Magnesium in PDB 6gqt: Kras-169 Q61H Gppnhp + Ppin-2

The structure of Kras-169 Q61H Gppnhp + Ppin-2, PDB code: 6gqt 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)	59.78 / 1.69
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.270, 119.550, 158.590, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 21.4

The binding sites of Magnesium atom in the Kras-169 Q61H Gppnhp + Ppin-2 (pdb code 6gqt). 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-2, PDB code: 6gqt:
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-2


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-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:17.1 occ:1.00 O2B A:GNP201 2.0 16.4 1.0 O2G A:GNP201 2.0 18.6 1.0 O A:HOH335 2.1 16.2 1.0 O A:HOH345 2.1 16.2 1.0 OG1 A:THR35 2.1 18.3 1.0 OG A:SER17 2.2 17.6 1.0 CB A:THR35 3.2 20.9 1.0 PB A:GNP201 3.2 16.9 1.0 CB A:SER17 3.3 16.9 1.0 PG A:GNP201 3.3 18.5 1.0 N3B A:GNP201 3.5 17.1 1.0 N A:SER17 3.9 14.7 1.0 N A:THR35 3.9 18.1 1.0 O3G A:GNP201 4.1 19.5 1.0 OD2 A:ASP57 4.1 20.4 1.0 CA A:SER17 4.1 16.4 1.0 O A:HOH304 4.1 48.7 1.0 CA A:THR35 4.2 18.9 1.0 O1A A:GNP201 4.2 19.1 1.0 CG2 A:THR35 4.2 20.9 1.0 OD1 A:ASP57 4.3 21.1 1.0 O1B A:GNP201 4.3 17.1 1.0 O3A A:GNP201 4.3 16.2 1.0 O A:HOH359 4.4 31.6 1.0 O A:ASP33 4.4 22.5 0.5 O1G A:GNP201 4.4 20.5 1.0 O A:ASP33 4.4 21.9 0.5 O A:THR58 4.5 20.8 1.0 CG A:ASP57 4.6 20.0 1.0 PA A:GNP201 4.6 16.9 1.0 O2A A:GNP201 4.7 16.3 1.0 C A:PRO34 4.8 24.4 1.0 CB A:LYS16 4.8 16.6 1.0 C A:LYS16 4.9 16.4 1.0 CE A:LYS16 5.0 16.7 1.0

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


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-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:25.0 occ:1.00 O2B B:GNP201 2.0 18.2 1.0 O B:HOH315 2.1 20.7 1.0 O2G B:GNP201 2.1 25.8 1.0 OG B:SER17 2.1 20.4 1.0 O B:HOH343 2.2 22.2 1.0 OG1 B:THR35 2.2 23.3 1.0 CB B:THR35 3.2 27.2 1.0 CB B:SER17 3.2 19.6 1.0 PB B:GNP201 3.2 19.0 1.0 PG B:GNP201 3.4 25.2 1.0 N3B B:GNP201 3.5 18.9 1.0 N B:SER17 3.8 16.5 1.0 N B:THR35 3.9 29.7 1.0 CA B:SER17 4.1 18.2 1.0 OD2 B:ASP57 4.1 28.1 0.5 OD2 B:ASP57 4.1 28.0 0.5 CA B:THR35 4.2 27.8 1.0 CG2 B:THR35 4.2 28.7 1.0 O3G B:GNP201 4.2 25.4 1.0 O1A B:GNP201 4.2 18.4 1.0 OD1 B:ASP57 4.2 28.0 0.5 OD1 B:ASP57 4.2 27.8 0.5 O B:HOH331 4.3 44.7 1.0 O3A B:GNP201 4.3 18.4 1.0 O1B B:GNP201 4.4 18.2 1.0 O1G B:GNP201 4.4 23.7 1.0 O B:THR58 4.4 27.7 1.0 O B:ASP33 4.5 28.4 1.0 CG B:ASP57 4.5 27.2 0.5 CG B:ASP57 4.5 27.1 0.5 PA B:GNP201 4.6 18.4 1.0 O2A B:GNP201 4.6 17.4 1.0 CB B:LYS16 4.7 15.7 1.0 C B:LYS16 4.9 16.7 1.0 C B:PRO34 4.9 30.0 1.0

Magnesium binding site 3 out of 6 in the Kras-169 Q61H Gppnhp + Ppin-2


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-2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:57.6 occ:1.00 O1B C:GNP201 1.8 39.1 1.0 O1G C:GNP201 2.1 62.0 1.0 OG C:SER17 2.2 31.6 1.0 O C:HOH322 2.3 58.0 1.0 O C:HOH303 2.4 46.8 1.0 PB C:GNP201 3.0 34.8 1.0 CB C:SER17 3.1 33.2 1.0 PG C:GNP201 3.4 58.1 1.0 N3B C:GNP201 3.5 39.0 1.0 N C:SER17 3.6 26.7 1.0 CA C:SER17 3.9 31.6 1.0 O3A C:GNP201 4.0 32.8 1.0 O2B C:GNP201 4.0 31.4 1.0 O2A C:GNP201 4.1 31.4 1.0 OD1 C:ASP57 4.2 50.8 1.0 OD2 C:ASP57 4.2 51.2 1.0 O2G C:GNP201 4.2 53.9 1.0 PA C:GNP201 4.3 32.6 1.0 O1A C:GNP201 4.3 34.2 1.0 O3G C:GNP201 4.4 54.7 1.0 CB C:LYS16 4.5 30.7 1.0 CG C:ASP57 4.6 51.5 1.0 C C:LYS16 4.6 27.6 1.0 O C:THR58 4.7 49.2 1.0 NZ C:LYS16 5.0 45.9 1.0 CE C:LYS16 5.0 37.8 1.0 CA C:LYS16 5.0 27.2 1.0

