Magnesium in PDB 6fa2: Antibody Derived (Abd-5) Small Molecule Binding to Kras.

The structure of Antibody Derived (Abd-5) Small Molecule Binding to Kras., PDB code: 6fa2 was solved by C.E.Quevedo, A.Cruz-Migoni, M.T.Ehebauer, 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)	93.81 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.230, 117.215, 156.446, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 23.3

The binding sites of Magnesium atom in the Antibody Derived (Abd-5) Small Molecule Binding to Kras. (pdb code 6fa2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Antibody Derived (Abd-5) Small Molecule Binding to Kras., PDB code: 6fa2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Antibody Derived (Abd-5) Small Molecule Binding to Kras.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Antibody Derived (Abd-5) Small Molecule Binding to Kras. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:37.0 occ:1.00 O2G A:GNP202 1.9 35.8 1.0 O2B A:GNP202 2.0 32.9 1.0 O A:HOH301 2.0 38.5 1.0 OG A:SER17 2.1 29.9 1.0 O A:HOH304 2.1 26.1 1.0 OG1 A:THR35 2.2 44.3 1.0 CB A:THR35 3.1 41.8 1.0 CB A:SER17 3.2 36.7 1.0 PB A:GNP202 3.2 34.5 1.0 PG A:GNP202 3.2 34.7 1.0 N3B A:GNP202 3.4 34.4 1.0 N A:SER17 3.8 36.1 1.0 O3G A:GNP202 3.9 34.8 1.0 N A:THR35 4.0 39.9 1.0 CA A:SER17 4.0 38.8 1.0 OD1 A:ASP57 4.0 56.8 1.0 O1B A:GNP202 4.1 34.5 1.0 OD2 A:ASP57 4.1 63.9 1.0 CG2 A:THR35 4.1 41.2 1.0 CA A:THR35 4.2 42.0 1.0 O1A A:GNP202 4.3 33.7 1.0 O A:THR58 4.3 48.5 1.0 O3A A:GNP202 4.4 35.6 1.0 O A:ASP33 4.5 53.6 1.0 CG A:ASP57 4.5 54.3 1.0 O1G A:GNP202 4.5 39.6 1.0 O2A A:GNP202 4.5 35.4 1.0 PA A:GNP202 4.6 37.9 1.0 CB A:LYS16 4.7 44.3 1.0 C A:LYS16 4.8 37.5 1.0 C A:PRO34 4.9 42.4 1.0 NZ A:LYS16 4.9 46.5 1.0 CE A:LYS16 4.9 50.0 1.0

Magnesium binding site 2 out of 6 in the Antibody Derived (Abd-5) Small Molecule Binding to Kras.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Antibody Derived (Abd-5) Small Molecule Binding to Kras. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:62.9 occ:1.00 O2G B:GNP202 1.9 45.4 1.0 O B:HOH303 2.0 56.8 1.0 O B:HOH301 2.1 46.9 1.0 O2B B:GNP202 2.1 33.1 1.0 OG1 B:THR35 2.2 52.0 1.0 OG B:SER17 2.4 38.6 1.0 PG B:GNP202 3.1 43.1 1.0 PB B:GNP202 3.1 37.2 1.0 CB B:THR35 3.2 55.4 1.0 N3B B:GNP202 3.2 39.6 1.0 CB B:SER17 3.4 37.4 1.0 O3G B:GNP202 3.9 43.9 1.0 N B:THR35 3.9 60.2 1.0 O1A B:GNP202 3.9 36.4 1.0 N B:SER17 4.0 37.0 1.0 CA B:THR35 4.2 59.0 1.0 CG2 B:THR35 4.2 57.1 1.0 O3A B:GNP202 4.2 38.7 1.0 CA B:SER17 4.3 37.4 1.0 PA B:GNP202 4.3 40.2 1.0 OD1 B:ASP57 4.3 71.4 1.0 O2A B:GNP202 4.3 37.9 1.0 O B:THR58 4.3 67.2 1.0 O1G B:GNP202 4.3 47.5 1.0 O1B B:GNP202 4.4 35.9 1.0 OD2 B:ASP57 4.4 60.6 1.0 O B:ASP33 4.4 59.9 1.0 C B:PRO34 4.7 56.5 1.0 CG B:ASP57 4.8 63.4 1.0 CA B:PRO34 4.8 62.2 1.0 CB B:LYS16 4.9 37.5 1.0 NZ B:LYS16 5.0 41.7 1.0

