Magnesium in PDB 6ark: Crystal Structure of Compound 10 Covalently Bound to K-Ras G12C

The structure of Crystal Structure of Compound 10 Covalently Bound to K-Ras G12C, PDB code: 6ark was solved by C.I.Nnadi, M.L.Jenkins, D.R.Gentile, L.A.Bateman, D.Zaidman, T.E.Balius, D.K.Nomura, J.E.Burke, K.M.Shokat, N.London, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.88 / 1.75
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	94.280, 94.280, 119.550, 90.00, 90.00, 120.00
R / Rfree (%)	19.4 / 23.1

The structure of Crystal Structure of Compound 10 Covalently Bound to K-Ras G12C also contains other interesting chemical elements:

Bromine

(Br)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of Compound 10 Covalently Bound to K-Ras G12C (pdb code 6ark). 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 Crystal Structure of Compound 10 Covalently Bound to K-Ras G12C, PDB code: 6ark:

Magnesium binding site 1 out of 1 in the Crystal Structure of Compound 10 Covalently Bound to K-Ras G12C


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 Compound 10 Covalently Bound to K-Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:74.6 occ:1.00 OG A:SER17 2.0 52.8 1.0 O A:HOH310 2.1 40.5 1.0 O A:HOH305 2.1 59.1 1.0 O A:HOH314 2.2 59.4 1.0 O2B A:GDP201 2.2 44.8 1.0 O A:HOH308 2.3 44.5 1.0 HG A:SER17 2.4 63.4 1.0 CB A:SER17 3.2 54.4 1.0 HB2 A:SER17 3.3 65.2 1.0 H A:SER17 3.3 54.4 1.0 HD2 A:TYR32 3.4 0.6 1.0 PB A:GDP201 3.4 34.9 1.0 O3B A:GDP201 3.6 35.6 1.0 OD2 A:ASP57 3.6 48.9 1.0 HB3 A:SER17 3.9 65.2 1.0 N A:SER17 3.9 45.3 1.0 OD1 A:ASP57 3.9 60.8 1.0 HB2 A:LYS16 4.0 48.6 1.0 O2A A:GDP201 4.1 46.3 1.0 CA A:SER17 4.1 40.5 1.0 CG A:ASP57 4.2 64.7 1.0 CD2 A:TYR32 4.3 92.2 1.0 HB2 A:ALA59 4.3 93.7 1.0 HA A:SER17 4.3 48.6 1.0 HE2 A:LYS16 4.3 47.1 1.0 O1B A:GDP201 4.5 40.1 1.0 CA A:PRO34 4.5 0.8 1.0 HE2 A:TYR32 4.5 0.9 1.0 O A:ILE36 4.5 86.9 1.0 O3A A:GDP201 4.5 33.0 1.0 O A:ASP33 4.5 0.8 1.0 HB3 A:TYR32 4.6 0.4 1.0 O1A A:GDP201 4.6 37.9 1.0 PA A:GDP201 4.6 38.7 1.0 O A:THR58 4.6 60.8 1.0 O A:PRO34 4.7 0.1 1.0 CE2 A:TYR32 4.8 90.8 1.0 HZ1 A:LYS16 4.8 45.7 1.0 C A:PRO34 4.9 0.5 1.0 CB A:LYS16 4.9 40.5 1.0 HZ3 A:LYS16 5.0 45.7 1.0 O A:TYR32 5.0 92.9 1.0 C A:LYS16 5.0 45.3 1.0

C.I.Nnadi, M.L.Jenkins, D.R.Gentile, L.A.Bateman, D.Zaidman, T.E.Balius, D.K.Nomura, J.E.Burke, K.M.Shokat, N.London. Novel K-Ras G12C Switch-II Covalent Binders Destabilize Ras and Accelerate Nucleotide Exchange. J Chem Inf Model V. 58 464 2018.
ISSN: ESSN 1549-960X
PubMed: 29320178
DOI: 10.1021/ACS.JCIM.7B00399