Magnesium in PDB 6wgn: Crystal Structure of K-Ras(G12D) Gppnhp Bound to Cyclic Peptide Ligand KD2

The structure of Crystal Structure of K-Ras(G12D) Gppnhp Bound to Cyclic Peptide Ligand KD2, PDB code: 6wgn was solved by Z.Zhang, R.Gao, Q.Hu, H.Peacock, D.M.Peacock, K.M.Shokat, H.Suga, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.52 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.437, 79.155, 90.982, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 21.4

The binding sites of Magnesium atom in the Crystal Structure of K-Ras(G12D) Gppnhp Bound to Cyclic Peptide Ligand KD2 (pdb code 6wgn). 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 K-Ras(G12D) Gppnhp Bound to Cyclic Peptide Ligand KD2, PDB code: 6wgn:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of K-Ras(G12D) Gppnhp Bound to Cyclic Peptide Ligand KD2


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 K-Ras(G12D) Gppnhp Bound to Cyclic Peptide Ligand KD2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:12.9 occ:1.00 O A:HOH346 2.0 14.0 1.0 O1B A:GNP201 2.0 8.8 1.0 O1G A:GNP201 2.1 15.5 1.0 OG A:SER17 2.1 11.1 1.0 O A:HOH401 2.1 15.8 1.0 O A:HOH359 2.2 12.4 1.0 CB A:SER17 3.1 10.5 1.0 PB A:GNP201 3.2 9.2 1.0 PG A:GNP201 3.2 13.1 1.0 N3B A:GNP201 3.4 11.2 1.0 N A:SER17 3.8 8.4 1.0 O A:HOH415 4.0 29.9 1.0 OD2 A:ASP57 4.0 17.8 1.0 CA A:SER17 4.0 9.3 1.0 OD1 A:ASP57 4.2 19.1 1.0 O2A A:GNP201 4.2 13.5 1.0 O2B A:GNP201 4.2 10.8 1.0 O3G A:GNP201 4.2 17.2 1.0 O2G A:GNP201 4.3 13.7 1.0 O3A A:GNP201 4.3 8.7 1.0 O A:HOH375 4.5 33.5 1.0 O A:HOH388 4.5 25.1 1.0 O A:THR58 4.5 17.7 1.0 CG A:ASP57 4.5 18.2 1.0 PA A:GNP201 4.6 10.4 1.0 CB A:LYS16 4.7 8.5 1.0 O1A A:GNP201 4.7 11.8 1.0 CE A:LYS16 4.8 9.9 1.0 CB A:ALA59 4.9 19.1 1.0 C A:LYS16 4.9 10.2 1.0 O A:ASP33 4.9 45.1 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of K-Ras(G12D) Gppnhp Bound to Cyclic Peptide Ligand KD2


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 K-Ras(G12D) Gppnhp Bound to Cyclic Peptide Ligand KD2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:13.7 occ:1.00 O B:HOH353 2.0 14.7 1.0 O1B B:GNP201 2.1 10.0 1.0 O1G B:GNP201 2.1 17.5 1.0 OG B:SER17 2.1 13.1 1.0 O B:HOH327 2.1 13.9 1.0 O B:HOH398 2.1 16.9 1.0 CB B:SER17 3.2 13.2 1.0 PG B:GNP201 3.2 14.6 1.0 PB B:GNP201 3.2 11.6 1.0 N3B B:GNP201 3.4 11.6 1.0 N B:SER17 3.8 11.8 1.0 OD2 B:ASP57 4.0 20.2 1.0 CA B:SER17 4.1 12.0 1.0 O2A B:GNP201 4.1 13.2 1.0 OD1 B:ASP57 4.2 19.0 1.0 O B:HOH406 4.2 28.0 1.0 O3G B:GNP201 4.2 18.6 1.0 O2B B:GNP201 4.3 11.9 1.0 O2G B:GNP201 4.3 16.9 1.0 O B:HOH340 4.3 23.6 1.0 O3A B:GNP201 4.3 10.5 1.0 CG B:ASP57 4.5 18.7 1.0 PA B:GNP201 4.6 13.2 1.0 O B:THR58 4.6 20.4 1.0 O1A B:GNP201 4.7 14.1 1.0 CB B:LYS16 4.7 9.1 1.0 CE B:LYS16 4.8 9.9 1.0 C B:LYS16 4.9 12.0 1.0 O B:HOH405 4.9 39.3 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of K-Ras(G12D) Gppnhp Bound to Cyclic Peptide Ligand KD2


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 K-Ras(G12D) Gppnhp Bound to Cyclic Peptide Ligand KD2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:11.5 occ:1.00 O1B C:GNP201 2.0 10.1 1.0 O C:HOH372 2.1 12.9 1.0 O1G C:GNP201 2.1 15.2 1.0 OG C:SER17 2.1 11.2 1.0 O C:HOH333 2.1 13.3 1.0 O C:HOH399 2.1 15.2 1.0 CB C:SER17 3.2 11.3 1.0 PB C:GNP201 3.2 10.3 1.0 PG C:GNP201 3.3 12.4 1.0 N3B C:GNP201 3.5 9.9 1.0 N C:SER17 3.8 8.2 1.0 O C:HOH396 4.0 26.3 1.0 CA C:SER17 4.1 10.6 1.0 O C:HOH423 4.1 28.4 1.0 OD2 C:ASP57 4.1 17.6 1.0 O2A C:GNP201 4.2 11.2 1.0 OD1 C:ASP57 4.2 18.6 1.0 O2B C:GNP201 4.2 10.0 1.0 O3G C:GNP201 4.2 15.2 1.0 O C:HOH425 4.3 25.7 1.0 O2G C:GNP201 4.3 15.0 1.0 O3A C:GNP201 4.3 9.3 1.0 CG C:ASP57 4.6 16.9 1.0 O C:THR58 4.6 16.9 1.0 PA C:GNP201 4.6 10.4 1.0 CB C:LYS16 4.8 9.2 1.0 O1A C:GNP201 4.8 12.6 1.0 CE C:LYS16 4.8 11.2 1.0 C C:LYS16 4.9 7.5 1.0 CB C:ALA59 5.0 27.5 1.0

Z.Zhang, R.Gao, Q.Hu, H.Peacock, D.M.Peacock, S.Dai, K.M.Shokat, H.Suga. Gtp-State-Selective Cyclic Peptide Ligands of K-Ras(G12D) Block Its Interaction with Raf. Acs Cent.Sci. V. 6 1753 2020.
ISSN: ESSN 2374-7951
PubMed: 33145412
DOI: 10.1021/ACSCENTSCI.0C00514