Magnesium in PDB 6gqw: Kras-169 Q61H Gppnhp + Ch-1

The structure of Kras-169 Q61H Gppnhp + Ch-1, PDB code: 6gqw was solved by A.Cruz-Migoni, 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)	94.50 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.484, 118.538, 156.527, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 22.4

The binding sites of Magnesium atom in the Kras-169 Q61H Gppnhp + Ch-1 (pdb code 6gqw). 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 + Ch-1, PDB code: 6gqw:
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 + Ch-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 + Ch-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:32.2 occ:1.00 OG A:SER17 2.2 26.7 1.0 OG1 A:THR35 2.4 30.1 1.0 O2B A:GNP202 2.4 28.6 1.0 O2G A:GNP202 2.4 28.3 1.0 O A:HOH302 2.8 10.3 1.0 OD1 A:ASP57 3.0 46.9 1.0 CB A:THR35 3.1 32.9 1.0 OD2 A:ASP57 3.2 43.4 1.0 O A:THR58 3.4 35.8 1.0 CB A:SER17 3.4 28.8 1.0 CG A:ASP57 3.5 42.3 1.0 PB A:GNP202 3.6 29.5 1.0 N A:SER17 3.6 29.9 1.0 PG A:GNP202 3.6 31.4 1.0 CG2 A:THR35 3.9 32.5 1.0 CA A:SER17 3.9 29.6 1.0 O3G A:GNP202 4.0 35.8 1.0 N3B A:GNP202 4.0 31.2 1.0 CB A:LYS16 4.1 31.9 1.0 O1B A:GNP202 4.2 31.1 1.0 CE A:LYS16 4.3 32.7 1.0 C A:LYS16 4.4 30.1 1.0 NZ A:LYS16 4.5 32.7 1.0 CA A:THR35 4.5 32.2 1.0 N A:THR35 4.6 33.3 1.0 C A:THR58 4.6 35.8 1.0 O A:HOH306 4.7 40.8 1.0 CA A:LYS16 4.8 29.9 1.0 O3A A:GNP202 4.9 26.3 1.0 CB A:ASP57 4.9 35.0 1.0 O1G A:GNP202 5.0 31.9 1.0

Magnesium binding site 2 out of 6 in the Kras-169 Q61H Gppnhp + Ch-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 + Ch-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:42.4 occ:1.00 O B:HOH302 2.0 29.5 1.0 O2G B:GNP202 2.0 33.7 1.0 O B:HOH304 2.1 24.2 1.0 OG1 B:THR35 2.1 46.0 1.0 OG B:SER17 2.2 27.9 1.0 O2B B:GNP202 2.2 29.8 1.0 PG B:GNP202 3.1 39.3 1.0 CB B:THR35 3.2 45.4 1.0 CB B:SER17 3.2 29.1 1.0 PB B:GNP202 3.2 34.0 1.0 N3B B:GNP202 3.3 36.5 1.0 N B:THR35 3.8 44.8 1.0 O1A B:GNP202 3.9 24.5 1.0 N B:SER17 4.1 32.4 1.0 CA B:THR35 4.1 46.8 1.0 O1G B:GNP202 4.1 43.2 1.0 OD2 B:ASP57 4.1 46.7 1.0 O3A B:GNP202 4.2 29.7 1.0 O B:ASP33 4.2 36.7 1.0 O3G B:GNP202 4.2 37.8 1.0 CA B:SER17 4.2 31.2 1.0 CG2 B:THR35 4.2 49.0 1.0 PA B:GNP202 4.3 26.6 1.0 O1B B:GNP202 4.4 31.0 1.0 OD1 B:ASP57 4.5 49.0 1.0 O2A B:GNP202 4.5 28.5 1.0 C B:PRO34 4.6 44.3 1.0 O B:THR58 4.6 41.0 1.0 CG B:ASP57 4.7 46.6 1.0 CA B:PRO34 4.8 46.5 1.0

Magnesium binding site 3 out of 6 in the Kras-169 Q61H Gppnhp + Ch-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 + Ch-1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg201 b:54.3 occ:1.00 OG C:SER17 2.0 49.6 1.0 O1G C:GNP202 2.2 0.1 1.0 O1B C:GNP202 2.2 62.0 1.0 OG1 C:THR35 2.3 0.3 1.0 CB C:THR35 3.1 0.7 1.0 CB C:SER17 3.2 43.8 1.0 OD1 C:ASP57 3.4 62.1 1.0 OD2 C:ASP57 3.4 59.9 1.0 PB C:GNP202 3.5 58.7 1.0 PG C:GNP202 3.5 90.0 1.0 N C:SER17 3.7 43.0 1.0 CG C:ASP57 3.8 62.9 1.0 N3B C:GNP202 3.8 72.8 1.0 O C:THR58 3.9 63.7 1.0 CA C:SER17 3.9 44.0 1.0 CG2 C:THR35 3.9 0.1 1.0 O2B C:GNP202 4.2 51.0 1.0 N C:THR35 4.2 94.5 1.0 CA C:THR35 4.3 94.9 1.0 O3G C:GNP202 4.4 0.7 1.0 O2G C:GNP202 4.4 98.9 1.0 CB C:LYS16 4.4 48.9 1.0 C C:LYS16 4.6 48.0 1.0 O3A C:GNP202 4.6 51.5 1.0 O1A C:GNP202 4.6 50.4 1.0 CE C:LYS16 4.7 52.4 1.0 O2A C:GNP202 4.7 44.5 1.0 NZ C:LYS16 4.8 57.1 1.0 PA C:GNP202 4.9 44.7 1.0 CA C:LYS16 5.0 46.5 1.0

