Magnesium in PDB 6gqy: Kras-169 Q61H Gppnhp + Ch-3

The structure of Kras-169 Q61H Gppnhp + Ch-3, PDB code: 6gqy 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)	94.67 / 2.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.531, 118.678, 156.996, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 24.7

The structure of Kras-169 Q61H Gppnhp + Ch-3 also contains other interesting chemical elements:

Fluorine

(F)

4 atoms

The binding sites of Magnesium atom in the Kras-169 Q61H Gppnhp + Ch-3 (pdb code 6gqy). 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-3, PDB code: 6gqy:
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-3


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-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:19.9 occ:1.00 OG A:SER17 2.1 14.2 1.0 OG1 A:THR35 2.3 22.7 1.0 O2G A:GNP202 2.3 17.5 1.0 O2B A:GNP202 2.3 17.7 1.0 O A:HOH301 2.4 3.0 1.0 OD1 A:ASP57 3.1 41.9 1.0 CB A:THR35 3.1 23.9 1.0 CB A:SER17 3.3 15.6 1.0 OD2 A:ASP57 3.4 41.7 1.0 PB A:GNP202 3.5 17.8 1.0 PG A:GNP202 3.5 19.5 1.0 N A:SER17 3.5 16.7 1.0 O A:THR58 3.6 29.8 1.0 CG A:ASP57 3.7 39.0 1.0 N3B A:GNP202 3.8 18.6 1.0 CA A:SER17 3.9 16.6 1.0 CG2 A:THR35 3.9 24.8 1.0 O3G A:GNP202 4.0 20.2 1.0 CB A:LYS16 4.2 17.2 1.0 O1B A:GNP202 4.3 18.6 1.0 CA A:THR35 4.4 25.4 1.0 C A:LYS16 4.4 18.5 1.0 N A:THR35 4.4 28.0 1.0 CE A:LYS16 4.5 17.4 1.0 NZ A:LYS16 4.6 17.8 1.0 O A:HOH307 4.7 35.3 1.0 O3A A:GNP202 4.8 17.6 1.0 O1G A:GNP202 4.8 20.0 1.0 CA A:LYS16 4.8 18.3 1.0 C A:THR58 4.8 28.5 1.0 O2A A:GNP202 4.9 18.4 1.0 O1A A:GNP202 4.9 20.4 1.0

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


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-3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:20.6 occ:1.00 O2B B:GNP202 2.2 15.5 1.0 O2G B:GNP202 2.3 19.6 1.0 OG B:SER17 2.5 17.2 1.0 OG1 B:THR35 2.6 31.9 1.0 O B:HOH301 2.7 13.9 1.0 O1A B:GNP202 2.9 15.1 1.0 N3B B:GNP202 3.1 19.8 1.0 PB B:GNP202 3.1 16.8 1.0 CB B:SER17 3.2 18.8 1.0 PG B:GNP202 3.2 23.7 1.0 O B:ASP33 3.6 37.7 1.0 PA B:GNP202 3.6 16.0 1.0 O3A B:GNP202 3.7 16.2 1.0 CB B:THR35 3.8 34.7 1.0 O2A B:GNP202 3.9 16.8 1.0 O1G B:GNP202 3.9 20.7 1.0 N B:THR35 4.0 36.6 1.0 N B:SER17 4.2 20.5 1.0 CA B:SER17 4.3 20.3 1.0 O3G B:GNP202 4.4 22.1 1.0 O1B B:GNP202 4.5 17.7 1.0 C B:ASP33 4.5 38.8 1.0 CA B:THR35 4.5 37.5 1.0 CA B:PRO34 4.6 39.2 1.0 C B:PRO34 4.6 37.2 1.0 OD2 B:ASP57 4.9 46.1 1.0 N B:PRO34 4.9 38.0 1.0 CG2 B:THR35 5.0 34.2 1.0

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


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-3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg201 b:57.8 occ:1.00 O1B C:GNP202 2.2 41.4 1.0 OG C:SER17 2.2 34.3 1.0 O1G C:GNP202 2.3 93.6 1.0 OG1 C:THR35 2.4 94.5 1.0 CB C:THR35 3.2 99.5 1.0 OD1 C:ASP57 3.2 61.8 1.0 PB C:GNP202 3.3 43.6 1.0 CB C:SER17 3.4 32.3 1.0 PG C:GNP202 3.4 81.5 1.0 N C:SER17 3.6 32.2 1.0 OD2 C:ASP57 3.6 62.1 1.0 O C:THR58 3.7 62.2 1.0 O2G C:GNP202 3.7 69.2 1.0 N3B C:GNP202 3.8 58.6 1.0 CG C:ASP57 3.8 58.0 1.0 O2B C:GNP202 3.9 38.6 1.0 CA C:SER17 3.9 32.9 1.0 CG2 C:THR35 4.0 99.9 1.0 CB C:LYS16 4.2 35.0 1.0 N C:THR35 4.4 0.0 1.0 CA C:THR35 4.4 0.1 1.0 C C:LYS16 4.4 33.6 1.0 CE C:LYS16 4.5 33.4 1.0 NZ C:LYS16 4.5 34.3 1.0 O3A C:GNP202 4.6 41.8 1.0 O3G C:GNP202 4.7 89.0 1.0 O1A C:GNP202 4.8 41.2 1.0 O2A C:GNP202 4.8 36.4 1.0 CA C:LYS16 4.8 33.5 1.0 C C:THR58 4.9 53.8 1.0 PA C:GNP202 4.9 36.4 1.0

