Magnesium in PDB 4k81: Crystal Structure of the GRB14 Ra and pH Domains in Complex with Gtp- Loaded H-Ras

The structure of Crystal Structure of the GRB14 Ra and pH Domains in Complex with Gtp- Loaded H-Ras, PDB code: 4k81 was solved by R.Qamra, S.R.Hubbard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	79.727, 115.593, 103.107, 90.00, 96.75, 90.00
R / Rfree (%)	21.9 / 27.7

The binding sites of Magnesium atom in the Crystal Structure of the GRB14 Ra and pH Domains in Complex with Gtp- Loaded H-Ras (pdb code 4k81). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the GRB14 Ra and pH Domains in Complex with Gtp- Loaded H-Ras, PDB code: 4k81:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the GRB14 Ra and pH Domains in Complex with Gtp- Loaded H-Ras


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 the GRB14 Ra and pH Domains in Complex with Gtp- Loaded H-Ras within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:40.3 occ:1.00 O2G B:GTP202 1.7 39.1 1.0 O2B B:GTP202 2.0 36.2 1.0 O B:HOH315 2.1 23.6 1.0 OG1 B:THR35 2.2 30.0 1.0 OG B:SER17 2.4 31.4 1.0 PG B:GTP202 2.9 42.0 1.0 PB B:GTP202 3.1 37.9 1.0 O3B B:GTP202 3.1 39.0 1.0 CB B:THR35 3.2 31.0 1.0 CB B:SER17 3.4 31.8 1.0 N B:THR35 3.8 33.2 1.0 O2A B:GTP202 3.8 34.5 1.0 O3G B:GTP202 3.9 42.5 1.0 O B:ASP33 3.9 44.5 1.0 O3A B:GTP202 4.0 36.0 1.0 O1G B:GTP202 4.0 39.2 1.0 CA B:THR35 4.1 31.5 1.0 PA B:GTP202 4.1 36.6 1.0 N B:SER17 4.2 31.3 1.0 O B:HOH310 4.2 34.3 1.0 O1A B:GTP202 4.3 38.1 1.0 CG2 B:THR35 4.3 30.4 1.0 OD1 B:ASP57 4.3 41.8 1.0 O1B B:GTP202 4.4 40.6 1.0 OD2 B:ASP57 4.4 40.6 1.0 CA B:SER17 4.4 31.5 1.0 C B:PRO34 4.7 34.4 1.0 CG B:ASP57 4.8 39.9 1.0 CE1 B:TYR32 4.9 37.8 1.0 O B:THR58 4.9 38.0 1.0 C B:ASP33 4.9 41.7 1.0 CA B:PRO34 5.0 36.8 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the GRB14 Ra and pH Domains in Complex with Gtp- Loaded H-Ras


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 the GRB14 Ra and pH Domains in Complex with Gtp- Loaded H-Ras within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg201 b:45.2 occ:1.00 O2G D:GTP200 1.9 43.3 1.0 O2B D:GTP200 2.1 38.6 1.0 OG D:SER17 2.2 33.9 1.0 OG1 D:THR35 2.4 38.8 1.0 O D:HOH314 2.5 42.8 1.0 CB D:SER17 3.0 35.9 1.0 PG D:GTP200 3.2 44.1 1.0 PB D:GTP200 3.2 40.2 1.0 O2A D:GTP200 3.3 44.8 1.0 O D:ASP33 3.3 54.0 1.0 O3B D:GTP200 3.4 41.5 1.0 CB D:THR35 3.6 40.5 1.0 N D:THR35 3.9 44.4 1.0 PA D:GTP200 3.9 43.1 1.0 O3A D:GTP200 3.9 42.4 1.0 O1A D:GTP200 4.1 43.2 1.0 O1G D:GTP200 4.1 45.5 1.0 N D:SER17 4.2 34.8 1.0 CA D:SER17 4.2 36.1 1.0 O3G D:GTP200 4.3 46.9 1.0 CA D:THR35 4.3 42.3 1.0 C D:ASP33 4.4 53.6 1.0 C D:PRO34 4.6 48.8 1.0 OD1 D:ASP57 4.6 42.9 1.0 O1B D:GTP200 4.6 40.8 1.0 CE1 D:TYR32 4.6 60.1 1.0 CA D:PRO34 4.7 50.8 1.0 CG2 D:THR35 4.7 39.9 1.0 OD2 D:ASP57 4.9 42.6 1.0 N D:PRO34 5.0 51.7 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the GRB14 Ra and pH Domains in Complex with Gtp- Loaded H-Ras