Magnesium binding site 3 out of 6 in the Antibody Derived (Abd-5) Small Molecule Binding to Kras.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Antibody Derived (Abd-5) Small Molecule Binding to Kras. within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg201 b:88.5 occ:1.00 O1G C:GNP202 2.0 97.1 1.0 O1B C:GNP202 2.1 65.0 1.0 OG C:SER17 2.3 62.5 1.0 OG1 C:THR35 2.4 0.9 1.0 CB C:THR35 3.2 0.4 1.0 PB C:GNP202 3.3 69.3 1.0 PG C:GNP202 3.4 74.1 1.0 CB C:SER17 3.4 53.4 1.0 OD1 C:ASP57 3.5 92.9 1.0 N C:SER17 3.6 54.6 1.0 N3B C:GNP202 3.6 71.6 1.0 O C:THR58 3.8 79.0 1.0 OD2 C:ASP57 3.9 95.7 1.0 CA C:SER17 4.0 56.2 1.0 O2B C:GNP202 4.0 56.8 1.0 CG2 C:THR35 4.1 0.2 1.0 CG C:ASP57 4.1 89.4 1.0 CB C:LYS16 4.2 57.9 1.0 O2G C:GNP202 4.3 72.3 1.0 O3G C:GNP202 4.3 72.0 1.0 N C:THR35 4.4 0.6 1.0 CE C:LYS16 4.4 58.3 1.0 CA C:THR35 4.4 0.7 1.0 C C:LYS16 4.5 57.9 1.0 O3A C:GNP202 4.6 72.0 1.0 NZ C:LYS16 4.6 58.9 1.0 O1A C:GNP202 4.7 71.0 1.0 O2A C:GNP202 4.8 60.5 1.0 CA C:LYS16 4.8 57.0 1.0 PA C:GNP202 4.8 77.0 1.0 N C:LYS16 4.9 58.6 1.0 C C:THR58 5.0 75.2 1.0

Magnesium binding site 4 out of 6 in the Antibody Derived (Abd-5) Small Molecule Binding to Kras.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Antibody Derived (Abd-5) Small Molecule Binding to Kras. within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg201 b:74.0 occ:1.00 O2G D:GNP202 2.6 71.7 1.0 OG D:SER17 2.7 49.5 1.0 O2B D:GNP202 2.8 51.6 1.0 O D:THR58 3.1 74.1 1.0 OD1 D:ASP57 3.4 83.3 1.0 OD2 D:ASP57 3.7 85.1 1.0 PG D:GNP202 3.8 65.8 1.0 CG D:ASP57 3.8 81.7 1.0 O3G D:GNP202 4.0 63.5 1.0 CB D:SER17 4.0 48.5 1.0 PB D:GNP202 4.1 54.3 1.0 C D:THR58 4.2 72.6 1.0 N D:SER17 4.4 51.0 1.0 N3B D:GNP202 4.4 58.9 1.0 CE D:LYS16 4.5 60.6 1.0 CA D:SER17 4.7 51.8 1.0 CA D:ALA59 4.7 92.6 1.0 CB D:LYS16 4.7 53.8 1.0 N D:ALA59 4.8 82.8 1.0 O1B D:GNP202 4.9 46.8 1.0 NZ D:LYS16 4.9 62.8 1.0

Magnesium binding site 5 out of 6 in the Antibody Derived (Abd-5) Small Molecule Binding to Kras.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Antibody Derived (Abd-5) Small Molecule Binding to Kras. within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg201 b:66.0 occ:1.00 OG1 E:THR35 2.3 0.9 1.0 O1B E:GNP202 2.4 49.6 1.0 O1G E:GNP202 2.4 60.9 1.0 OG E:SER17 2.5 57.9 1.0 OD1 E:ASP57 3.1 81.8 1.0 O E:THR58 3.1 55.2 1.0 O E:HOH303 3.4 53.1 1.0 CB E:THR35 3.5 0.8 1.0 CG2 E:THR35 3.6 0.3 1.0 PB E:GNP202 3.7 50.2 1.0 OD2 E:ASP57 3.7 87.9 1.0 CG E:ASP57 3.7 79.8 1.0 PG E:GNP202 3.7 59.4 1.0 CB E:SER17 3.8 47.7 1.0 N E:SER17 3.8 48.1 1.0 CB E:LYS16 4.0 49.2 1.0 O2G E:GNP202 4.0 62.7 1.0 CE E:LYS16 4.1 53.4 1.0 N3B E:GNP202 4.2 59.2 1.0 O2B E:GNP202 4.2 48.6 1.0 CA E:SER17 4.2 48.9 1.0 C E:THR58 4.3 63.8 1.0 NZ E:LYS16 4.4 51.7 1.0 C E:LYS16 4.5 49.6 1.0 N E:THR35 4.6 0.3 1.0 CA E:THR35 4.6 0.8 1.0 CA E:LYS16 4.8 52.5 1.0 O3A E:GNP202 4.9 55.9 1.0 CA E:ALA59 5.0 77.5 1.0 CG E:LYS16 5.0 49.4 1.0

Magnesium binding site 6 out of 6 in the Antibody Derived (Abd-5) Small Molecule Binding to Kras.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Antibody Derived (Abd-5) Small Molecule Binding to Kras. within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg201 b:74.1 occ:1.00 OG F:SER17 2.4 43.5 1.0 O1G F:GNP202 2.4 61.5 1.0 O1B F:GNP202 2.7 44.4 1.0 OD1 F:ASP57 3.4 0.8 1.0 O F:THR58 3.4 74.2 1.0 OD2 F:ASP57 3.6 92.5 1.0 CB F:SER17 3.7 41.0 1.0 PG F:GNP202 3.7 54.1 1.0 CG F:ASP57 3.8 87.6 1.0 PB F:GNP202 4.0 43.1 1.0 O2G F:GNP202 4.0 59.8 1.0 N F:SER17 4.2 45.7 1.0 N3B F:GNP202 4.3 48.6 1.0 CA F:SER17 4.4 45.0 1.0 C F:THR58 4.5 69.3 1.0 O2B F:GNP202 4.6 44.0 1.0 CE F:LYS16 4.7 51.7 1.0 CB F:LYS16 4.7 41.4 1.0 NZ F:LYS16 4.9 52.7 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