Magnesium in PDB 5oco: Discovery of Small Molecules Binding to Kras Via High Affinity Antibody Fragment Competition Method.

The structure of Discovery of Small Molecules Binding to Kras Via High Affinity Antibody Fragment Competition Method., PDB code: 5oco was solved by A.Cruz-Migoni, M.T.Ehebauer, S.E.V.Phillips, C.E.Quevedo, T.H.Rabbitts, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.38 / 1.66
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.600, 118.760, 156.900, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 20.5

The binding sites of Magnesium atom in the Discovery of Small Molecules Binding to Kras Via High Affinity Antibody Fragment Competition Method. (pdb code 5oco). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Discovery of Small Molecules Binding to Kras Via High Affinity Antibody Fragment Competition Method., PDB code: 5oco:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Discovery of Small Molecules Binding to Kras Via High Affinity Antibody Fragment Competition Method.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Discovery of Small Molecules Binding to Kras Via High Affinity Antibody Fragment Competition Method. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg204 b:19.7 occ:1.00 O2B B:GNP201 1.9 15.9 1.0 O2G B:GNP201 2.1 20.9 1.0 O B:HOH323 2.1 17.7 1.0 OG B:SER17 2.1 19.4 1.0 OG1 B:THR35 2.1 19.7 1.0 O B:HOH334 2.1 20.5 1.0 CB B:THR35 3.1 23.3 1.0 CB B:SER17 3.1 18.3 1.0 PB B:GNP201 3.2 16.7 1.0 PG B:GNP201 3.3 20.3 1.0 N3B B:GNP201 3.4 18.4 1.0 N B:SER17 3.8 14.5 1.0 N B:THR35 3.8 27.3 1.0 CA B:SER17 4.0 17.3 1.0 OD2 B:ASP57 4.0 26.3 1.0 O B:HOH313 4.1 42.8 1.0 CA B:THR35 4.1 24.7 1.0 O1A B:GNP201 4.1 18.2 1.0 CG2 B:THR35 4.1 24.8 1.0 O3G B:GNP201 4.1 21.4 1.0 OD1 B:ASP57 4.2 25.2 1.0 O3A B:GNP201 4.3 17.4 1.0 O1B B:GNP201 4.3 17.0 1.0 O1G B:GNP201 4.3 20.5 1.0 O B:THR58 4.4 23.9 1.0 O B:ASP33 4.5 24.6 1.0 CG B:ASP57 4.5 24.3 1.0 PA B:GNP201 4.5 17.6 1.0 O2A B:GNP201 4.6 16.6 1.0 CB B:LYS16 4.7 14.1 1.0 C B:PRO34 4.8 26.0 1.0 C B:LYS16 4.9 17.1 1.0 CE B:LYS16 5.0 19.4 1.0

Magnesium binding site 2 out of 6 in the Discovery of Small Molecules Binding to Kras Via High Affinity Antibody Fragment Competition Method.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Discovery of Small Molecules Binding to Kras Via High Affinity Antibody Fragment Competition Method. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:16.6 occ:1.00 O2G A:GNP201 2.0 20.8 1.0 O A:HOH325 2.0 16.2 1.0 O2B A:GNP201 2.0 15.7 1.0 OG A:SER17 2.1 16.6 1.0 OG1 A:THR35 2.1 17.2 1.0 O A:HOH341 2.1 16.3 1.0 CB A:THR35 3.1 18.6 1.0 CB A:SER17 3.2 16.9 1.0 PB A:GNP201 3.2 16.7 1.0 PG A:GNP201 3.2 18.8 1.0 N3B A:GNP201 3.4 15.7 1.0 N A:THR35 3.8 17.7 1.0 N A:SER17 3.8 14.3 1.0 OD2 A:ASP57 4.0 20.7 0.5 OD2 A:ASP57 4.0 22.2 0.5 CA A:SER17 4.0 14.2 1.0 O3G A:GNP201 4.0 19.8 1.0 O1A A:GNP201 4.1 18.1 1.0 CA A:THR35 4.1 17.8 1.0 CG2 A:THR35 4.2 19.9 1.0 OD1 A:ASP57 4.2 21.3 0.5 OD1 A:ASP57 4.2 23.6 0.5 O A:HOH369 4.2 29.1 1.0 O3A A:GNP201 4.3 15.8 1.0 O1B A:GNP201 4.3 16.1 1.0 O A:ASP33 4.4 22.7 1.0 O1G A:GNP201 4.4 19.1 1.0 O A:THR58 4.5 20.1 1.0 CG A:ASP57 4.5 19.4 0.5 CG A:ASP57 4.5 20.7 0.5 PA A:GNP201 4.5 16.7 1.0 O2A A:GNP201 4.6 16.4 1.0 C A:PRO34 4.7 22.3 1.0 CB A:LYS16 4.8 14.4 1.0 C A:LYS16 4.9 16.0 1.0 CE A:LYS16 5.0 16.3 1.0 NZ A:LYS16 5.0 16.1 1.0