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 the GRB14 Ra and pH Domains in Complex with Gtp- Loaded H-Ras within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg201 b:54.2 occ:1.00 OG F:SER17 2.1 38.4 1.0 O2B F:GTP200 2.2 39.4 1.0 O F:HOH310 2.2 35.3 1.0 O2G F:GTP200 2.3 41.3 1.0 OG1 F:THR35 2.3 40.0 1.0 OD2 F:ASP57 3.0 52.7 1.0 CB F:THR35 3.0 41.8 1.0 OD1 F:ASP57 3.3 51.1 1.0 CB F:SER17 3.3 39.9 1.0 PB F:GTP200 3.5 41.2 1.0 CG F:ASP57 3.5 47.5 1.0 PG F:GTP200 3.5 45.5 1.0 N F:SER17 3.6 40.6 1.0 CG2 F:THR35 3.8 38.7 1.0 O F:THR58 3.8 42.0 1.0 O3B F:GTP200 3.9 43.6 1.0 CA F:SER17 3.9 42.2 1.0 O3G F:GTP200 4.0 44.2 1.0 CB F:LYS16 4.1 42.5 1.0 CA F:THR35 4.3 42.7 1.0 O1B F:GTP200 4.3 45.0 1.0 N F:THR35 4.4 44.8 1.0 C F:LYS16 4.4 43.2 1.0 O F:HOH313 4.5 42.4 1.0 CE F:LYS16 4.5 40.0 1.0 O3A F:GTP200 4.7 43.1 1.0 O2A F:GTP200 4.7 46.1 1.0 CA F:LYS16 4.8 43.3 1.0 O1G F:GTP200 4.8 44.8 1.0 O1A F:GTP200 4.8 43.5 1.0 NZ F:LYS16 4.9 38.6 1.0 CB F:ASP57 4.9 43.5 1.0 PA F:GTP200 5.0 45.9 1.0 C F:THR58 5.0 38.7 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the GRB14 Ra and pH Domains in Complex with Gtp- Loaded H-Ras


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the GRB14 Ra and pH Domains in Complex with Gtp- Loaded H-Ras within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg201 b:63.9 occ:1.00 O2G H:GTP200 1.9 75.7 1.0 O2B H:GTP200 1.9 69.9 1.0 OG1 H:THR35 2.1 69.0 1.0 O H:HOH301 2.3 48.4 1.0 OG H:SER17 2.4 63.9 1.0 PG H:GTP200 3.1 77.1 1.0 PB H:GTP200 3.1 72.9 1.0 O3B H:GTP200 3.4 73.5 1.0 OD1 H:ASP57 3.5 70.2 1.0 CB H:THR35 3.5 70.4 1.0 CB H:SER17 3.6 61.6 1.0 OD2 H:ASP57 3.6 76.9 1.0 O3G H:GTP200 3.6 77.2 1.0 N H:SER17 3.9 60.0 1.0 CG H:ASP57 3.9 71.6 1.0 CG2 H:THR35 4.0 71.6 1.0 O1B H:GTP200 4.0 75.7 1.0 O H:THR58 4.1 77.6 1.0 CA H:SER17 4.2 59.2 1.0 N H:THR35 4.2 73.1 1.0 O2A H:GTP200 4.3 72.2 1.0 O3A H:GTP200 4.4 71.6 1.0 O1G H:GTP200 4.4 78.0 1.0 CA H:THR35 4.4 69.3 1.0 CB H:LYS16 4.4 63.9 1.0 NZ H:LYS16 4.5 63.9 1.0 CE H:LYS16 4.6 64.3 1.0 PA H:GTP200 4.7 71.1 1.0 O1A H:GTP200 4.7 71.7 1.0 C H:LYS16 4.8 61.9 1.0 O H:THR35 5.0 72.3 1.0

R.Qamra, S.R.Hubbard. Structural Basis For the Interaction of the Adaptor Protein GRB14 with Activated Ras. Plos One V. 8 72473 2013.
ISSN: ESSN 1932-6203
PubMed: 23967305
DOI: 10.1371/JOURNAL.PONE.0072473