Magnesium in PDB 8v39: Crystal Structure of Active Kras-G12C (Gmppnp-Bound) in Complex with Bbo-8520

All present enzymatic activity of Crystal Structure of Active Kras-G12C (Gmppnp-Bound) in Complex with Bbo-8520:
3.6.5.2;

The structure of Crystal Structure of Active Kras-G12C (Gmppnp-Bound) in Complex with Bbo-8520, PDB code: 8v39 was solved by A.H.Chan, M.Ashraf, S.Dharmaiah, D.K.Simanshu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.78 / 2.10
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	115.96, 115.96, 180.5, 90, 90, 120
R / Rfree (%)	26.6 / 31.2

The structure of Crystal Structure of Active Kras-G12C (Gmppnp-Bound) in Complex with Bbo-8520 also contains other interesting chemical elements:

Fluorine

(F)

18 atoms

The binding sites of Magnesium atom in the Crystal Structure of Active Kras-G12C (Gmppnp-Bound) in Complex with Bbo-8520 (pdb code 8v39). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Active Kras-G12C (Gmppnp-Bound) in Complex with Bbo-8520, PDB code: 8v39:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Active Kras-G12C (Gmppnp-Bound) in Complex with Bbo-8520


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 Active Kras-G12C (Gmppnp-Bound) in Complex with Bbo-8520 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:24.5 occ:1.00 O2G A:GNP201 1.9 26.2 1.0 OG A:SER17 2.1 25.2 1.0 O A:HOH305 2.1 21.0 1.0 O1B A:GNP201 2.1 22.4 1.0 O A:HOH355 2.2 25.7 1.0 O A:HOH325 2.2 25.6 1.0 CB A:SER17 3.2 25.5 1.0 PG A:GNP201 3.2 26.9 1.0 PB A:GNP201 3.3 24.6 1.0 N3B A:GNP201 3.5 24.9 1.0 O A:HOH359 3.8 34.1 1.0 N A:SER17 3.9 22.8 1.0 O1G A:GNP201 4.0 25.8 1.0 OD2 A:ASP57 4.1 22.9 1.0 CA A:SER17 4.1 25.2 1.0 OD1 A:ASP57 4.1 22.4 1.0 O1A A:GNP201 4.2 26.1 1.0 O2B A:GNP201 4.3 22.2 1.0 O3G A:GNP201 4.4 27.3 1.0 O A:PRO34 4.4 39.8 1.0 O3A A:GNP201 4.5 22.8 1.0 CG A:ASP57 4.5 23.8 1.0 O A:THR58 4.5 19.2 1.0 CB A:ALA59 4.5 23.3 1.0 PA A:GNP201 4.7 24.1 1.0 CB A:LYS16 4.9 21.6 1.0 CE A:LYS16 4.9 20.5 1.0 O2A A:GNP201 4.9 23.5 1.0 O A:ILE36 4.9 28.5 1.0 NZ A:LYS16 5.0 20.2 1.0 CB A:PRO34 5.0 35.1 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Active Kras-G12C (Gmppnp-Bound) in Complex with Bbo-8520


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 Active Kras-G12C (Gmppnp-Bound) in Complex with Bbo-8520 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:33.3 occ:1.00 O2G B:GNP201 1.9 31.4 1.0 OG B:SER17 2.0 34.2 1.0 O B:HOH325 2.1 33.3 1.0 O1B B:GNP201 2.1 25.4 1.0 O B:HOH326 2.1 38.4 1.0 O B:HOH318 2.2 30.1 1.0 CB B:SER17 3.0 35.0 1.0 PG B:GNP201 3.2 36.5 1.0 PB B:GNP201 3.3 30.1 1.0 N3B B:GNP201 3.6 33.3 1.0 N B:SER17 3.9 32.5 1.0 CA B:SER17 4.0 33.6 1.0 OD2 B:ASP57 4.0 33.0 1.0 O1G B:GNP201 4.1 32.4 1.0 O1A B:GNP201 4.1 38.3 1.0 OD1 B:ASP57 4.2 31.5 1.0 O2B B:GNP201 4.3 30.7 1.0 O3G B:GNP201 4.4 40.5 1.0 O B:PRO34 4.5 69.7 1.0 O3A B:GNP201 4.5 34.9 1.0 O B:THR58 4.5 32.1 1.0 O B:HOH301 4.5 44.5 1.0 CG B:ASP57 4.5 32.0 1.0 PA B:GNP201 4.7 34.4 1.0 CB B:ALA59 4.7 34.8 1.0 O2A B:GNP201 4.9 36.4 1.0 CB B:LYS16 4.9 30.9 1.0 O B:ILE36 4.9 43.5 1.0 CE B:LYS16 4.9 31.6 1.0 CB B:PRO34 4.9 66.0 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Active Kras-G12C (Gmppnp-Bound) in Complex with Bbo-8520


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Active Kras-G12C (Gmppnp-Bound) in Complex with Bbo-8520 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:45.5 occ:1.00 OG C:SER17 1.9 50.7 1.0 O C:HOH312 2.0 42.9 1.0 O2G C:GNP201 2.1 43.4 1.0 O1B C:GNP201 2.1 39.8 1.0 O C:HOH304 2.4 46.5 1.0 O C:HOH325 2.5 44.8 1.0 CB C:SER17 3.0 52.5 1.0 PG C:GNP201 3.3 44.3 1.0 PB C:GNP201 3.3 40.5 1.0 N3B C:GNP201 3.5 44.0 1.0 N C:SER17 3.8 52.3 1.0 OD2 C:ASP57 3.9 50.9 1.0 CA C:SER17 4.0 53.3 1.0 O1G C:GNP201 4.1 47.0 1.0 OD1 C:ASP57 4.1 49.7 1.0 O1A C:GNP201 4.2 45.3 1.0 O2B C:GNP201 4.3 47.3 1.0 O C:PRO34 4.3 58.8 1.0 CG C:ASP57 4.4 50.3 1.0 O3A C:GNP201 4.4 47.9 1.0 O3G C:GNP201 4.5 46.3 1.0 PA C:GNP201 4.6 45.6 1.0 O2A C:GNP201 4.7 43.8 1.0 O C:THR58 4.7 45.0 1.0 CB C:ALA59 4.8 44.0 1.0 CB C:LYS16 4.8 49.8 1.0 CE C:LYS16 4.9 46.2 1.0 C C:LYS16 4.9 52.7 1.0 CB C:PRO34 5.0 56.4 1.0

A.E.Maciag, J.P.Stice, B.Wang, A.K.Sharma, A.H.Chan, K.Lin, D.Singh, M.Dyba, Y.Yang, S.Setoodeh, B.P.Smith, J.H.Ju, S.Jeknic, D.Rabara, Z.Zhang, E.K.Larsen, D.Esposito, J.P.Denson, M.Ranieri, M.Meynardie, S.Mehdizadeh, P.A.Alexander, M.Abreu Blanco, D.M.Turner, R.Xu, F.C.Lightstone, K.K.Wong, A.G.Stephen, K.Wang, D.K.Simanshu, K.W.Sinkevicius, D.V.Nissley, E.Wallace, F.Mccormick, P.J.Beltran. Discovery of Bbo-8520, A First-in-Class Direct and Covalent Dual Inhibitor of Gtp-Bound (on) and Gdp-Bound (Off) KRASG12C. Cancer Discov 2024.
ISSN: ESSN 2159-8290
PubMed: 39642212
DOI: 10.1158/2159-8290.CD-24-0840