Magnesium in PDB 8ely: Hras R97M Crystal Form 2

All present enzymatic activity of Hras R97M Crystal Form 2:
3.6.5.2;

The structure of Hras R97M Crystal Form 2, PDB code: 8ely was solved by C.W.Johnson, C.Mattos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.98 / 1.75
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	39.241, 39.241, 157.693, 90, 90, 120
R / Rfree (%)	17.9 / 22.7

The structure of Hras R97M Crystal Form 2 also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Magnesium atom in the Hras R97M Crystal Form 2 (pdb code 8ely). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Hras R97M Crystal Form 2, PDB code: 8ely:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Hras R97M Crystal Form 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Hras R97M Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:17.3 occ:1.00 O A:HOH337 2.0 17.6 1.0 O2B A:GNP202 2.0 19.0 1.0 OG A:SER17 2.0 17.3 1.0 OG1 A:THR35 2.0 18.6 1.0 O2G A:GNP202 2.0 20.5 1.0 O A:HOH347 2.1 20.1 1.0 CB A:THR35 3.1 21.7 1.0 CB A:SER17 3.1 17.9 1.0 PB A:GNP202 3.2 18.5 1.0 PG A:GNP202 3.2 21.4 1.0 N3B A:GNP202 3.3 19.3 1.0 N A:SER17 3.7 15.7 1.0 N A:THR35 3.8 21.4 1.0 OD2 A:ASP57 4.0 20.1 1.0 CA A:SER17 4.0 19.6 1.0 CA A:THR35 4.0 23.8 1.0 OD1 A:ASP57 4.1 18.3 1.0 CG2 A:THR35 4.2 25.3 1.0 O2A A:GNP202 4.2 23.1 1.0 O3G A:GNP202 4.2 20.0 1.0 O1B A:GNP202 4.2 17.4 1.0 O3A A:GNP202 4.2 17.1 1.0 O A:HOH394 4.3 35.1 1.0 O A:THR58 4.4 24.6 1.0 O1G A:GNP202 4.4 21.4 1.0 CG A:ASP57 4.4 18.4 1.0 O A:ASP33 4.5 24.8 1.0 PA A:GNP202 4.5 19.9 1.0 O1A A:GNP202 4.6 21.3 1.0 C A:PRO34 4.7 27.2 1.0 CB A:LYS16 4.7 15.6 1.0 C A:LYS16 4.8 18.1 1.0 CE A:LYS16 4.9 19.6 1.0 CA A:PRO34 5.0 26.3 1.0

Magnesium binding site 2 out of 2 in the Hras R97M Crystal Form 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Hras R97M Crystal Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:18.0 occ:1.00 O A:HOH399 2.4 35.3 1.0 OD1 A:ASP107 2.5 26.0 1.0 OD1 A:ASP108 2.5 31.9 1.0 OD2 A:ASP108 2.5 31.5 1.0 CG A:ASP108 2.9 30.4 1.0 CG A:ASP107 3.6 30.8 1.0 O A:HOH413 4.0 48.2 1.0 OD2 A:ASP107 4.0 29.4 1.0 CB A:ASP108 4.4 26.0 1.0 O A:HOH359 4.4 41.0 1.0 O A:HOH395 4.5 34.8 1.0 C A:ASP107 4.6 23.0 1.0 N A:ASP108 4.7 22.3 1.0 O A:ASP107 4.8 24.8 1.0 CB A:ASP107 4.8 26.7 1.0 N A:ASP107 4.9 21.3 1.0 O A:HOH364 5.0 41.5 1.0

C.W.Johnson, S.K.Fetics, K.P.Davis, J.A.Rodrigues, C.Mattos. Allosteric Site Variants Affect Gtp Hydrolysis on Ras. Protein Sci. E4767 2023.
ISSN: ESSN 1469-896X
PubMed: 37615343
DOI: 10.1002/PRO.4767