Magnesium in PDB 7rov: Kras G12D Mutant in Complex with Gmppcp and Cyclic Peptide Mp-9903

All present enzymatic activity of Kras G12D Mutant in Complex with Gmppcp and Cyclic Peptide Mp-9903:
3.6.5.2;

The structure of Kras G12D Mutant in Complex with Gmppcp and Cyclic Peptide Mp-9903, PDB code: 7rov was solved by P.Orth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.94 / 1.32
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.793, 71.764, 65.481, 90, 100.29, 90
R / Rfree (%)	19.4 / 21.6

The binding sites of Magnesium atom in the Kras G12D Mutant in Complex with Gmppcp and Cyclic Peptide Mp-9903 (pdb code 7rov). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Kras G12D Mutant in Complex with Gmppcp and Cyclic Peptide Mp-9903, PDB code: 7rov:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Kras G12D Mutant in Complex with Gmppcp and Cyclic Peptide Mp-9903


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Kras G12D Mutant in Complex with Gmppcp and Cyclic Peptide Mp-9903 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2002 b:11.0 occ:1.00 O2B A:GCP2001 2.0 11.1 1.0 O A:HOH2180 2.1 15.4 1.0 O1G A:GCP2001 2.1 14.8 1.0 O A:HOH2114 2.1 12.8 1.0 OG A:SER17 2.1 12.0 1.0 O A:HOH2130 2.1 12.9 1.0 CB A:SER17 3.2 10.9 1.0 PG A:GCP2001 3.2 15.1 1.0 PB A:GCP2001 3.3 10.9 1.0 C3B A:GCP2001 3.5 12.2 1.0 N A:SER17 3.9 9.0 1.0 O A:HOH2104 4.0 37.9 1.0 O A:HOH2131 4.0 29.3 1.0 CA A:SER17 4.1 9.6 1.0 OD2 A:ASP57 4.1 18.3 1.0 O1A A:GCP2001 4.1 13.2 1.0 OD1 A:ASP57 4.2 15.6 1.0 O2G A:GCP2001 4.2 17.2 1.0 O1B A:GCP2001 4.3 10.9 1.0 O3G A:GCP2001 4.4 16.0 1.0 O3A A:GCP2001 4.4 11.1 1.0 O A:THR58 4.5 14.2 1.0 CB A:ALA59 4.5 15.6 1.0 CG A:ASP57 4.6 16.4 1.0 O A:HOH2198 4.6 36.0 1.0 PA A:GCP2001 4.7 12.0 1.0 O A:THR35 4.8 29.9 1.0 CB A:LYS16 4.8 9.7 1.0 CE A:LYS16 4.9 11.0 1.0 O2A A:GCP2001 5.0 12.2 1.0 C A:LYS16 5.0 9.2 1.0

Magnesium binding site 2 out of 2 in the Kras G12D Mutant in Complex with Gmppcp and Cyclic Peptide Mp-9903


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Kras G12D Mutant in Complex with Gmppcp and Cyclic Peptide Mp-9903 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2003 b:13.0 occ:1.00 O B:HOH2115 2.1 16.2 1.0 O2B B:GCP2001 2.1 13.2 1.0 O2G B:GCP2001 2.1 17.7 1.0 O B:HOH2171 2.1 17.0 1.0 OG B:SER17 2.1 14.1 1.0 O B:HOH2132 2.2 15.8 1.0 CB B:SER17 3.2 12.3 1.0 PB B:GCP2001 3.3 12.5 1.0 PG B:GCP2001 3.3 17.3 1.0 C3B B:GCP2001 3.5 14.3 1.0 N B:SER17 3.9 10.6 1.0 CA B:SER17 4.1 10.9 1.0 O2A B:GCP2001 4.2 13.9 1.0 OD2 B:ASP57 4.2 20.8 1.0 OD1 B:ASP57 4.2 18.9 1.0 O1B B:GCP2001 4.3 12.3 1.0 O1G B:GCP2001 4.4 17.7 1.0 CB B:ALA59 4.4 28.0 1.0 O3G B:GCP2001 4.4 18.3 1.0 O3A B:GCP2001 4.4 12.3 1.0 O B:ASP33 4.5 38.7 1.0 O B:THR58 4.5 17.6 1.0 O B:PRO34 4.6 41.5 1.0 CG B:ASP57 4.6 19.4 1.0 PA B:GCP2001 4.7 12.6 1.0 O B:ILE36 4.7 35.0 1.0 CD2 B:TYR32 4.8 33.5 1.0 CA B:PRO34 4.8 40.0 1.0 CB B:LYS16 4.8 10.7 1.0 CE B:LYS16 4.8 13.6 1.0 O1A B:GCP2001 4.9 12.4 1.0 C B:LYS16 5.0 10.5 1.0 C B:PRO34 5.0 40.8 1.0

S.Lim, N.Boyer, N.Boo, C.Huang, G.Venkatachalam, Y.C.A.Juang, M.Garrigou, K.Kaan, K.M.Peh, A.Sadruddin, P.Gopal, R.Duggal, T.Y.Yuen, S.Ng, S.Kannan, C.J.Brown, C.Verma, P.Orth, A.Peier, L.Ge, X.Yu, B.Bhatt, F.Chen, E.Wang, N.J.Li, R.Gonzalez, A.Stoeck, B.Henry, T.K.Sawyer, D.P.Lane, C.W.Johannes, K.Biswas, A.W.Partridge. Discovery of Cell Active Macrocyclic Peptides with on-Target Inhibition of Kras Signaling Biorxiv 2021.
DOI: 10.1101/2021.09.11.459913