Magnesium in PDB 6gom: Kras-169 Q61H Gppnhp + Ppin-1

The structure of Kras-169 Q61H Gppnhp + Ppin-1, PDB code: 6gom was solved by A.Cruz-Migoni, P.Canning, C.E.Quevedo, S.B.Carr, S.E.V.Phillips, T.H.Rabbitts, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	66.13 / 1.63
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.180, 119.840, 158.600, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 20.7

The binding sites of Magnesium atom in the Kras-169 Q61H Gppnhp + Ppin-1 (pdb code 6gom). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Kras-169 Q61H Gppnhp + Ppin-1, PDB code: 6gom:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Kras-169 Q61H Gppnhp + Ppin-1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Kras-169 Q61H Gppnhp + Ppin-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:16.1 occ:1.00 O2G A:GNP201 2.0 18.7 1.0 O A:HOH336 2.0 15.2 1.0 O2B A:GNP201 2.1 15.5 1.0 OG A:SER17 2.1 16.1 1.0 OG1 A:THR35 2.1 16.9 1.0 O A:HOH341 2.1 15.7 1.0 CB A:THR35 3.2 19.8 1.0 CB A:SER17 3.2 15.4 1.0 PB A:GNP201 3.2 16.7 1.0 PG A:GNP201 3.2 17.5 1.0 N3B A:GNP201 3.5 15.8 1.0 N A:THR35 3.9 16.5 1.0 N A:SER17 3.9 14.7 1.0 OD2 A:ASP57 4.1 22.1 1.0 O3G A:GNP201 4.1 19.4 1.0 CA A:SER17 4.1 14.8 1.0 CA A:THR35 4.1 19.0 1.0 O1A A:GNP201 4.1 18.3 1.0 CG2 A:THR35 4.2 19.3 1.0 OD1 A:ASP57 4.3 20.5 1.0 O A:HOH306 4.3 40.4 1.0 O1B A:GNP201 4.3 16.7 1.0 O3A A:GNP201 4.3 16.6 1.0 O1G A:GNP201 4.4 19.1 1.0 O A:HOH347 4.5 32.6 1.0 O A:THR58 4.5 19.3 1.0 O A:ASP33 4.5 21.2 1.0 CG A:ASP57 4.6 20.1 1.0 PA A:GNP201 4.6 16.6 1.0 O2A A:GNP201 4.7 16.3 1.0 CB A:LYS16 4.8 15.1 1.0 C A:PRO34 4.8 22.4 1.0 C A:LYS16 5.0 15.9 1.0 CE A:LYS16 5.0 15.7 1.0

Magnesium binding site 2 out of 6 in the Kras-169 Q61H Gppnhp + Ppin-1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Kras-169 Q61H Gppnhp + Ppin-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:20.7 occ:1.00 O2B B:GNP201 2.0 16.1 1.0 O2G B:GNP201 2.1 22.7 1.0 O B:HOH309 2.1 20.1 1.0 OG B:SER17 2.1 19.0 1.0 OG1 B:THR35 2.1 21.3 1.0 O B:HOH340 2.2 21.9 1.0 CB B:THR35 3.1 25.9 1.0 CB B:SER17 3.2 16.9 1.0 PB B:GNP201 3.2 17.4 1.0 PG B:GNP201 3.3 22.1 1.0 N3B B:GNP201 3.5 17.9 1.0 N B:SER17 3.9 14.3 1.0 N B:THR35 3.9 26.1 1.0 OD2 B:ASP57 4.0 28.5 1.0 CA B:SER17 4.1 15.1 1.0 CG2 B:THR35 4.1 25.5 1.0 O3G B:GNP201 4.1 23.8 1.0 CA B:THR35 4.2 24.0 1.0 OD1 B:ASP57 4.2 27.6 1.0 O1A B:GNP201 4.2 18.4 1.0 O3A B:GNP201 4.3 17.9 1.0 O1B B:GNP201 4.3 16.6 1.0 O B:THR58 4.4 26.1 1.0 O1G B:GNP201 4.4 23.3 1.0 CG B:ASP57 4.5 27.3 1.0 O B:ASP33 4.6 25.7 1.0 PA B:GNP201 4.6 17.1 1.0 O2A B:GNP201 4.6 17.5 1.0 CB B:LYS16 4.8 14.4 1.0 C B:LYS16 4.9 15.0 1.0 C B:PRO34 4.9 25.6 1.0

Magnesium binding site 3 out of 6 in the Kras-169 Q61H Gppnhp + Ppin-1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Kras-169 Q61H Gppnhp + Ppin-1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:51.4 occ:1.00 O1B C:GNP201 1.9 37.6 1.0 O1G C:GNP201 2.0 50.0 1.0 OG C:SER17 2.1 31.2 1.0 O C:HOH301 2.2 39.5 1.0 O C:HOH309 2.3 53.7 1.0 CB C:SER17 3.1 30.3 1.0 PB C:GNP201 3.1 34.0 1.0 PG C:GNP201 3.3 55.8 1.0 N3B C:GNP201 3.6 39.0 1.0 N C:SER17 3.6 24.8 1.0 CA C:SER17 3.9 27.6 1.0 OD2 C:ASP57 4.0 49.1 1.0 OD1 C:ASP57 4.0 49.1 1.0 O2G C:GNP201 4.1 48.1 1.0 O2B C:GNP201 4.2 31.7 1.0 O3A C:GNP201 4.2 31.7 1.0 O2A C:GNP201 4.2 31.4 1.0 O1A C:GNP201 4.4 34.0 1.0 CG C:ASP57 4.4 44.0 1.0 PA C:GNP201 4.4 32.1 1.0 O3G C:GNP201 4.5 51.4 1.0 CB C:LYS16 4.5 29.9 1.0 O C:THR58 4.6 50.8 1.0 O C:ASP33 4.6 84.8 1.0 C C:LYS16 4.6 29.2 1.0 CE C:LYS16 4.9 35.7 1.0 CA C:LYS16 5.0 29.2 1.0 NZ C:LYS16 5.0 39.4 1.0