Magnesium binding site 3 out of 6 in the Discovery of Small Molecules Binding to Kras Via High Affinity Antibody Fragment Competition Method.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Discovery of Small Molecules Binding to Kras Via High Affinity Antibody Fragment Competition Method. within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg203 b:30.3 occ:1.00 O1B C:GNP201 2.0 27.2 1.0 O C:HOH321 2.0 28.4 1.0 O1G C:GNP201 2.1 33.9 1.0 OG C:SER17 2.1 26.8 1.0 OG1 C:THR35 2.1 37.9 1.0 O C:HOH312 2.1 33.3 1.0 CB C:THR35 3.1 40.0 1.0 CB C:SER17 3.1 29.6 1.0 PB C:GNP201 3.1 28.4 1.0 PG C:GNP201 3.3 33.0 1.0 N3B C:GNP201 3.4 29.8 1.0 N C:SER17 3.8 23.4 1.0 N C:THR35 3.8 39.6 1.0 CA C:SER17 4.0 26.2 1.0 OD2 C:ASP57 4.0 25.1 0.5 O2A C:GNP201 4.1 28.9 1.0 O2G C:GNP201 4.1 33.9 1.0 CA C:THR35 4.1 38.1 1.0 CG2 C:THR35 4.2 43.9 1.0 OD1 C:ASP57 4.2 20.9 0.5 O2B C:GNP201 4.2 26.4 1.0 O3A C:GNP201 4.2 26.2 1.0 O C:ASP33 4.4 43.7 1.0 O3G C:GNP201 4.4 33.6 1.0 PA C:GNP201 4.5 30.2 1.0 O C:THR58 4.5 33.5 1.0 CG C:ASP57 4.5 24.2 0.5 O1A C:GNP201 4.5 28.5 1.0 CB C:LYS16 4.7 22.9 1.0 C C:PRO34 4.8 43.5 1.0 C C:LYS16 4.8 24.2 1.0 CE C:LYS16 5.0 29.9 1.0 NZ C:LYS16 5.0 32.4 1.0

Magnesium binding site 4 out of 6 in the Discovery of Small Molecules Binding to Kras Via High Affinity Antibody Fragment Competition Method.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Discovery of Small Molecules Binding to Kras Via High Affinity Antibody Fragment Competition Method. within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg204 b:47.0 occ:1.00 O2B D:GNP201 2.0 28.8 1.0 OG D:SER17 2.1 31.8 1.0 OG1 D:THR35 2.1 54.5 1.0 O D:HOH312 2.2 41.8 1.0 O2G D:GNP201 2.3 40.7 1.0 O D:HOH308 2.3 39.2 1.0 CB D:SER17 3.1 35.0 1.0 CB D:THR35 3.1 68.5 1.0 PB D:GNP201 3.1 30.0 1.0 PG D:GNP201 3.3 38.0 1.0 N3B D:GNP201 3.5 34.9 1.0 OD2 D:ASP57 3.7 59.7 0.5 N D:SER17 3.8 26.4 1.0 N D:THR35 3.9 70.6 1.0 CA D:SER17 4.0 25.5 1.0 O1A D:GNP201 4.0 32.0 1.0 OD2 D:ASP57 4.1 36.4 0.5 CA D:THR35 4.1 71.7 1.0 CG2 D:THR35 4.2 60.9 1.0 O1B D:GNP201 4.2 27.8 1.0 O1G D:GNP201 4.2 38.2 1.0 OD1 D:ASP57 4.3 31.7 0.5 O3A D:GNP201 4.3 26.8 1.0 O3G D:GNP201 4.4 40.3 1.0 O2A D:GNP201 4.4 28.8 1.0 O D:ASP33 4.4 82.8 1.0 PA D:GNP201 4.4 30.1 1.0 O D:THR58 4.5 42.3 1.0 CG D:ASP57 4.5 34.9 0.5 C D:PRO34 4.8 79.8 1.0 CB D:LYS16 4.8 25.6 1.0 C D:LYS16 4.9 27.1 1.0 CG D:ASP57 5.0 50.1 0.5

