.9 1.0 C A:PRO34 4.2 117.3 1.0 O3A A:GDP201 4.4 114.2 1.0 O3B A:GDP201 4.6 89.8 1.0 CA A:ALA59 4.7 85.4 1.0 C A:ASP33 4.7 101.8 1.0 PA A:GDP201 4.8 114.9 1.0 O A:ILE36 4.8 70.4 1.0 N A:PRO34 4.9 114.3 1.0 CD A:LYS16 4.9 75.3 1.0 C A:LYS16 5.0 95.0 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