Magnesium binding site 4 out of 6 in the Kras-169 Q61H Gppnhp + Ch-3


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-3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg201 b:0.7 occ:1.00 O2G D:GNP202 2.2 99.1 1.0 OG D:SER17 2.3 32.1 1.0 OG1 D:THR35 2.4 0.8 1.0 O2B D:GNP202 2.5 36.8 1.0 CB D:THR35 3.0 0.8 1.0 OD1 D:ASP57 3.2 55.7 1.0 O D:THR58 3.4 64.0 1.0 CB D:SER17 3.5 29.4 1.0 OD2 D:ASP57 3.5 72.0 1.0 PG D:GNP202 3.6 84.5 1.0 PB D:GNP202 3.7 36.1 1.0 CG D:ASP57 3.7 64.9 1.0 N D:SER17 3.8 27.6 1.0 CG2 D:THR35 3.8 0.0 1.0 CA D:SER17 4.1 29.3 1.0 N3B D:GNP202 4.1 53.7 1.0 CA D:THR35 4.2 0.5 1.0 N D:THR35 4.3 0.4 1.0 CB D:LYS16 4.4 29.7 1.0 O1B D:GNP202 4.4 32.5 1.0 O3G D:GNP202 4.4 82.2 1.0 O1G D:GNP202 4.5 78.0 1.0 CE D:LYS16 4.6 29.8 1.0 C D:THR58 4.6 57.3 1.0 C D:LYS16 4.6 28.3 1.0 NZ D:LYS16 4.7 31.3 1.0 O1A D:GNP202 4.9 35.1 1.0 O2A D:GNP202 4.9 34.9 1.0 O3A D:GNP202 4.9 35.8 1.0

Magnesium binding site 5 out of 6 in the Kras-169 Q61H Gppnhp + Ch-3


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-3 within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg201 b:80.7 occ:1.00 O1G E:GNP202 2.3 60.8 1.0 OG1 E:THR35 2.6 0.3 1.0 OG E:SER17 2.7 35.5 1.0 O1B E:GNP202 2.8 39.1 1.0 CB E:THR35 2.9 0.3 1.0 O E:THR58 3.0 63.2 1.0 OD1 E:ASP57 3.2 77.9 1.0 PG E:GNP202 3.5 70.1 1.0 OD2 E:ASP57 3.8 78.1 1.0 O2G E:GNP202 3.8 70.4 1.0 CG2 E:THR35 3.8 0.6 1.0 CG E:ASP57 3.8 75.8 1.0 PB E:GNP202 3.8 40.4 1.0 CB E:SER17 4.0 33.4 1.0 N3B E:GNP202 4.1 48.4 1.0 N E:SER17 4.1 33.0 1.0 C E:THR58 4.2 60.2 1.0 CA E:THR35 4.2 0.6 1.0 CE E:LYS16 4.2 29.9 1.0 N E:THR35 4.2 0.3 1.0 CB E:LYS16 4.3 30.2 1.0 NZ E:LYS16 4.4 30.2 1.0 O2B E:GNP202 4.5 38.6 1.0 CA E:SER17 4.5 34.4 1.0 O3G E:GNP202 4.7 75.6 1.0 CA E:ALA59 4.8 76.8 1.0 C E:LYS16 4.9 31.2 1.0 O E:THR35 4.9 0.4 1.0 N E:ALA59 4.9 68.4 1.0 C E:THR35 4.9 0.8 1.0

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


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-3 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg201 b:72.5 occ:1.00 OG F:SER17 2.1 26.6 1.0 OG1 F:THR35 2.4 0.5 1.0 O1B F:GNP202 2.4 39.9 1.0 O1G F:GNP202 2.5 80.9 1.0 CB F:THR35 3.1 0.6 1.0 OD1 F:ASP57 3.1 74.9 1.0 CB F:SER17 3.3 26.6 1.0 OD2 F:ASP57 3.5 75.5 1.0 N F:SER17 3.5 27.9 1.0 O F:THR58 3.6 56.9 1.0 PB F:GNP202 3.6 31.6 1.0 CG F:ASP57 3.7 69.1 1.0 PG F:GNP202 3.8 67.1 1.0 CA F:SER17 3.9 28.1 1.0 CG2 F:THR35 3.9 0.9 1.0 N3B F:GNP202 4.1 47.9 1.0 CB F:LYS16 4.1 26.4 1.0 O2G F:GNP202 4.3 65.0 1.0 CA F:THR35 4.4 0.3 1.0 N F:THR35 4.4 0.5 1.0 O2B F:GNP202 4.4 34.7 1.0 C F:LYS16 4.4 28.0 1.0 CE F:LYS16 4.6 29.8 1.0 O1A F:GNP202 4.6 26.1 1.0 NZ F:LYS16 4.7 29.5 1.0 O3A F:GNP202 4.8 29.7 1.0 CA F:LYS16 4.8 28.5 1.0 C F:THR58 4.8 55.8 1.0 O3G F:GNP202 4.9 71.3 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