Magnesium in PDB 6ob3: Crystal Structure of G13D-Kras (Gmppnp-Bound) in Complex with Gap- Related Domain (Grd) of Neurofibromin (NF1)

The structure of Crystal Structure of G13D-Kras (Gmppnp-Bound) in Complex with Gap- Related Domain (Grd) of Neurofibromin (NF1), PDB code: 6ob3 was solved by T.H.Tran, S.Dharmaiah, D.K.Simanshu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	77.76 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	81.677, 97.169, 155.525, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 22.6

The structure of Crystal Structure of G13D-Kras (Gmppnp-Bound) in Complex with Gap- Related Domain (Grd) of Neurofibromin (NF1) also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Magnesium atom in the Crystal Structure of G13D-Kras (Gmppnp-Bound) in Complex with Gap- Related Domain (Grd) of Neurofibromin (NF1) (pdb code 6ob3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of G13D-Kras (Gmppnp-Bound) in Complex with Gap- Related Domain (Grd) of Neurofibromin (NF1), PDB code: 6ob3:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of G13D-Kras (Gmppnp-Bound) in Complex with Gap- Related Domain (Grd) of Neurofibromin (NF1)


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 G13D-Kras (Gmppnp-Bound) in Complex with Gap- Related Domain (Grd) of Neurofibromin (NF1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:38.2 occ:1.00 O1G A:GNP201 2.0 39.8 1.0 O2B A:GNP201 2.0 32.0 1.0 O A:HOH328 2.0 35.1 1.0 O A:HOH332 2.1 42.4 1.0 OG1 A:THR35 2.1 39.5 1.0 OG A:SER17 2.2 40.7 1.0 PG A:GNP201 3.0 44.8 1.0 CB A:THR35 3.1 38.1 1.0 PB A:GNP201 3.2 41.6 1.0 N3B A:GNP201 3.3 34.8 1.0 CB A:SER17 3.3 42.9 1.0 N A:THR35 3.7 44.7 1.0 O3G A:GNP201 3.9 42.5 1.0 N A:SER17 4.0 34.4 1.0 CA A:THR35 4.1 38.2 1.0 O2A A:GNP201 4.1 39.3 1.0 O1B A:GNP201 4.2 35.9 1.0 OD2 A:ASP57 4.2 51.6 1.0 O2G A:GNP201 4.2 46.6 1.0 CA A:SER17 4.2 40.4 1.0 CG2 A:THR35 4.3 34.1 1.0 O A:HOH308 4.3 46.3 1.0 O3A A:GNP201 4.4 41.3 1.0 O A:THR58 4.4 39.9 1.0 OD1 A:ASP57 4.4 53.3 1.0 O A:ASP33 4.4 40.9 1.0 PA A:GNP201 4.6 40.8 1.0 CG A:ASP57 4.6 55.0 1.0 C A:PRO34 4.7 44.1 1.0 O1A A:GNP201 4.8 42.5 1.0 CA A:PRO34 4.9 47.1 1.0 CE A:LYS16 4.9 42.3 1.0 CB A:LYS16 4.9 34.5 1.0 NZ A:LYS16 4.9 35.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of G13D-Kras (Gmppnp-Bound) in Complex with Gap- Related Domain (Grd) of Neurofibromin (NF1)


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 G13D-Kras (Gmppnp-Bound) in Complex with Gap- Related Domain (Grd) of Neurofibromin (NF1) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:44.7 occ:1.00 O1G C:GNP201 2.0 47.4 1.0 OG C:SER17 2.0 44.2 1.0 O2B C:GNP201 2.1 45.9 1.0 O C:HOH314 2.1 41.1 1.0 OG1 C:THR35 2.1 42.7 1.0 O C:HOH306 2.2 40.1 1.0 CB C:THR35 3.1 41.6 1.0 CB C:SER17 3.2 44.7 1.0 PG C:GNP201 3.2 45.7 1.0 PB C:GNP201 3.3 48.5 1.0 N3B C:GNP201 3.5 42.6 1.0 N C:SER17 3.9 47.2 1.0 N C:THR35 3.9 48.8 1.0 O2A C:GNP201 4.0 52.5 1.0 O2G C:GNP201 4.0 48.4 1.0 OD2 C:ASP57 4.0 62.4 1.0 CA C:SER17 4.1 48.0 1.0 CA C:THR35 4.1 44.4 1.0 O C:HOH307 4.2 47.9 1.0 CG2 C:THR35 4.2 38.4 1.0 O1B C:GNP201 4.3 47.9 1.0 OD1 C:ASP57 4.3 65.9 1.0 O C:ASP33 4.4 55.5 1.0 O3A C:GNP201 4.4 52.0 1.0 O3G C:GNP201 4.4 50.7 1.0 PA C:GNP201 4.5 53.9 1.0 O C:THR58 4.5 44.3 1.0 CG C:ASP57 4.5 59.5 1.0 O1A C:GNP201 4.6 53.2 1.0 C C:PRO34 4.8 53.5 1.0 CB C:LYS16 4.9 50.4 1.0 NZ D:LYS1436 5.0 57.7 1.0 C C:LYS16 5.0 51.6 1.0

D.Rabara, T.H.Tran, S.Dharmaiah, R.M.Stephens, F.Mccormick, D.K.Simanshu, M.Holderfield. Kras G13D Sensitivity to Neurofibromin-Mediated Gtp Hydrolysis. Proc.Natl.Acad.Sci.Usa V. 116 22122 2019.
ISSN: ESSN 1091-6490
PubMed: 31611389
DOI: 10.1073/PNAS.1908353116