Magnesium in PDB 8f0m: Monobody 12D5 Bound to Kras(G12D)

All present enzymatic activity of Monobody 12D5 Bound to Kras(G12D):
3.6.5.2;

The structure of Monobody 12D5 Bound to Kras(G12D), PDB code: 8f0m was solved by T.Hattori, E.Glasser, P.Akkapeddi, G.Ketavarapu, K.W.Teng, A.Koide, S.Koide, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.90 / 2.44
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	151.386, 44.733, 88.162, 90, 90, 90
R / Rfree (%)	20.1 / 24.5

The binding sites of Magnesium atom in the Monobody 12D5 Bound to Kras(G12D) (pdb code 8f0m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Monobody 12D5 Bound to Kras(G12D), PDB code: 8f0m:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Monobody 12D5 Bound to Kras(G12D)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Monobody 12D5 Bound to Kras(G12D) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:35.8 occ:1.00 O A:HOH315 2.0 34.4 1.0 O2B A:GDP202 2.1 41.1 1.0 O A:HOH312 2.1 35.7 1.0 O A:HOH313 2.1 38.8 1.0 OG A:SER17 2.2 34.2 1.0 O A:HOH305 2.4 44.4 1.0 O1B A:GDP202 3.1 29.1 1.0 PB A:GDP202 3.1 33.5 1.0 CB A:SER17 3.3 33.8 1.0 O2A A:GDP202 3.9 39.6 1.0 N A:SER17 3.9 32.4 1.0 OD2 A:ASP57 4.1 41.4 1.0 O3B A:GDP202 4.1 30.7 1.0 O A:THR58 4.1 43.7 1.0 CA A:SER17 4.2 35.2 1.0 O3A A:GDP202 4.2 37.8 1.0 PA A:GDP202 4.4 31.1 1.0 O1A A:GDP202 4.6 36.6 1.0 O A:HOH310 4.7 36.2 1.0 CE A:LYS16 4.8 35.4 1.0 NZ A:LYS16 4.8 32.7 1.0 OD1 A:ASP57 4.8 36.9 1.0 CG A:ASP57 4.9 42.5 1.0 CB A:LYS16 4.9 30.4 1.0

Magnesium binding site 2 out of 2 in the Monobody 12D5 Bound to Kras(G12D)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Monobody 12D5 Bound to Kras(G12D) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg201 b:41.4 occ:1.00 O1B C:GSP202 1.9 44.2 1.0 O3G C:GSP202 2.0 33.1 1.0 OG C:SER17 2.0 51.0 1.0 O C:HOH313 2.3 40.4 1.0 O C:HOH312 2.4 34.0 1.0 CB C:SER17 3.1 38.5 1.0 PB C:GSP202 3.3 38.9 1.0 PG C:GSP202 3.3 51.4 1.0 O3B C:GSP202 3.7 43.5 1.0 N C:SER17 3.8 38.1 1.0 OD2 C:ASP57 3.9 44.2 1.0 O2B C:GSP202 4.0 43.8 1.0 CA C:SER17 4.0 43.3 1.0 O1A C:GSP202 4.1 34.2 1.0 O C:THR58 4.2 38.7 1.0 O2G C:GSP202 4.3 49.1 1.0 O3A C:GSP202 4.4 40.3 1.0 S1G C:GSP202 4.4 56.0 1.0 PA C:GSP202 4.6 38.5 1.0 CG C:ASP57 4.6 47.6 1.0 O2A C:GSP202 4.6 34.7 1.0 OD1 C:ASP57 4.6 40.7 1.0 CB C:LYS16 5.0 42.6 1.0 C C:LYS16 5.0 40.7 1.0

P.Akkapeddi, T.Hattori, I.Khan, E.Glasser, A.Koide, G.Ketavarapu, M.Whaby, M.Zuberi, K.W.Teng, J.Lefler, L.Maso, I.Bang, M.C.Ostrowski, J.P.O'bryan, S.Koide. Exploring Switch II Pocket Conformation of Kras(G12D) with Mutant-Selective Monobody Inhibitors. Proc.Natl.Acad.Sci.Usa V. 120 85120 2023.
ISSN: ESSN 1091-6490
PubMed: 37399416
DOI: 10.1073/PNAS.2302485120