Magnesium in PDB 3x1y: Ras-Related Protein RAP1B(L9V) with Gppnhp

The structure of Ras-Related Protein RAP1B(L9V) with Gppnhp, PDB code: 3x1y was solved by H.Noguchi, T.Ikegami, S.Y.Park, J.R.H.Tame, S.Unzai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.42 / 1.17
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	43.600, 52.600, 60.720, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 21.9

The structure of Ras-Related Protein RAP1B(L9V) with Gppnhp also contains other interesting chemical elements:

Cadmium

(Cd)

1 atom

The binding sites of Magnesium atom in the Ras-Related Protein RAP1B(L9V) with Gppnhp (pdb code 3x1y). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Ras-Related Protein RAP1B(L9V) with Gppnhp, PDB code: 3x1y:

Magnesium binding site 1 out of 1 in the Ras-Related Protein RAP1B(L9V) with Gppnhp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ras-Related Protein RAP1B(L9V) with Gppnhp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:5.1 occ:1.00 O1G A:GNP201 2.0 7.5 1.0 O A:HOH302 2.0 6.9 1.0 O1B A:GNP201 2.0 4.5 1.0 O A:HOH303 2.1 6.3 1.0 O A:HOH301 2.1 6.1 1.0 OG A:SER17 2.1 5.4 1.0 CB A:SER17 3.2 4.8 1.0 PB A:GNP201 3.2 4.9 1.0 PG A:GNP201 3.3 7.4 1.0 N3B A:GNP201 3.5 6.3 1.0 N A:SER17 3.9 4.3 1.0 O A:HOH305 4.1 14.1 1.0 OD2 A:ASP57 4.1 7.2 1.0 O2A A:GNP201 4.1 6.8 1.0 CA A:SER17 4.1 4.4 1.0 OD1 A:ASP57 4.1 6.8 1.0 O2G A:GNP201 4.2 8.1 1.0 O A:HOH304 4.2 10.3 1.0 OD1 A:ASP33 4.3 17.3 1.0 O3A A:GNP201 4.3 5.6 1.0 O2B A:GNP201 4.3 5.0 1.0 O3G A:GNP201 4.3 9.5 1.0 O A:PRO34 4.5 14.6 1.0 CG A:ASP57 4.5 7.0 1.0 PA A:GNP201 4.6 5.7 1.0 O A:THR58 4.6 6.7 1.0 CD A:PRO34 4.8 12.1 1.0 O1A A:GNP201 4.8 6.3 1.0 CB A:LYS16 4.9 4.6 1.0 CE A:LYS16 5.0 6.4 1.0

H.Noguchi, T.Ikegami, A.Nagadoi, Y.O.Kamatari, S.Y.Park, J.R.Tame, S.Unzai. The Structure and Conformational Switching of RAP1B Biochem.Biophys.Res.Commun. V. 462 46 2015.
ISSN: ISSN 0006-291X
PubMed: 25935485
DOI: 10.1016/J.BBRC.2015.04.103