Magnesium in PDB 8onv: Kras-G13D in Complex with Bi-2493

All present enzymatic activity of Kras-G13D in Complex with Bi-2493:
3.6.5.2;

The structure of Kras-G13D in Complex with Bi-2493, PDB code: 8onv was solved by J.Boettcher, L.Herdeis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.88 / 1.01
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	85.799, 40.845, 55.96, 90, 90, 90
R / Rfree (%)	13.4 / 15.7

The binding sites of Magnesium atom in the Kras-G13D in Complex with Bi-2493 (pdb code 8onv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Kras-G13D in Complex with Bi-2493, PDB code: 8onv:

Magnesium binding site 1 out of 1 in the Kras-G13D in Complex with Bi-2493


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Kras-G13D in Complex with Bi-2493 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:8.9 occ:1.00 O A:HOH343 2.0 10.0 1.0 O2B A:GDP201 2.1 8.7 1.0 O A:HOH330 2.1 9.3 1.0 OG A:SER17 2.1 9.3 1.0 O A:HOH377 2.1 9.9 1.0 O A:HOH390 2.1 9.4 1.0 HB2 A:SER17 3.1 10.2 1.0 CB A:SER17 3.2 8.5 1.0 PB A:GDP201 3.3 8.6 1.0 H A:SER17 3.4 10.3 1.0 HA A:PRO34 3.5 14.0 0.5 HA A:PRO34 3.6 14.0 0.5 O3B A:GDP201 3.6 9.7 1.0 HB3 A:SER17 3.8 10.2 1.0 HD2 A:TYR32 3.9 15.2 1.0 N A:SER17 3.9 8.6 1.0 HB2 A:LYS16 4.0 11.1 1.0 OD2 A:ASP57 4.1 10.9 1.0 CA A:SER17 4.1 8.3 1.0 O1A A:GDP201 4.1 10.2 1.0 HB2 A:ALA59 4.1 14.0 1.0 O A:PRO34 4.2 11.7 0.5 HE2 A:LYS16 4.2 13.8 1.0 OD1 A:ASP57 4.2 11.2 1.0 O A:PRO34 4.3 11.4 0.5 O3A A:GDP201 4.3 8.9 1.0 O A:ASP33 4.3 10.5 1.0 CA A:PRO34 4.4 11.7 0.5 O1B A:GDP201 4.4 9.0 1.0 HA A:SER17 4.4 10.0 1.0 CA A:PRO34 4.4 11.6 0.5 O A:ILE36 4.4 10.4 1.0 PA A:GDP201 4.5 8.8 1.0 CG A:ASP57 4.5 10.6 1.0 O A:THR58 4.6 10.1 1.0 C A:PRO34 4.6 11.2 0.5 C A:PRO34 4.6 11.2 0.5 HB3 A:TYR32 4.6 12.5 1.0 O2A A:GDP201 4.6 10.5 1.0 HZ3 A:LYS16 4.8 12.0 1.0 CD2 A:TYR32 4.8 12.6 1.0 HB1 A:ALA59 4.8 14.0 1.0 O A:TYR32 4.8 10.4 1.0 CB A:ALA59 4.9 11.7 1.0 O A:HOH360 4.9 19.0 1.0 CB A:LYS16 4.9 9.2 1.0 HZ1 A:LYS16 5.0 12.0 1.0

D.Kim, L.Herdeis, D.Rudolph, Y.Zhao, J.Boettcher, A.Vides, C.I.Ayala-Santos, Y.Pourfarjam, A.Cuevas-Navarro, J.Y.Xue, A.Mantoulidis, J.Broker, T.Wunberg, O.Schaaf, J.Popow, B.Wolkerstorfer, K.G.Kropatsch, R.Qu, E.De Stanchina, B.Sang, C.Li, D.B.Mcconnell, N.Kraut, P.Lito. Pan-Kras Inhibitor Disables Oncogenic Signalling and Tumour Growth. Nature 2023.
ISSN: ESSN 1476-4687
PubMed: 37258666
DOI: 10.1038/S41586-023-06123-3