Magnesium binding site 4 out of 6 in the Kras-169 Q61H Gppnhp + Ppin-1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Kras-169 Q61H Gppnhp + Ppin-1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg202 b:72.0 occ:1.00 O2B D:GNP201 1.7 30.6 1.0 O2G D:GNP201 2.1 63.0 1.0 OG D:SER17 2.2 33.0 1.0 O D:HOH307 2.4 52.9 1.0 PB D:GNP201 3.1 31.5 1.0 CB D:SER17 3.1 31.0 1.0 PG D:GNP201 3.2 59.7 1.0 N3B D:GNP201 3.4 39.4 1.0 N D:SER17 3.6 27.0 1.0 CA D:SER17 3.9 25.8 1.0 O1A D:GNP201 4.0 34.8 1.0 O3A D:GNP201 4.1 30.7 1.0 O2A D:GNP201 4.1 35.0 1.0 O1B D:GNP201 4.1 28.7 1.0 O3G D:GNP201 4.2 50.0 1.0 PA D:GNP201 4.2 32.2 1.0 OD2 D:ASP57 4.2 53.1 1.0 OD1 D:ASP57 4.3 52.8 1.0 O1G D:GNP201 4.3 58.4 1.0 CG D:ASP57 4.7 46.3 1.0 CB D:LYS16 4.7 25.5 1.0 C D:LYS16 4.7 27.1 1.0 O D:THR58 4.7 47.3 1.0

Magnesium binding site 5 out of 6 in the Kras-169 Q61H Gppnhp + Ppin-1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Kras-169 Q61H Gppnhp + Ppin-1 within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg202 b:44.0 occ:1.00 OG E:SER17 2.0 30.1 1.0 O1B E:GNP201 2.1 30.7 1.0 O1G E:GNP201 2.1 46.7 1.0 O E:HOH307 2.1 37.6 1.0 OG1 E:THR35 2.2 64.8 1.0 O E:HOH318 2.4 40.3 1.0 CB E:SER17 3.1 28.9 1.0 CB E:THR35 3.2 73.5 1.0 PB E:GNP201 3.4 30.5 1.0 PG E:GNP201 3.4 46.2 1.0 N3B E:GNP201 3.8 33.0 1.0 N E:SER17 3.8 24.6 1.0 OD2 E:ASP57 3.9 45.0 1.0 N E:THR35 4.0 69.7 1.0 CA E:SER17 4.0 25.1 1.0 OD1 E:ASP57 4.1 42.9 1.0 CG2 E:THR35 4.2 72.3 1.0 CA E:THR35 4.2 75.4 1.0 O2G E:GNP201 4.3 42.9 1.0 O2A E:GNP201 4.3 33.4 1.0 CG E:ASP57 4.4 40.8 1.0 O3A E:GNP201 4.4 28.2 1.0 O E:THR58 4.5 39.5 1.0 O3G E:GNP201 4.5 46.0 1.0 O2B E:GNP201 4.5 30.3 1.0 O E:ASP33 4.6 64.8 1.0 O1A E:GNP201 4.7 32.0 1.0 PA E:GNP201 4.7 30.2 1.0 CB E:LYS16 4.8 27.7 1.0 C E:LYS16 4.9 27.0 1.0 C E:PRO34 5.0 69.6 1.0

Magnesium binding site 6 out of 6 in the Kras-169 Q61H Gppnhp + Ppin-1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Kras-169 Q61H Gppnhp + Ppin-1 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg202 b:48.9 occ:1.00 O1B F:GNP201 2.0 25.3 1.0 O F:HOH302 2.0 37.7 1.0 O1G F:GNP201 2.1 42.9 1.0 OG F:SER17 2.2 26.0 1.0 O F:HOH347 2.2 42.3 1.0 CB F:SER17 3.3 23.6 1.0 PB F:GNP201 3.3 24.6 1.0 PG F:GNP201 3.4 41.7 1.0 N3B F:GNP201 3.7 28.1 1.0 N F:SER17 3.9 22.0 1.0 OD2 F:ASP57 3.9 31.5 0.5 OD1 F:ASP57 4.0 32.5 0.5 CA F:SER17 4.1 21.1 1.0 O2G F:GNP201 4.2 35.8 1.0 CG F:ASP57 4.4 33.6 0.5 O2B F:GNP201 4.4 23.3 1.0 O3A F:GNP201 4.4 25.5 1.0 O2A F:GNP201 4.4 27.3 1.0 O F:THR58 4.4 44.1 1.0 O3G F:GNP201 4.5 40.7 1.0 PA F:GNP201 4.7 25.1 1.0 O1A F:GNP201 4.7 24.7 1.0 CB F:LYS16 4.7 20.5 1.0 O F:ASP33 4.8 71.1 1.0 C F:LYS16 4.9 22.4 1.0

A.Cruz-Migoni, P.Canning, C.E.Quevedo, C.J.R.Bataille, N.Bery, A.Miller, A.J.Russell, S.E.V.Phillips, S.B.Carr, T.H.Rabbitts. Structure-Based Development of New Ras-Effector Inhibitors From A Combination of Active and Inactive Ras-Binding Compounds. Proc. Natl. Acad. Sci. V. 116 2545 2019U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30683716
DOI: 10.1073/PNAS.1811360116