Magnesium in PDB 6yxw: Affimer K3 - Kras Protein Complex

The structure of Affimer K3 - Kras Protein Complex, PDB code: 6yxw was solved by C.H.Trinh, K.Z.Haza, A.Rao, H.L.Martin, C.Tiede, T.A.Edwards, M.J.Mcpherson, D.C.Tomlinson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.16 / 2.06
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.126, 39.490, 113.212, 90.00, 106.91, 90.00
R / Rfree (%)	23.7 / 27.8

The binding sites of Magnesium atom in the Affimer K3 - Kras Protein Complex (pdb code 6yxw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Affimer K3 - Kras Protein Complex, PDB code: 6yxw:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Affimer K3 - Kras Protein Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Affimer K3 - Kras Protein Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:34.1 occ:1.00 O A:HOH301 1.9 33.8 1.0 O A:HOH314 2.0 34.2 1.0 O2B A:GDP201 2.0 39.0 1.0 OG A:SER17 2.1 41.5 1.0 O A:HOH304 2.2 34.9 1.0 O A:HOH308 2.3 39.0 1.0 CB A:SER17 3.0 42.3 1.0 PB A:GDP201 3.3 38.7 1.0 O3B A:GDP201 3.5 39.7 1.0 O2A A:GDP201 3.9 43.8 1.0 N A:SER17 3.9 40.2 1.0 CA A:SER17 4.0 41.2 1.0 OD2 A:ASP57 4.0 42.4 1.0 OD1 A:ASP57 4.2 39.5 1.0 O3A A:GDP201 4.3 40.6 1.0 O1B A:GDP201 4.3 37.3 1.0 PA A:GDP201 4.3 42.7 1.0 O A:ASP33 4.3 48.9 1.0 O A:PRO34 4.4 44.5 1.0 CD2 A:TYR32 4.4 53.9 1.0 CA A:PRO34 4.4 47.4 1.0 O1A A:GDP201 4.4 41.8 1.0 CG A:ASP57 4.5 40.4 1.0 O A:ILE36 4.6 42.7 1.0 O A:THR58 4.7 36.6 1.0 C A:PRO34 4.7 46.3 1.0 CB A:ALA59 4.8 41.8 1.0 O A:TYR32 4.8 53.9 1.0 CB A:LYS16 4.9 38.2 1.0 C A:LYS16 5.0 39.5 1.0

Magnesium binding site 2 out of 2 in the Affimer K3 - Kras Protein Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Affimer K3 - Kras Protein Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:24.9 occ:1.00 O C:HOH322 2.0 31.2 1.0 O1B C:GDP201 2.1 27.6 1.0 O C:HOH303 2.2 27.5 1.0 O C:HOH309 2.2 27.7 1.0 O C:HOH302 2.2 29.4 1.0 OG C:SER17 2.2 30.0 1.0 CB C:SER17 3.2 29.8 1.0 PB C:GDP201 3.3 27.7 1.0 O3B C:GDP201 3.5 29.4 1.0 OD2 C:ASP57 4.0 30.1 1.0 N C:SER17 4.1 27.1 1.0 O1A C:GDP201 4.1 30.4 1.0 CD1 C:TYR32 4.2 38.7 1.0 CA C:SER17 4.2 28.5 1.0 OD1 C:ASP57 4.2 29.2 1.0 O C:PRO34 4.3 35.4 1.0 O3A C:GDP201 4.4 29.1 1.0 O C:ILE36 4.4 33.8 1.0 O C:ASP33 4.4 35.9 1.0 CA C:PRO34 4.4 36.4 1.0 O2B C:GDP201 4.4 26.8 1.0 CE1 C:TYR32 4.5 39.0 1.0 CG C:ASP57 4.5 29.3 1.0 PA C:GDP201 4.6 29.7 1.0 C C:PRO34 4.7 36.0 1.0 CB C:ALA59 4.7 30.1 1.0 O C:THR58 4.7 28.0 1.0 O2A C:GDP201 4.8 28.8 1.0 O C:TYR32 4.8 37.0 1.0 O C:HOH314 4.9 31.6 1.0 CB C:LYS16 4.9 25.0 1.0

K.Z.Haza, H.L.Martin, A.Rao, A.Turner, S.E.Saunders, B.Petersen, C.Tiede, K.Tipping, M.Ajayi, K.M.Fishwick, T.L.Adams, C.H.Trinh, A.L.Breeze, T.A.Edwards, M.J.Mcpherson, D.C.Tomlinson. Ras-Inhibiting Biologics Identify and Probe Druggable Pockets Including An Sii-ALPHA3 Allosteric Site Biorxiv 2020.
DOI: 10.1101/2020.06.04.133728