Magnesium binding site 5 out of 6 in the Discovery of Small Molecules Binding to Kras Via High Affinity Antibody Fragment Competition Method.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Discovery of Small Molecules Binding to Kras Via High Affinity Antibody Fragment Competition Method. within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg203 b:33.7 occ:1.00 O1B E:GNP201 2.0 27.0 1.0 OG1 E:THR35 2.1 40.6 1.0 O1G E:GNP201 2.1 39.1 1.0 OG E:SER17 2.1 31.9 1.0 O E:HOH307 2.1 30.0 1.0 O E:HOH313 2.2 32.8 1.0 CB E:THR35 3.1 41.9 1.0 CB E:SER17 3.1 28.2 1.0 PB E:GNP201 3.3 27.9 1.0 PG E:GNP201 3.3 35.8 1.0 N3B E:GNP201 3.6 31.5 1.0 OD2 E:ASP57 3.8 54.8 0.5 N E:THR35 3.8 45.7 1.0 N E:SER17 3.8 23.9 1.0 OD2 E:ASP57 4.0 28.2 0.5 O2G E:GNP201 4.0 38.4 1.0 CA E:SER17 4.0 23.1 1.0 CA E:THR35 4.1 42.3 1.0 O2A E:GNP201 4.1 32.5 1.0 CG2 E:THR35 4.1 45.1 1.0 OD1 E:ASP57 4.2 25.1 0.5 O3A E:GNP201 4.3 28.1 1.0 O E:THR58 4.4 37.5 1.0 O2B E:GNP201 4.4 29.9 1.0 O3G E:GNP201 4.4 42.3 1.0 CG E:ASP57 4.4 27.7 0.5 O E:ASP33 4.5 45.4 1.0 PA E:GNP201 4.6 30.3 1.0 O1A E:GNP201 4.7 30.2 1.0 CB E:LYS16 4.7 27.2 1.0 C E:PRO34 4.8 48.1 1.0 CG E:ASP57 4.9 49.2 0.5 C E:LYS16 4.9 25.6 1.0 CE E:LYS16 5.0 31.5 1.0

Magnesium binding site 6 out of 6 in the Discovery of Small Molecules Binding to Kras Via High Affinity Antibody Fragment Competition Method.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Discovery of Small Molecules Binding to Kras Via High Affinity Antibody Fragment Competition Method. within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg203 b:34.1 occ:1.00 O1B F:GNP201 1.9 23.4 1.0 O F:HOH319 1.9 30.8 1.0 OG1 F:THR35 2.1 41.1 1.0 OG F:SER17 2.2 25.8 1.0 O F:HOH316 2.2 36.9 1.0 O1G F:GNP201 2.2 34.5 1.0 CB F:THR35 3.1 50.6 1.0 PB F:GNP201 3.2 23.8 1.0 CB F:SER17 3.2 28.0 1.0 PG F:GNP201 3.3 31.0 1.0 N3B F:GNP201 3.5 24.5 1.0 N F:SER17 3.7 22.5 1.0 N F:THR35 3.9 52.4 1.0 OD2 F:ASP57 4.0 25.0 0.5 CA F:SER17 4.0 23.1 1.0 CG2 F:THR35 4.1 50.6 1.0 OD1 F:ASP57 4.1 27.5 0.5 CA F:THR35 4.1 56.9 1.0 O2G F:GNP201 4.1 32.5 1.0 O2B F:GNP201 4.3 21.2 1.0 O3A F:GNP201 4.3 23.1 1.0 O2A F:GNP201 4.3 25.0 1.0 O F:THR58 4.3 36.0 1.0 CG F:ASP57 4.4 28.4 0.5 O3G F:GNP201 4.4 33.2 1.0 CB F:LYS16 4.5 20.7 1.0 O F:ASP33 4.6 42.6 1.0 PA F:GNP201 4.6 24.3 1.0 O1A F:GNP201 4.7 24.1 1.0 C F:LYS16 4.8 21.0 1.0 C F:PRO34 4.9 61.2 1.0 CE F:LYS16 4.9 24.0 1.0 NZ F:LYS16 5.0 22.3 1.0

C.E.Quevedo, A.Cruz-Migoni, N.Bery, A.Miller, T.Tanaka, D.Petch, C.J.R.Bataille, L.Y.W.Lee, P.S.Fallon, H.Tulmin, M.T.Ehebauer, N.Fernandez-Fuentes, A.J.Russell, S.B.Carr, S.E.V.Phillips, T.H.Rabbitts. Small Molecule Inhibitors of Ras-Effector Protein Interactions Derived Using An Intracellular Antibody Fragment. Nat Commun V. 9 3169 2018.
ISSN: ESSN 2041-1723
PubMed: 30093669
DOI: 10.1038/S41467-018-05707-2