Magnesium in PDB 6ob2: Crystal Structure of Wild-Type Kras (Gmppnp-Bound) in Complex with Gap-Related Domain (Grd) of Neurofibromin (NF1)

The structure of Crystal Structure of Wild-Type Kras (Gmppnp-Bound) in Complex with Gap-Related Domain (Grd) of Neurofibromin (NF1), PDB code: 6ob2 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)	46.00 / 2.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	83.728, 99.736, 155.514, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 24.7

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

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of Wild-Type Kras (Gmppnp-Bound) in Complex with Gap-Related Domain (Grd) of Neurofibromin (NF1) (pdb code 6ob2). 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 Wild-Type Kras (Gmppnp-Bound) in Complex with Gap-Related Domain (Grd) of Neurofibromin (NF1), PDB code: 6ob2:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Wild-Type 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 Wild-Type 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:Mg203 b:55.1 occ:1.00 OG A:SER17 2.0 48.6 1.0 O2B A:GNP202 2.0 42.9 1.0 OG1 A:THR35 2.0 55.4 1.0 O1G A:GNP202 2.1 47.0 1.0 O A:HOH305 2.1 46.4 1.0 O A:HOH304 2.1 52.3 1.0 CB A:THR35 2.9 54.3 1.0 CB A:SER17 3.2 46.9 1.0 PG A:GNP202 3.2 46.7 1.0 PB A:GNP202 3.3 51.1 1.0 N3B A:GNP202 3.5 46.2 1.0 N A:THR35 3.7 54.7 1.0 OD2 A:ASP57 3.8 63.4 1.0 CA A:THR35 3.9 55.4 1.0 O2A A:GNP202 3.9 48.7 1.0 N A:SER17 4.0 41.0 1.0 O3G A:GNP202 4.1 48.8 1.0 CG2 A:THR35 4.1 53.9 1.0 CA A:SER17 4.1 47.0 1.0 O1B A:GNP202 4.2 39.4 1.0 OD1 A:ASP57 4.3 68.1 1.0 O2G A:GNP202 4.4 53.0 1.0 O A:ASP33 4.4 60.2 1.0 O3A A:GNP202 4.4 38.2 1.0 CG A:ASP57 4.5 60.3 1.0 PA A:GNP202 4.5 50.3 1.0 O A:THR58 4.6 50.5 1.0 O1A A:GNP202 4.7 52.5 1.0 C A:PRO34 4.7 57.2 1.0 CA A:PRO34 4.9 55.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Wild-Type 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 Wild-Type 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:80.5 occ:1.00 O C:HOH302 1.9 80.4 0.5 O C:HOH301 1.9 84.1 0.5 O1G C:GNP201 2.0 92.3 1.0 OG1 C:THR35 2.0 82.2 0.8 O2B C:GNP201 2.1 92.0 1.0 OG C:SER17 2.1 87.7 0.8 CB C:THR35 2.9 80.2 0.8 CB C:SER17 3.1 89.6 0.8 PG C:GNP201 3.3 94.8 1.0 PB C:GNP201 3.4 91.7 1.0 O2A C:GNP201 3.5 0.8 1.0 N3B C:GNP201 3.7 89.3 1.0 N C:THR35 3.7 79.5 0.8 OD2 C:ASP57 3.8 99.8 1.0 N C:SER17 3.8 90.2 0.8 CA C:THR35 3.9 81.0 0.8 CG2 C:THR35 3.9 80.6 0.8 CA C:SER17 4.0 92.7 0.8 O3G C:GNP201 4.1 93.5 1.0 OD1 C:ASP57 4.2 0.7 1.0 O C:THR58 4.2 85.8 1.0 O1B C:GNP201 4.3 87.0 1.0 CG C:ASP57 4.3 0.7 1.0 O2G C:GNP201 4.3 98.0 1.0 O3A C:GNP201 4.4 88.9 1.0 PA C:GNP201 4.5 96.7 1.0 O C:ASP33 4.5 0.8 1.0 C C:PRO34 4.8 82.7 1.0 C C:LYS16 4.8 93.8 1.0 CB C:LYS16 4.8 90.6 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