Magnesium in PDB 6cu6: Crystal Structure of Gmppnp-Bound G12R Mutant of Human KRAS4B

The structure of Crystal Structure of Gmppnp-Bound G12R Mutant of Human KRAS4B, PDB code: 6cu6 was solved by T.H.Tran, D.K.Simanshu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.58 / 1.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	67.790, 83.295, 86.040, 90.00, 110.10, 90.00
R / Rfree (%)	20.2 / 23

The binding sites of Magnesium atom in the Crystal Structure of Gmppnp-Bound G12R Mutant of Human KRAS4B (pdb code 6cu6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Gmppnp-Bound G12R Mutant of Human KRAS4B, PDB code: 6cu6:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Gmppnp-Bound G12R Mutant of Human KRAS4B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Gmppnp-Bound G12R Mutant of Human KRAS4B within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:26.4 occ:1.00 O A:HOH541 2.0 26.3 1.0 OG A:SER17 2.1 26.0 1.0 O1B A:GNP402 2.1 26.3 1.0 O2G A:GNP402 2.1 30.6 1.0 OG1 A:THR35 2.1 26.8 1.0 O A:HOH519 2.2 28.1 1.0 CB A:THR35 3.1 26.9 1.0 CB A:SER17 3.2 23.8 1.0 PB A:GNP402 3.3 25.4 1.0 PG A:GNP402 3.3 25.9 1.0 N3B A:GNP402 3.5 25.1 1.0 N A:SER17 3.8 24.5 1.0 N A:THR35 3.9 30.4 1.0 OD1 A:ASP57 4.1 28.6 1.0 CA A:SER17 4.1 23.8 1.0 CA A:THR35 4.1 31.9 1.0 O3G A:GNP402 4.1 25.9 1.0 CG2 A:THR35 4.2 29.2 1.0 O1A A:GNP402 4.3 29.8 1.0 O3A A:GNP402 4.3 25.5 1.0 OD2 A:ASP57 4.3 28.8 1.0 O2B A:GNP402 4.4 24.1 1.0 O1G A:GNP402 4.4 30.2 1.0 O A:ASP33 4.4 36.8 1.0 O A:THR58 4.5 28.0 1.0 O A:HOH524 4.5 42.0 1.0 CG A:ASP57 4.5 28.2 1.0 PA A:GNP402 4.6 26.2 1.0 O2A A:GNP402 4.7 25.5 1.0 C A:PRO34 4.8 37.2 1.0 CB A:LYS16 4.8 23.1 1.0 C A:LYS16 4.9 23.1 1.0 CE A:LYS16 5.0 25.9 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Gmppnp-Bound G12R Mutant of Human KRAS4B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Gmppnp-Bound G12R Mutant of Human KRAS4B within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:34.1 occ:1.00 O3G B:GNP403 2.0 38.7 1.0 O B:HOH501 2.1 35.5 1.0 O2B B:GNP403 2.2 27.1 1.0 OG1 B:THR35 2.2 46.0 1.0 O B:HOH528 2.2 38.6 1.0 OG B:SER17 2.2 32.6 1.0 CB B:THR35 3.0 47.6 1.0 PG B:GNP403 3.2 31.2 1.0 CB B:SER17 3.3 29.2 1.0 PB B:GNP403 3.3 25.9 1.0 N3B B:GNP403 3.5 29.6 1.0 OD2 B:ASP57 3.8 53.7 1.0 OD1 B:ASP57 3.9 50.8 1.0 CG2 B:THR35 4.0 52.4 1.0 N B:SER17 4.0 24.4 1.0 O2G B:GNP403 4.0 37.2 1.0 N B:THR35 4.0 54.9 1.0 CA B:THR35 4.1 59.8 1.0 CA B:SER17 4.2 24.9 1.0 CG B:ASP57 4.2 46.7 1.0 O1A B:GNP403 4.3 33.3 1.0 O3A B:GNP403 4.3 26.8 1.0 O1G B:GNP403 4.3 39.4 1.0 O B:ASP33 4.4 61.9 1.0 O1B B:GNP403 4.4 27.0 1.0 O B:THR58 4.4 43.6 1.0 PA B:GNP403 4.6 28.2 1.0 O2A B:GNP403 4.7 25.9 1.0 CB B:LYS16 4.9 23.1 1.0 CE B:LYS16 5.0 26.3 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Gmppnp-Bound G12R Mutant of Human KRAS4B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Gmppnp-Bound G12R Mutant of Human KRAS4B within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:55.3 occ:1.00 O1G C:GNP402 2.4 61.9 1.0 OG C:SER17 2.5 53.2 1.0 O1B C:GNP402 2.6 42.9 1.0 OD1 C:ASP57 2.6 72.7 1.0 O C:HOH530 2.6 51.8 1.0 OD2 C:ASP57 2.8 70.9 1.0 CG C:ASP57 3.0 71.1 1.0 O C:HOH523 3.4 66.8 1.0 CB C:SER17 3.6 44.8 1.0 PG C:GNP402 3.7 53.7 1.0 PB C:GNP402 3.8 40.1 1.0 N3B C:GNP402 4.0 43.9 1.0 N C:SER17 4.1 39.5 1.0 O3G C:GNP402 4.3 53.0 1.0 CA C:SER17 4.3 40.4 1.0 CB C:ASP57 4.5 71.9 1.0 CE C:LYS16 4.7 46.0 1.0 CB C:LYS16 4.7 36.3 1.0 O2B C:GNP402 4.7 36.8 1.0 O2G C:GNP402 4.8 57.6 1.0 O3A C:GNP402 5.0 38.0 1.0 C C:LYS16 5.0 36.1 1.0

G.A.Hobbs, N.M.Baker, A.M.Miermont, R.D.Thurman, M.Pierobon, T.H.Tran, A.O.Anderson, A.M.Waters, J.N.Diehl, B.Papke, R.G.Hodge, J.E.Klomp, C.M.Goodwin, J.M.Deliberty, J.Wang, R.W.S.Ng, P.Gautam, K.L.Bryant, D.Esposito, S.L.Campbell, E.F.Petricoin, D.K.Simanshu, A.J.Aguirre, B.M.Wolpin, K.Wennerberg, U.Rudloff, A.D.Cox, C.J.Der. Atypical KRASG12R Mutant Is Impaired in PI3K Signaling and Macropinocytosis in Pancreatic Cancer. Cancer Discov 2019.
ISSN: ESSN 2159-8290
PubMed: 31649109
DOI: 10.1158/2159-8290.CD-19-1006