Sodium in PDB 8ezg: Monobody 12D1 Bound to Kras(G12D)

All present enzymatic activity of Monobody 12D1 Bound to Kras(G12D):
3.6.5.2;

The structure of Monobody 12D1 Bound to Kras(G12D), PDB code: 8ezg 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)	45.17 / 2.52
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	156.477, 156.477, 64.624, 90, 90, 120
R / Rfree (%)	17.1 / 21.3

The structure of Monobody 12D1 Bound to Kras(G12D) also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Monobody 12D1 Bound to Kras(G12D) (pdb code 8ezg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Monobody 12D1 Bound to Kras(G12D), PDB code: 8ezg:

Sodium binding site 1 out of 1 in the Monobody 12D1 Bound to Kras(G12D)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Monobody 12D1 Bound to Kras(G12D) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:23.6 occ:1.00 O B:TRP22 2.4 26.1 1.0 OG B:SER21 2.5 23.2 1.0 O B:HOH324 2.5 27.8 0.5 OG B:SER55 2.6 28.3 1.0 O B:SER55 2.6 29.4 1.0 CB B:SER55 3.1 27.7 1.0 C B:SER55 3.4 29.3 1.0 N B:TRP22 3.4 23.0 1.0 C B:TRP22 3.5 26.1 1.0 CB B:SER21 3.7 24.2 1.0 CA B:SER55 3.8 29.6 1.0 CG2 B:THR56 3.8 22.7 1.0 CA B:SER21 4.0 27.2 1.0 CA B:TRP22 4.1 29.6 1.0 C B:SER21 4.1 28.1 1.0 O B:HOH320 4.3 24.5 1.0 N B:THR56 4.4 26.8 1.0 OD1 B:ASP23 4.5 32.2 1.0 O B:HOH302 4.5 34.2 1.0 N B:ASP23 4.6 26.7 1.0 N B:SER55 4.7 26.6 1.0 CA B:THR56 4.9 31.4 1.0 CA B:ASP23 4.9 29.6 1.0 CB B:THR56 5.0 26.0 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