Magnesium binding site 4 out of 6 in the Kras-169 Q61H Gppnhp + Ppin-2


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-2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg202 b:73.5 occ:1.00 O2B D:GNP201 2.0 33.9 1.0 OG D:SER17 2.1 36.6 1.0 O2G D:GNP201 2.1 69.8 1.0 O D:HOH301 2.3 60.9 1.0 CB D:SER17 3.1 35.0 1.0 PB D:GNP201 3.3 34.2 1.0 PG D:GNP201 3.5 64.1 1.0 N D:SER17 3.7 28.1 1.0 N3B D:GNP201 3.8 44.8 1.0 OD2 D:ASP57 3.9 57.1 1.0 CA D:SER17 3.9 27.8 1.0 OD1 D:ASP57 4.0 56.8 1.0 O3G D:GNP201 4.3 58.0 1.0 O1B D:GNP201 4.3 33.0 1.0 CG D:ASP57 4.3 48.9 1.0 O1A D:GNP201 4.3 36.4 1.0 O3A D:GNP201 4.4 33.1 1.0 O2A D:GNP201 4.5 37.6 1.0 PA D:GNP201 4.5 35.0 1.0 O D:THR58 4.5 56.6 1.0 CB D:LYS16 4.6 28.3 1.0 O1G D:GNP201 4.7 62.5 1.0 C D:LYS16 4.7 33.0 1.0

Magnesium binding site 5 out of 6 in the Kras-169 Q61H Gppnhp + Ppin-2


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-2 within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg202 b:54.0 occ:1.00 O1G E:GNP201 2.0 54.6 1.0 OG E:SER17 2.1 35.4 1.0 O E:HOH306 2.2 46.3 1.0 O1B E:GNP201 2.2 36.0 1.0 OG1 E:THR35 2.4 72.2 1.0 O E:HOH332 2.5 47.3 1.0 CB E:THR35 3.2 78.6 1.0 CB E:SER17 3.2 30.9 1.0 PG E:GNP201 3.3 51.5 1.0 PB E:GNP201 3.5 32.3 1.0 N3B E:GNP201 3.8 36.6 1.0 N E:SER17 3.9 25.9 1.0 N E:THR35 3.9 71.1 1.0 OD2 E:ASP57 4.0 43.8 1.0 CA E:SER17 4.1 27.2 1.0 O2G E:GNP201 4.2 47.2 1.0 OD1 E:ASP57 4.2 46.5 1.0 CA E:THR35 4.2 77.7 1.0 CG2 E:THR35 4.3 80.4 1.0 O2A E:GNP201 4.3 36.8 1.0 O3G E:GNP201 4.4 49.7 1.0 O2B E:GNP201 4.4 32.5 1.0 O E:THR58 4.4 44.9 1.0 CG E:ASP57 4.5 45.3 1.0 O3A E:GNP201 4.5 30.7 1.0 PA E:GNP201 4.7 33.3 1.0 O1A E:GNP201 4.7 33.2 1.0 O E:ASP33 4.7 74.9 1.0 CB E:LYS16 4.8 30.0 1.0 C E:PRO34 4.9 72.8 1.0 C E:LYS16 5.0 30.4 1.0

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


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-2 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg202 b:61.4 occ:1.00 O F:HOH304 2.1 41.7 1.0 O1B F:GNP201 2.2 28.2 1.0 OG F:SER17 2.2 28.9 1.0 O1G F:GNP201 2.2 54.3 1.0 CB F:SER17 3.3 28.0 1.0 PB F:GNP201 3.4 27.2 1.0 PG F:GNP201 3.5 47.4 1.0 N3B F:GNP201 3.7 29.3 1.0 OD2 F:ASP57 3.9 55.4 1.0 N F:SER17 3.9 26.2 1.0 OD1 F:ASP57 4.1 55.8 1.0 CA F:SER17 4.2 24.8 1.0 O2G F:GNP201 4.3 37.7 1.0 CG F:ASP57 4.3 51.9 1.0 O2A F:GNP201 4.4 29.6 1.0 O F:THR58 4.5 48.4 1.0 O3A F:GNP201 4.5 28.4 1.0 O2B F:GNP201 4.5 24.8 1.0 O3G F:GNP201 4.6 44.9 1.0 O1A F:GNP201 4.8 26.1 1.0 PA F:GNP201 4.8 26.5 1.0 CB F:LYS16 4.8 21.0 1.0 C F:LYS16 5.0 22.6 1.0 O F:HOH302 5.0 49.1 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