Magnesium in PDB 8ebz: Crystal Structure of Gmppnp-Bound Kras-G13D Mutant at 1.2 Ang Resolution

All present enzymatic activity of Crystal Structure of Gmppnp-Bound Kras-G13D Mutant at 1.2 Ang Resolution:
3.6.5.2;

The structure of Crystal Structure of Gmppnp-Bound Kras-G13D Mutant at 1.2 Ang Resolution, PDB code: 8ebz was solved by A.H.Chan, D.K.Simanshu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.35 / 1.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	120.93, 38.23, 36.32, 90, 103.28, 90
R / Rfree (%)	15.9 / 17.1

The binding sites of Magnesium atom in the Crystal Structure of Gmppnp-Bound Kras-G13D Mutant at 1.2 Ang Resolution (pdb code 8ebz). 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 Gmppnp-Bound Kras-G13D Mutant at 1.2 Ang Resolution, PDB code: 8ebz:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Gmppnp-Bound Kras-G13D Mutant at 1.2 Ang Resolution


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 Kras-G13D Mutant at 1.2 Ang Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:9.3 occ:1.00 O3G A:GNP201 2.0 9.5 1.0 OG A:SER17 2.1 10.6 1.0 O A:HOH331 2.1 9.6 1.0 O2B A:GNP201 2.1 9.2 1.0 O A:HOH355 2.1 10.9 1.0 O A:HOH403 2.1 11.2 1.0 CB A:SER17 3.2 9.3 1.0 PB A:GNP201 3.3 8.9 1.0 PG A:GNP201 3.3 9.2 1.0 N3B A:GNP201 3.5 9.0 1.0 O A:HOH377 3.7 14.5 1.0 N A:SER17 3.9 8.9 1.0 CA A:SER17 4.1 9.5 1.0 O2A A:GNP201 4.2 10.3 1.0 OD1 A:ASP57 4.2 14.6 1.0 OD2 A:ASP57 4.2 15.5 1.0 O1G A:GNP201 4.2 11.0 1.0 O A:HOH379 4.3 25.0 1.0 O1B A:GNP201 4.3 9.7 1.0 O3A A:GNP201 4.3 9.0 1.0 O2G A:GNP201 4.3 10.1 1.0 O A:HOH410 4.4 14.3 1.0 O A:HOH467 4.4 44.0 1.0 CG A:ASP57 4.6 14.0 1.0 PA A:GNP201 4.6 9.4 1.0 O A:THR58 4.6 12.8 1.0 O A:HOH416 4.7 15.9 1.0 CA A:ALA59 4.7 12.6 1.0 O1A A:GNP201 4.8 10.7 1.0 CB A:LYS16 4.8 9.8 1.0 CE A:LYS16 4.9 10.2 1.0 C A:THR58 4.9 12.3 1.0 N A:ALA59 5.0 11.7 1.0 C A:LYS16 5.0 8.8 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Gmppnp-Bound Kras-G13D Mutant at 1.2 Ang Resolution


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 Kras-G13D Mutant at 1.2 Ang Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:12.9 occ:1.00 O2G A:GNP201 2.0 10.1 1.0 O A:HOH359 2.0 12.8 1.0 O A:HOH432 2.1 15.4 1.0 O A:HOH416 2.1 15.9 1.0 O A:HOH377 2.1 14.5 1.0 PG A:GNP201 3.3 9.2 1.0 O3G A:GNP201 3.7 9.5 1.0 NE2 A:GLN61 3.7 15.1 1.0 N3B A:GNP201 3.8 9.0 1.0 OD1 A:ASP13 4.0 17.2 1.0 O A:HOH445 4.2 21.9 1.0 O A:HOH353 4.2 16.7 1.0 O A:HOH355 4.2 10.9 1.0 OE1 A:GLN61 4.3 19.5 1.0 CD A:GLN61 4.4 15.4 1.0 O1G A:GNP201 4.5 11.0 1.0 O2A A:GNP201 4.8 10.3 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Gmppnp-Bound Kras-G13D Mutant at 1.2 Ang Resolution


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 Kras-G13D Mutant at 1.2 Ang Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:13.1 occ:0.67 O A:HOH393 2.0 29.1 1.0 O A:HOH319 2.1 20.6 1.0 O A:GLY138 2.2 16.9 1.0 O A:HOH454 2.2 17.6 1.0 O A:HOH341 2.3 17.8 1.0 C A:GLY138 3.3 16.1 1.0 CA A:GLY138 3.9 16.7 1.0 O A:HOH382 4.2 17.2 1.0 OD1 A:ASP108 4.2 22.7 1.0 O A:TYR137 4.3 20.0 1.0 O A:HOH420 4.4 27.4 1.0 O A:HOH380 4.4 21.8 1.0 O A:HOH340 4.4 15.8 1.0 N A:ILE139 4.4 14.8 1.0 O A:HOH398 4.5 19.3 0.5 CG2 A:ILE139 4.6 15.2 1.0 CA A:ILE139 4.8 15.4 1.0 OE1 A:GLU162 4.9 21.6 1.0 N A:GLY138 5.0 16.2 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Gmppnp-Bound Kras-G13D Mutant at 1.2 Ang Resolution


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 Gmppnp-Bound Kras-G13D Mutant at 1.2 Ang Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg205 b:17.6 occ:0.62 O A:HOH431 2.0 24.9 1.0 O A:HOH448 2.0 21.1 1.0 O A:HOH426 2.1 21.6 1.0 O A:ASP119 2.1 15.1 1.0 C A:ASP119 3.3 13.8 1.0 CA A:ASP119 4.0 13.0 1.0 O A:HOH330 4.1 21.8 1.0 O A:HOH356 4.2 22.1 1.0 C A:LEU120 4.3 14.9 1.0 N A:LEU120 4.3 13.5 1.0 CB A:ASP119 4.4 14.1 1.0 N A:PRO121 4.5 14.8 1.0 O A:LEU120 4.5 16.2 1.0 CA A:LEU120 4.5 14.4 1.0 CD A:PRO121 4.8 15.6 1.0

F.A.Chao, A.H.Chan, S.Dharmaiah, C.D.Schwieters, T.H.Tran, T.Taylor, N.Ramakrishnan, D.Esposito, D.V.Nissley, F.Mccormick, D.K.Simanshu, G.Cornilescu. Identification and Structure Elucidation of An Excited State in A Kras G13D Oncogenic Mutant with Reduced Dynamic Complexity Commun Biol 2023.
ISSN: ESSN 2399-3642
DOI: 10.1038/S42003-023-04960-6