Magnesium binding site 4 out of 6 in the Kras-169 Q61H Gppnhp + Ch-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 + Ch-1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg201 b:0.5 occ:1.00 OG D:SER17 2.3 33.4 1.0 O2G D:GNP202 2.5 93.4 1.0 O2B D:GNP202 2.5 47.1 1.0 OD1 D:ASP57 3.0 52.1 1.0 O D:THR58 3.2 72.9 1.0 OD2 D:ASP57 3.2 60.0 1.0 CG D:ASP57 3.4 56.5 1.0 CB D:SER17 3.6 33.6 1.0 N D:SER17 3.8 32.6 1.0 PB D:GNP202 3.8 48.1 1.0 PG D:GNP202 3.8 85.5 1.0 CA D:SER17 4.1 35.0 1.0 CB D:LYS16 4.2 36.9 1.0 N3B D:GNP202 4.3 59.3 1.0 CE D:LYS16 4.3 35.9 1.0 C D:THR58 4.4 65.8 1.0 O1G D:GNP202 4.4 77.3 1.0 O1B D:GNP202 4.5 41.2 1.0 NZ D:LYS16 4.5 35.4 1.0 C D:LYS16 4.5 35.1 1.0 CB D:ASP57 4.9 55.8 1.0 CA D:LYS16 4.9 36.5 1.0 O3G D:GNP202 4.9 76.8 1.0 O3A D:GNP202 5.0 45.7 1.0 N D:THR58 5.0 51.6 1.0

Magnesium binding site 5 out of 6 in the Kras-169 Q61H Gppnhp + Ch-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 + Ch-1 within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg201 b:82.6 occ:1.00 OG E:SER17 2.3 40.7 1.0 O1G E:GNP202 2.4 74.8 1.0 O1B E:GNP202 2.6 54.2 1.0 OD1 E:ASP57 3.0 64.1 1.0 O E:THR58 3.2 67.0 1.0 OD2 E:ASP57 3.3 68.3 1.0 CG E:ASP57 3.5 65.3 1.0 CB E:SER17 3.6 40.6 1.0 PG E:GNP202 3.7 78.3 1.0 PB E:GNP202 3.7 53.2 1.0 N E:SER17 3.8 42.3 1.0 N3B E:GNP202 4.1 62.4 1.0 CA E:SER17 4.1 43.5 1.0 CB E:LYS16 4.2 44.2 1.0 CE E:LYS16 4.2 45.5 1.0 O2G E:GNP202 4.3 74.5 1.0 O2B E:GNP202 4.3 51.1 1.0 C E:THR58 4.5 67.4 1.0 NZ E:LYS16 4.5 46.2 1.0 C E:LYS16 4.6 42.0 1.0 O3G E:GNP202 4.8 72.9 1.0 CA E:LYS16 4.9 42.1 1.0 CB E:ASP57 4.9 62.4 1.0 O3A E:GNP202 5.0 51.2 1.0

Magnesium binding site 6 out of 6 in the Kras-169 Q61H Gppnhp + Ch-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 + Ch-1 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg201 b:71.7 occ:1.00 OG F:SER17 2.3 34.1 1.0 O1B F:GNP202 2.4 43.7 1.0 O1G F:GNP202 2.5 69.2 1.0 OD1 F:ASP57 3.1 56.8 1.0 OD2 F:ASP57 3.4 60.6 1.0 CB F:SER17 3.4 34.3 1.0 O F:THR58 3.5 65.9 1.0 PB F:GNP202 3.6 40.8 1.0 N F:SER17 3.6 34.8 1.0 CG F:ASP57 3.6 59.7 1.0 PG F:GNP202 3.6 70.7 1.0 CA F:SER17 4.0 36.4 1.0 N3B F:GNP202 4.0 50.4 1.0 O2G F:GNP202 4.1 59.7 1.0 CB F:LYS16 4.1 35.6 1.0 O2B F:GNP202 4.2 43.1 1.0 CE F:LYS16 4.3 42.5 1.0 C F:LYS16 4.4 37.1 1.0 NZ F:LYS16 4.5 43.7 1.0 CA F:THR35 4.5 0.1 1.0 N F:THR35 4.6 0.7 1.0 C F:THR58 4.7 62.1 1.0 CA F:LYS16 4.7 37.2 1.0 O3A F:GNP202 4.8 40.5 1.0 O1A F:GNP202 4.8 38.7 1.0 O3G F:GNP202 4.9 70.1 1.0 N F:LYS16 5.0 37.2 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