Magnesium in PDB 6gog: Kras-169 Q61H Gppnhp

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

Resolution Low / High (Å)	29.47 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.565, 118.748, 156.595, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 19.1

The binding sites of Magnesium atom in the Kras-169 Q61H Gppnhp (pdb code 6gog). 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, PDB code: 6gog:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:16.0 occ:1.00 O2G A:GNP201 2.0 16.2 1.0 O A:HOH316 2.0 13.6 1.0 O2B A:GNP201 2.0 13.3 1.0 O A:HOH365 2.0 16.2 1.0 OG1 A:THR35 2.1 13.8 1.0 OG A:SER17 2.1 12.8 1.0 CB A:THR35 3.1 15.1 1.0 CB A:SER17 3.2 12.2 1.0 PB A:GNP201 3.2 14.5 1.0 PG A:GNP201 3.2 16.0 1.0 N3B A:GNP201 3.5 14.6 1.0 N A:THR35 3.8 17.1 1.0 N A:SER17 3.8 13.6 1.0 OD2 A:ASP57 4.0 20.9 1.0 O3G A:GNP201 4.0 16.5 1.0 CA A:SER17 4.1 13.4 1.0 CA A:THR35 4.1 16.2 1.0 OD1 A:ASP57 4.2 21.4 1.0 O1A A:GNP201 4.2 15.9 1.0 CG2 A:THR35 4.2 16.8 1.0 O3A A:GNP201 4.3 15.4 1.0 O A:HOH393 4.3 32.0 1.0 O1B A:GNP201 4.3 16.8 1.0 O1G A:GNP201 4.3 16.0 1.0 O A:ASP33 4.4 23.0 1.0 O A:THR58 4.4 17.3 1.0 CG A:ASP57 4.4 19.1 1.0 PA A:GNP201 4.5 14.8 1.0 O2A A:GNP201 4.6 15.3 1.0 C A:PRO34 4.7 19.1 1.0 CB A:LYS16 4.8 12.7 1.0 C A:LYS16 4.9 12.6 1.0 CE A:LYS16 5.0 13.4 1.0 CA A:PRO34 5.0 21.6 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:17.3 occ:1.00 O2B B:GNP201 2.0 12.9 1.0 O2G B:GNP201 2.1 16.6 1.0 OG1 B:THR35 2.1 17.9 1.0 O B:HOH316 2.1 12.4 1.0 OG B:SER17 2.1 16.5 1.0 O B:HOH347 2.2 15.1 1.0 CB B:THR35 3.1 20.1 1.0 PB B:GNP201 3.2 14.4 1.0 CB B:SER17 3.2 14.7 1.0 PG B:GNP201 3.2 18.0 1.0 N3B B:GNP201 3.4 16.1 1.0 N B:SER17 3.8 15.0 1.0 N B:THR35 3.9 20.6 1.0 OD2 B:ASP57 4.0 22.5 1.0 CA B:SER17 4.1 15.7 1.0 O3G B:GNP201 4.1 15.5 1.0 CA B:THR35 4.1 20.6 1.0 O1A B:GNP201 4.1 14.6 1.0 O B:HOH324 4.1 37.6 1.0 OD1 B:ASP57 4.2 21.9 1.0 CG2 B:THR35 4.2 20.4 1.0 O1B B:GNP201 4.2 13.6 1.0 O1G B:GNP201 4.2 17.0 1.0 O3A B:GNP201 4.3 13.7 1.0 O B:THR58 4.3 21.1 1.0 O B:ASP33 4.5 19.5 1.0 CG B:ASP57 4.5 23.9 1.0 PA B:GNP201 4.5 14.2 1.0 O2A B:GNP201 4.5 12.6 1.0 CB B:LYS16 4.7 14.2 1.0 C B:PRO34 4.8 19.2 1.0 C B:LYS16 4.9 14.1 1.0 CE B:LYS16 5.0 17.3 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:28.6 occ:1.00 O1B C:GNP201 2.0 21.5 1.0 O C:HOH318 2.1 23.5 1.0 O1G C:GNP201 2.1 25.9 1.0 OG1 C:THR35 2.1 31.9 1.0 O C:HOH338 2.1 29.4 1.0 OG C:SER17 2.2 23.9 1.0 CB C:THR35 3.1 34.6 1.0 CB C:SER17 3.2 25.4 1.0 PB C:GNP201 3.2 27.0 1.0 PG C:GNP201 3.2 31.5 1.0 N3B C:GNP201 3.4 28.9 1.0 N C:SER17 3.8 23.9 1.0 N C:THR35 3.8 35.4 1.0 OD2 C:ASP57 4.0 33.0 1.0 CA C:SER17 4.0 25.4 1.0 O2G C:GNP201 4.0 30.9 1.0 CA C:THR35 4.1 34.9 1.0 O C:HOH302 4.1 44.1 1.0 OD1 C:ASP57 4.1 30.6 1.0 CG2 C:THR35 4.2 37.3 1.0 O2A C:GNP201 4.2 23.5 1.0 O3A C:GNP201 4.3 22.8 1.0 O2B C:GNP201 4.3 23.8 1.0 O3G C:GNP201 