Magnesium in PDB 9qu1: Crystal Structure of the Human RALGAPA2 N-Terminal Domain with Human Kappab-RAS1

The structure of Crystal Structure of the Human RALGAPA2 N-Terminal Domain with Human Kappab-RAS1, PDB code: 9qu1 was solved by R.Rasche, D.Kuemmel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.63 / 2.72
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	163.564, 63.43, 104.163, 90, 91.26, 90
R / Rfree (%)	19.5 / 25.3

The binding sites of Magnesium atom in the Crystal Structure of the Human RALGAPA2 N-Terminal Domain with Human Kappab-RAS1 (pdb code 9qu1). 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 the Human RALGAPA2 N-Terminal Domain with Human Kappab-RAS1, PDB code: 9qu1:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Human RALGAPA2 N-Terminal Domain with Human Kappab-RAS1


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 Human RALGAPA2 N-Terminal Domain with Human Kappab-RAS1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:45.5 occ:1.00 HB C:THR38 2.1 79.9 1.0 OG1 C:THR38 2.1 68.9 1.0 OG1 C:THR18 2.2 43.4 1.0 O2B C:GNP201 2.4 71.1 1.0 O C:HOH301 2.4 43.3 1.0 CB C:THR38 2.5 65.3 1.0 O2G C:GNP201 2.6 59.4 1.0 HG21 C:THR38 3.1 67.0 1.0 OD2 C:ASP61 3.3 72.2 1.0 CG2 C:THR38 3.3 54.6 1.0 H C:THR38 3.4 73.1 1.0 PB C:GNP201 3.4 60.6 1.0 HE2 C:LYS17 3.5 77.0 1.0 H C:THR18 3.6 69.2 1.0 CB C:THR18 3.6 56.4 1.0 HB2 C:LYS17 3.6 80.5 1.0 N3B C:GNP201 3.6 51.9 1.0 PG C:GNP201 3.6 55.0 1.0 HNB3 C:GNP201 3.6 63.8 1.0 CA C:THR38 3.8 67.3 1.0 O C:THR62 3.8 51.8 1.0 HG22 C:THR38 3.8 67.0 1.0 OD1 C:ASP61 3.8 66.4 1.0 CG C:ASP61 3.9 67.0 1.0 N C:THR38 3.9 59.7 1.0 HB C:THR18 4.0 69.1 1.0 N C:THR18 4.1 56.4 1.0 HG23 C:THR38 4.1 67.0 1.0 HG21 C:THR18 4.2 62.4 1.0 O3G C:GNP201 4.3 62.3 1.0 O1B C:GNP201 4.3 50.8 1.0 HA C:THR38 4.3 82.2 1.0 CG2 C:THR18 4.4 50.8 1.0 HG23 C:THR18 4.4 62.4 1.0 CA C:THR18 4.4 62.6 1.0 CE C:LYS17 4.4 62.9 1.0 CB C:LYS17 4.5 65.8 1.0 HB3 C:LYS17 4.6 80.5 1.0 HA C:THR18 4.7 76.6 1.0 C C:THR38 4.7 56.8 1.0 HZ3 C:LYS17 4.8 78.4 1.0 HE3 C:LYS17 4.8 77.0 1.0 O3A C:GNP201 4.8 53.1 1.0 HZ1 C:LYS17 4.8 78.4 1.0 HA C:ARG63 4.9 80.3 1.0 NZ C:LYS17 4.9 64.1 1.0 O1G C:GNP201 4.9 67.3 1.0 C C:THR62 4.9 59.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Human RALGAPA2 N-Terminal Domain with Human Kappab-RAS1


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 Human RALGAPA2 N-Terminal Domain with Human Kappab-RAS1 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg202 b:46.0 occ:1.00 HB F:THR38 2.0 55.2 1.0 O2G F:GNP201 2.3 52.6 1.0 OG1 F:THR18 2.3 27.2 1.0 HG1 F:THR38 2.4 70.5 1.0 O2B F:GNP201 2.5 50.6 1.0 O F:HOH301 2.5 34.7 1.0 CB F:THR38 2.7 49.9 1.0 OG1 F:THR38 2.8 57.5 1.0 HE2 F:LYS17 3.1 59.3 1.0 OD1 F:ASP61 3.2 62.8 1.0 HG21 F:THR38 3.3 52.5 1.0 O F:THR62 3.4 54.6 1.0 H F:THR18 3.4 73.2 1.0 PG F:GNP201 3.4 52.2 1.0 HB2 F:LYS17 3.4 66.5 1.0 PB F:GNP201 3.5 77.2 1.0 CG2 F:THR38 3.5 49.2 1.0 H F:THR38 3.6 53.6 1.0 HG22 F:THR38 3.7 52.5 1.0 CB F:THR18 3.7 41.1 1.0 N3B F:GNP201 3.8 47.1 1.0 HZ1 F:LYS17 3.8 56.2 1.0 CG F:ASP61 3.8 62.0 1.0 OD2 F:ASP61 3.8 69.2 1.0 O3G F:GNP201 3.8 64.7 1.0 CE F:LYS17 4.0 48.1 1.0 CA F:THR38 4.0 50.4 1.0 N F:THR18 4.0 59.7 1.0 HB F:THR18 4.0 50.8 1.0 HZ3 F:LYS17 4.1 56.2 1.0 O1B F:GNP201 4.1 50.7 1.0 N F:THR38 4.1 51.0 1.0 HNB3 F:GNP201 4.1 58.0 1.0 NZ F:LYS17 4.1 45.6 1.0 HE3 F:LYS17 4.4 59.3 1.0 HG23 F:THR38 4.4 52.5 1.0 CB F:LYS17 4.4 54.2 1.0 CA F:THR18 4.4 53.3 1.0 HA F:ARG63 4.4 59.6 1.0 C F:THR62 4.5 53.8 1.0 HA F:THR38 4.6 52.8 1.0 HA F:THR18 4.6 65.5 1.0 CG2 F:THR18 4.6 52.5 1.0 HG21 F:THR18 4.6 64.5 1.0 HG23 F:THR18 4.6 64.5 1.0 HB3 F:LYS17 4.7 66.5 1.0 H F:GLY64 4.7 67.8 1.0 O1G F:GNP201 4.8 53.5 1.0 C F:THR38 4.9 49.4 1.0 C F:LYS17 4.9 54.4 1.0 O3A F:GNP201 5.0 42.1 1.0 N F:GLY64 5.0 55.2 1.0 H F:LYS17 5.0 68.8 1.0 H F:THR62 5.0 48.9 1.0

R.Rasche, L.H.Apken, S.Titze, E.Michalke, R.K.Singh, A.Oeckinghaus, D.Kummel. The Gtpase Kappa B-Ras Is An Essential Subunit of the Ralgap Tumor Suppressor Complex. J.Biol.Chem. 10460 2025.
ISSN: ESSN 1083-351X
PubMed: 40619001
DOI: 10.1016/J.JBC.2025.110460