Magnesium in PDB 7yv1: Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor LUNA18 and KA30L Fab

The structure of Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor LUNA18 and KA30L Fab, PDB code: 7yv1 was solved by M.Irie, T.A.Fukami, A.Matsuo, K.Saka, M.Nishimura, H.Saito, T.Torizawa, M.Tanada, A.Ohta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.41 / 1.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.617, 90.373, 116.81, 90, 90, 90
R / Rfree (%)	23.8 / 27.7

The structure of Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor LUNA18 and KA30L Fab also contains other interesting chemical elements:

Fluorine

(F)

5 atoms

The binding sites of Magnesium atom in the Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor LUNA18 and KA30L Fab (pdb code 7yv1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor LUNA18 and KA30L Fab, PDB code: 7yv1:

Magnesium binding site 1 out of 1 in the Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor LUNA18 and KA30L Fab


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor LUNA18 and KA30L Fab within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:6.0 occ:1.00 O1B A:GDP201 2.0 4.8 1.0 OG A:SER17 2.0 4.8 1.0 O A:HOH316 2.0 3.8 1.0 O A:HOH327 2.2 3.5 1.0 O A:HOH309 2.2 3.5 1.0 O A:HOH313 2.2 3.1 1.0 CB A:SER17 3.1 3.4 1.0 PB A:GDP201 3.3 6.2 1.0 O2B A:GDP201 3.5 6.0 1.0 N A:SER17 3.9 3.3 1.0 CA A:SER17 4.1 3.6 1.0 O1A A:GDP201 4.1 6.5 1.0 OD1 A:ASP57 4.2 8.1 1.0 OD2 A:ASP57 4.2 5.1 1.0 CD1 A:TYR32 4.2 7.1 1.0 O A:ASP33 4.3 6.0 1.0 O3A A:GDP201 4.3 6.6 1.0 O3B A:GDP201 4.3 5.6 1.0 O A:PRO34 4.4 6.0 1.0 CE1 A:TYR32 4.5 7.7 1.0 CA A:PRO34 4.5 7.4 1.0 O A:THR58 4.5 4.7 1.0 O A:ILE36 4.5 4.9 1.0 CG A:ASP57 4.6 6.4 1.0 PA A:GDP201 4.6 6.7 1.0 O A:HOH317 4.6 6.6 1.0 O2A A:GDP201 4.7 5.7 1.0 O A:HOH363 4.7 41.8 1.0 C A:PRO34 4.7 5.8 1.0 CB A:LYS16 5.0 4.2 1.0

M.Tanada, A.Ohta. Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor LUNA18 and KA30L Fab To Be Published.