Magnesium in PDB 8b69: Heterotetramer of K-RAS4B(G12V) and RGL2(Rbd)

All present enzymatic activity of Heterotetramer of K-RAS4B(G12V) and RGL2(Rbd):
3.6.5.2;

The structure of Heterotetramer of K-RAS4B(G12V) and RGL2(Rbd), PDB code: 8b69 was solved by M.Tariq, L.Fairall, B.Romartinez-Alonso, C.Dominguez, J.W.R.Schwabe, K.Tanaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.45 / 3.07
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	77.843, 77.843, 163.728, 90, 90, 120
R / Rfree (%)	23.7 / 31.7

The binding sites of Magnesium atom in the Heterotetramer of K-RAS4B(G12V) and RGL2(Rbd) (pdb code 8b69). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Heterotetramer of K-RAS4B(G12V) and RGL2(Rbd), PDB code: 8b69:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Heterotetramer of K-RAS4B(G12V) and RGL2(Rbd)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Heterotetramer of K-RAS4B(G12V) and RGL2(Rbd) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:109.3 occ:1.00 OG B:SER17 2.2 85.5 1.0 O2B B:GNP202 2.2 106.1 1.0 O3G B:GNP202 2.3 102.7 1.0 HG1 B:THR35 2.5 83.6 1.0 HB2 B:SER17 2.6 94.0 1.0 O2A B:GNP202 2.6 69.4 1.0 HG23 B:THR35 2.8 89.0 1.0 CB B:SER17 2.9 77.5 1.0 O B:ASP33 3.2 98.4 1.0 PB B:GNP202 3.2 84.8 1.0 OG1 B:THR35 3.2 68.8 1.0 N3B B:GNP202 3.2 100.4 1.0 PG B:GNP202 3.3 74.1 1.0 PA B:GNP202 3.3 170.2 1.0 HB3 B:SER17 3.4 94.0 1.0 CG2 B:THR35 3.5 73.3 1.0 H B:THR35 3.5 117.0 1.0 HG21 B:THR35 3.5 89.0 1.0 O3A B:GNP202 3.5 51.7 1.0 H B:SER17 3.6 95.3 1.0 O1A B:GNP202 3.6 103.7 1.0 HNB3 B:GNP202 3.7 121.4 1.0 HA B:PRO34 3.9 116.6 1.0 O2G B:GNP202 3.9 87.3 1.0 CB B:THR35 3.9 75.0 1.0 N B:THR35 3.9 96.7 1.0 CA B:SER17 4.1 88.5 1.0 N B:SER17 4.2 78.6 1.0 C B:ASP33 4.2 95.7 1.0 HG22 B:THR35 4.3 89.0 1.0 CA B:PRO34 4.5 96.3 1.0 C B:PRO34 4.5 101.3 1.0 CA B:THR35 4.5 93.3 1.0 O1G B:GNP202 4.6 71.7 1.0 O1B B:GNP202 4.6 82.4 1.0 H B:ASP33 4.6 140.1 1.0 HA B:SER17 4.7 107.2 1.0 HB B:THR35 4.7 91.0 1.0 N B:PRO34 4.8 91.1 1.0 O5' B:GNP202 4.9 84.5 1.0 H B:ALA18 4.9 82.0 1.0 OD2 B:ASP57 4.9 101.2 1.0 HE3 B:LYS16 5.0 119.5 1.0

Magnesium binding site 2 out of 2 in the Heterotetramer of K-RAS4B(G12V) and RGL2(Rbd)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Heterotetramer of K-RAS4B(G12V) and RGL2(Rbd) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg201 b:97.7 occ:1.00 O3G D:GNP202 2.1 92.7 1.0 OG D:SER17 2.2 97.7 1.0 O2B D:GNP202 2.4 87.4 1.0 HG23 D:THR35 2.7 112.7 1.0 OG1 D:THR35 2.7 70.6 1.0 H D:THR35 2.8 84.3 1.0 HG1 D:THR35 2.8 85.7 1.0 HB2 D:SER17 3.0 98.0 1.0 PG D:GNP202 3.0 127.8 1.0 CB D:SER17 3.1 80.9 1.0 O2A D:GNP202 3.2 64.3 1.0 N3B D:GNP202 3.2 100.0 1.0 HA D:PRO34 3.2 114.2 1.0 N D:THR35 3.3 69.5 1.0 CG2 D:THR35 3.3 93.1 1.0 HE1 D:TYR32 3.4 113.7 1.0 PB D:GNP202 3.4 70.4 1.0 O D:ASP33 3.4 84.4 1.0 O2G D:GNP202 3.4 84.2 1.0 HG21 D:THR35 3.5 112.7 1.0 CB D:THR35 3.5 84.4 1.0 HB3 D:SER17 3.6 98.0 1.0 HNB3 D:GNP202 3.8 121.0 1.0 H D:SER17 3.9 83.4 1.0 CA D:PRO34 4.0 94.3 1.0 C D:PRO34 4.0 76.1 1.0 CA D:THR35 4.0 91.4 1.0 O3A D:GNP202 4.0 78.5 1.0 PA D:GNP202 4.1 75.3 1.0 HG22 D:THR35 4.2 112.7 1.0 CE1 D:TYR32 4.3 93.9 1.0 C D:ASP33 4.3 77.3 1.0 HB D:THR35 4.3 102.3 1.0 O1G D:GNP202 4.3 89.9 1.0 CA D:SER17 4.4 77.4 1.0 N D:SER17 4.5 68.7 1.0 N D:PRO34 4.5 86.5 1.0 HH D:TYR32 4.5 112.8 1.0 O1A D:GNP202 4.5 97.5 1.0 HD1 D:TYR32 4.6 121.8 1.0 HA D:THR35 4.6 110.6 1.0 O1B D:GNP202 4.7 88.8 1.0 HG3 D:LYS16 4.7 130.2 1.0 HA D:SER17 4.8 93.9 1.0 OD2 D:ASP57 4.8 80.6 1.0 OD1 D:ASP57 4.9 102.7 1.0 H D:ASP33 4.9 101.5 1.0 CD1 D:TYR32 4.9 100.7 1.0 HZ3 D:LYS16 5.0 123.6 1.0

M.Tariq, T.Ikeya, N.Togashi, L.Fairall, C.Bueno-Alejo, S.Kamei, B.Romartinez-Alonso, M.A.M.Campillo, A.J.Hudson, Y.Ito, J.W.R.Schwabe, C.Dominguez, K.Tanaka. Structural Insights Into the Complex of Oncogenic K-RAS4B^G12V and RGL2, A Rala/B Activator Biorxiv 2023.
ISSN: ISSN 2692-8205
DOI: 10.1101/2022.10.10.511529