Magnesium in PDB 6zj0: Crystal Structure of Hras-G12D in Complex with Gcp and Compound 18

The structure of Crystal Structure of Hras-G12D in Complex with Gcp and Compound 18, PDB code: 6zj0 was solved by D.Kessler, G.Fischer, J.Boettcher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	80.61 / 1.76
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	93.075, 93.075, 55.256, 90.00, 90.00, 120.00
R / Rfree (%)	19.8 / 22.8

The binding sites of Magnesium atom in the Crystal Structure of Hras-G12D in Complex with Gcp and Compound 18 (pdb code 6zj0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Hras-G12D in Complex with Gcp and Compound 18, PDB code: 6zj0:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Hras-G12D in Complex with Gcp and Compound 18


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 Hras-G12D in Complex with Gcp and Compound 18 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:45.9 occ:1.00 O A:HOH323 2.0 33.7 1.0 O2B A:GCP203 2.0 39.2 1.0 OG A:SER17 2.0 38.5 1.0 OG1 A:THR35 2.0 65.2 1.0 O3G A:GCP203 2.1 43.2 1.0 O A:HOH326 2.2 37.2 1.0 HB A:THR35 2.8 86.5 0.0 CB A:THR35 2.9 65.4 1.0 HB2 A:SER17 3.0 48.6 0.0 CB A:SER17 3.1 37.1 1.0 H A:SER17 3.1 42.7 0.0 PB A:GCP203 3.2 39.4 1.0 H A:THR35 3.2 89.8 0.0 H3B2 A:GCP203 3.3 54.6 0.0 PG A:GCP203 3.3 44.3 1.0 C3B A:GCP203 3.4 41.9 1.0 HG21 A:THR35 3.6 87.4 0.0 HB2 A:LYS16 3.7 39.9 0.0 N A:SER17 3.8 35.1 1.0 HB3 A:SER17 3.8 50.4 0.0 CG2 A:THR35 3.9 65.7 1.0 N A:THR35 3.9 67.1 1.0 CA A:SER17 3.9 36.2 1.0 HE2 A:LYS16 4.0 46.1 0.0 CA A:THR35 4.0 65.9 1.0 OD2 A:ASP57 4.1 46.6 1.0 O2A A:GCP203 4.1 40.4 1.0 OD1 A:ASP57 4.2 44.5 1.0 O1B A:GCP203 4.2 38.0 1.0 O3A A:GCP203 4.2 39.5 1.0 O1G A:GCP203 4.2 44.5 1.0 HA A:SER17 4.3 46.0 0.0 O2G A:GCP203 4.3 44.8 1.0 O A:THR58 4.3 45.5 1.0 H3B1 A:GCP203 4.3 53.0 0.0 O A:HOH375 4.4 64.7 1.0 CG A:ASP57 4.5 45.0 1.0 PA A:GCP203 4.5 40.4 1.0 HA A:THR35 4.5 92.8 0.0 HA A:PRO34 4.6 94.6 0.0 O A:ASP33 4.6 72.1 1.0 HG22 A:THR35 4.6 89.4 0.0 HG23 A:THR35 4.6 91.0 0.0 HZ3 A:LYS16 4.6 44.0 0.0 O1A A:GCP203 4.7 40.0 1.0 CB A:LYS16 4.7 33.8 1.0 HA A:ALA59 4.8 67.8 0.0 C A:LYS16 4.8 34.6 1.0 H A:LYS16 4.9 36.7 0.0 C A:PRO34 5.0 69.0 1.0 CE A:LYS16 5.0 37.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Hras-G12D in Complex with Gcp and Compound 18


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 Hras-G12D in Complex with Gcp and Compound 18 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:49.5 occ:0.53 HE21 A:GLN129 2.9 45.0 0.0 NE2 A:GLN129 3.4 37.5 1.0 HE22 A:GLN129 3.4 44.1 0.0 HH12 A:ARG128 3.8 85.4 0.0 CD A:GLN129 4.5 36.0 1.0 HG2 A:GLN129 4.5 40.6 0.0 HH22 A:ARG128 4.6 84.9 0.0 O A:HOH380 4.8 68.1 1.0 NH1 A:ARG128 4.8 68.4 1.0 O A:HOH463 4.9 92.8 0.3

D.Kessler, A.Bergner, J.Bottcher, G.Fischer, S.Dobel, M.Hinkel, B.Mullauer, A.Weiss-Puxbaum, D.B.Mcconnell. Drugging All Ras Isoforms with One Pocket. Future Med Chem V. 12 1911 2020.
ISSN: ISSN 1756-8927
PubMed: 32779487
DOI: 10.4155/FMC-2020-0221