4.3 31.0 1.0 O C:THR58 4.3 32.4 1.0 CG C:ASP57 4.4 30.0 1.0 O C:ASP33 4.5 36.8 1.0 PA C:GNP201 4.5 24.3 1.0 O1A C:GNP201 4.6 25.6 1.0 CB C:LYS16 4.7 20.1 1.0 C C:PRO34 4.8 35.3 1.0 C C:LYS16 4.8 22.2 1.0 CE C:LYS16 4.9 25.5 1.0 NZ C:LYS16 5.0 27.9 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg202 b:36.2 occ:1.00 O2B D:GNP201 2.0 23.0 1.0 O D:HOH320 2.0 28.2 1.0 O2G D:GNP201 2.1 32.0 1.0 OG D:SER17 2.2 25.2 1.0 OG1 D:THR35 2.2 38.3 1.0 O D:HOH312 2.3 30.3 1.0 PB D:GNP201 3.1 25.8 1.0 CB D:THR35 3.1 43.1 1.0 CB D:SER17 3.2 29.1 1.0 PG D:GNP201 3.2 31.5 1.0 N3B D:GNP201 3.3 31.4 1.0 N D:SER17 3.8 24.8 1.0 N D:THR35 3.8 44.4 1.0 OD2 D:ASP57 4.0 38.9 1.0 CA D:SER17 4.1 24.1 1.0 CA D:THR35 4.1 45.5 1.0 O1G D:GNP201 4.1 27.5 1.0 O1A D:GNP201 4.1 29.6 1.0 O3A D:GNP201 4.2 25.0 1.0 CG2 D:THR35 4.2 43.5 1.0 OD1 D:ASP57 4.2 35.7 1.0 O1B D:GNP201 4.2 24.8 1.0 O3G D:GNP201 4.3 32.5 1.0 O D:THR58 4.4 32.0 1.0 PA D:GNP201 4.4 27.9 1.0 O2A D:GNP201 4.5 26.5 1.0 CG D:ASP57 4.5 37.9 1.0 O D:ASP33 4.5 44.1 1.0 CB D:LYS16 4.8 24.7 1.0 C D:PRO34 4.8 49.6 1.0 C D:LYS16 4.9 25.2 1.0 CE D:LYS16 5.0 29.5 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg202 b:30.8 occ:1.00 OG1 E:THR35 2.0 33.1 1.0 O E:HOH315 2.0 25.0 1.0 OG E:SER17 2.1 27.4 1.0 O1B E:GNP201 2.1 24.4 1.0 O1G E:GNP201 2.2 29.9 1.0 O E:HOH314 2.2 28.2 1.0 CB E:THR35 3.1 35.1 1.0 CB E:SER17 3.1 24.4 1.0 PB E:GNP201 3.3 25.7 1.0 PG E:GNP201 3.3 32.9 1.0 N3B E:GNP201 3.5 27.9 1.0 N E:THR35 3.8 36.0 1.0 N E:SER17 3.8 22.9 1.0 OD2 E:ASP57 3.9 38.5 1.0 CA E:SER17 4.0 22.6 1.0 CA E:THR35 4.0 36.7 1.0 CG2 E:THR35 4.1 35.5 1.0 OD1 E:ASP57 4.1 33.0 1.0 O2A E:GNP201 4.2 27.9 1.0 O2G E:GNP201 4.2 33.2 1.0 O3A E:GNP201 4.3 26.9 1.0 O3G E:GNP201 4.3 36.9 1.0 O2B E:GNP201 4.4 26.3 1.0 O E:THR58 4.4 31.3 1.0 O E:ASP33 4.4 42.0 1.0 CG E:ASP57 4.4 31.3 1.0 PA E:GNP201 4.6 26.2 1.0 O1A E:GNP201 4.7 26.2 1.0 CB E:LYS16 4.8 23.6 1.0 C E:PRO34 4.8 39.4 1.0 C E:LYS16 4.9 23.4 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg202 b:26.5 occ:1.00 O1B F:GNP201 2.0 19.3 1.0 O F:HOH312 2.0 20.1 1.0 O F:HOH339 2.1 25.8 1.0 OG1 F:THR35 2.1 31.9 1.0 OG F:SER17 2.2 21.4 1.0 O1G F:GNP201 2.2 26.9 1.0 CB F:THR35 3.1 32.3 1.0 PB F:GNP201 3.2 20.9 1.0 CB F:SER17 3.2 21.5 1.0 PG F:GNP201 3.3 26.6 1.0 N3B F:GNP201 3.3 23.2 1.0 N F:SER17 3.8 21.2 1.0 N F:THR35 3.9 36.4 1.0 OD2 F:ASP57 4.0 37.0 1.0 CA F:SER17 4.1 21.2 1.0 CA F:THR35 4.1 37.1 1.0 O2G F:GNP201 4.1 25.8 1.0 OD1 F:ASP57 4.1 34.7 1.0 CG2 F:THR35 4.1 31.8 1.0 O3A F:GNP201 4.2 20.1 1.0 O2A F:GNP201 4.2 21.4 1.0 O2B F:GNP201 4.2 20.8 1.0 O3G F:GNP201 4.3 24.6 1.0 O F:THR58 4.3 28.1 1.0 CG F:ASP57 4.4 33.3 1.0 O F:ASP33 4.5 32.2 1.0 PA F:GNP201 4.6 20.8 1.0 O1A F:GNP201 4.6 19.9 1.0 CB F:LYS16 4.6 18.8 1.0 C F:PRO34 4.8 39.2 1.0 C F:LYS16 4.8 20.2 1.0 CE F:LYS16 4.9 20.5 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