Magnesium in PDB 5kho: RASIP1 Ra Domain in Complex with RAP1B

The structure of RASIP1 Ra Domain in Complex with RAP1B, PDB code: 5kho was solved by A.R.Gingras, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.24 / 2.78
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	101.540, 154.760, 38.800, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 28.6

The binding sites of Magnesium atom in the RASIP1 Ra Domain in Complex with RAP1B (pdb code 5kho). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the RASIP1 Ra Domain in Complex with RAP1B, PDB code: 5kho:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the RASIP1 Ra Domain in Complex with RAP1B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of RASIP1 Ra Domain in Complex with RAP1B within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg200 b:72.1 occ:1.00 O2G C:GNP201 1.8 78.4 1.0 O2B C:GNP201 1.9 78.2 1.0 O C:HOH303 2.1 79.5 1.0 O C:HOH302 2.2 54.3 1.0 OG1 C:THR35 2.3 73.7 1.0 OG C:SER17 2.5 59.6 1.0 PG C:GNP201 2.9 81.4 1.0 PB C:GNP201 3.0 71.2 1.0 N3B C:GNP201 3.0 77.4 1.0 CB C:THR35 3.3 73.8 1.0 CB C:SER17 3.4 65.9 1.0 O3G C:GNP201 3.6 78.3 1.0 O1A C:GNP201 3.6 75.1 1.0 N C:THR35 3.6 81.5 1.0 O1B C:GNP201 4.0 77.7 1.0 CA C:THR35 4.0 74.5 1.0 O3A C:GNP201 4.1 72.8 1.0 N C:SER17 4.2 65.9 1.0 PA C:GNP201 4.2 71.4 1.0 O1G C:GNP201 4.2 91.4 1.0 O C:ASP33 4.3 91.0 1.0 CA C:SER17 4.4 69.0 1.0 CG2 C:THR35 4.5 75.5 1.0 O2A C:GNP201 4.5 78.5 1.0 OD1 C:ASP57 4.5 89.6 1.0 OD2 C:ASP57 4.6 96.9 1.0 C C:PRO34 4.6 85.8 1.0 O C:THR58 4.6 87.9 1.0 CA C:PRO34 4.7 85.7 1.0 CG C:ASP57 4.9 88.2 1.0

Magnesium binding site 2 out of 2 in the RASIP1 Ra Domain in Complex with RAP1B


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of RASIP1 Ra Domain in Complex with RAP1B within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg200 b:96.6 occ:1.00 O D:HOH302 1.9 98.7 1.0 O D:HOH301 2.0 67.9 1.0 O1B D:GNP201 2.1 0.2 1.0 O1G D:GNP201 2.1 0.5 1.0 OG D:SER17 2.1 80.4 1.0 OG1 D:THR35 2.2 80.8 1.0 PG D:GNP201 3.1 0.8 1.0 PB D:GNP201 3.2 99.0 1.0 N3B D:GNP201 3.3 0.2 1.0 CB D:SER17 3.4 83.1 1.0 CB D:THR35 3.4 81.0 1.0 O2G D:GNP201 3.8 96.3 1.0 O2A D:GNP201 3.8 87.6 1.0 N D:THR35 4.0 89.8 1.0 N D:SER17 4.1 85.3 1.0 OD1 D:ASP57 4.2 0.9 1.0 O3A D:GNP201 4.2 96.4 1.0 O D:ASP33 4.3 0.7 1.0 O2B D:GNP201 4.3 93.6 1.0 CA D:SER17 4.3 81.1 1.0 OD2 D:ASP57 4.3 0.9 1.0 PA D:GNP201 4.3 98.5 1.0 CA D:THR35 4.4 82.4 1.0 CG2 D:THR35 4.4 76.9 1.0 O3G D:GNP201 4.5 0.9 1.0 O1A D:GNP201 4.6 0.1 1.0 CG D:ASP57 4.7 0.6 1.0 O D:THR58 4.7 70.4 1.0 CB D:LYS16 5.0 85.4 1.0

A.R.Gingras, W.Puzon-Mclaughlin, A.A.Bobkov, M.H.Ginsberg. Structural Basis of Dimeric RASIP1 Ra Domain Recognition of the Ras Subfamily of Gtp-Binding Proteins. Structure V. 24 2152 2016.
ISSN: ISSN 1878-4186
PubMed: 27839947
DOI: 10.1016/J.STR.2016.10.001