Magnesium in PDB 3x1z: Ras-Related Protein RAP1B(T65A) with Gppnhp

The structure of Ras-Related Protein RAP1B(T65A) with Gppnhp, PDB code: 3x1z 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)	33.96 / 1.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	37.420, 59.040, 68.070, 90.00, 93.68, 90.00
R / Rfree (%)	14.5 / 17.2

The binding sites of Magnesium atom in the Ras-Related Protein RAP1B(T65A) with Gppnhp (pdb code 3x1z). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Ras-Related Protein RAP1B(T65A) with Gppnhp, PDB code: 3x1z:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Ras-Related Protein RAP1B(T65A) 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(T65A) with Gppnhp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:6.2 occ:1.00 O1G A:GNP201 2.0 7.7 1.0 O1B A:GNP201 2.0 5.5 1.0 OG1 A:THR35 2.1 7.5 1.0 OG A:SER17 2.1 7.1 1.0 O A:HOH309 2.1 7.3 1.0 O A:HOH310 2.1 7.2 1.0 CB A:THR35 3.1 7.7 1.0 CB A:SER17 3.2 7.0 1.0 PG A:GNP201 3.2 7.2 1.0 PB A:GNP201 3.2 5.7 1.0 N3B A:GNP201 3.4 6.6 1.0 N A:THR35 3.8 7.8 1.0 N A:SER17 3.9 5.8 1.0 CA A:THR35 4.0 7.7 1.0 CA A:SER17 4.1 6.0 1.0 O3G A:GNP201 4.1 9.0 1.0 OD2 A:ASP57 4.1 10.0 1.0 O2A A:GNP201 4.1 7.0 1.0 CG2 A:THR35 4.1 8.4 1.0 OD1 A:ASP57 4.2 8.9 1.0 O A:HOH321 4.3 15.8 1.0 O2B A:GNP201 4.3 6.1 1.0 O3A A:GNP201 4.3 5.8 1.0 O2G A:GNP201 4.3 8.2 1.0 O A:THR58 4.5 8.0 1.0 O A:ASP33 4.5 8.9 1.0 CG A:ASP57 4.5 8.7 1.0 PA A:GNP201 4.5 6.4 1.0 O1A A:GNP201 4.6 7.3 1.0 CB A:LYS16 4.8 5.9 1.0 C A:PRO34 4.8 8.6 1.0 CE A:LYS16 4.9 7.6 1.0 C A:LYS16 4.9 5.0 1.0

Magnesium binding site 2 out of 2 in the Ras-Related Protein RAP1B(T65A) with Gppnhp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ras-Related Protein RAP1B(T65A) with Gppnhp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:9.5 occ:1.00 O3G B:GNP201 2.0 10.4 1.0 O2B B:GNP201 2.0 9.6 1.0 OG1 B:THR35 2.0 11.4 1.0 OG B:SER17 2.1 10.3 1.0 O B:HOH309 2.1 10.5 1.0 O B:HOH305 2.1 11.5 1.0 CB B:THR35 3.0 11.1 1.0 CB B:SER17 3.1 10.1 1.0 PB B:GNP201 3.2 8.9 1.0 PG B:GNP201 3.2 10.1 1.0 N3B B:GNP201 3.4 9.3 1.0 N B:SER17 3.8 9.7 1.0 N B:THR35 3.8 11.8 1.0 CA B:SER17 4.0 10.1 1.0 CA B:THR35 4.1 11.8 1.0 CG2 B:THR35 4.1 12.3 1.0 OD2 B:ASP57 4.1 12.7 1.0 O1A B:GNP201 4.1 12.1 1.0 OD1 B:ASP57 4.2 12.1 1.0 O2G B:GNP201 4.2 11.3 1.0 O1B B:GNP201 4.2 9.8 1.0 O1G B:GNP201 4.3 12.3 1.0 O3A B:GNP201 4.3 10.2 1.0 O B:HOH311 4.3 19.6 1.0 O B:THR58 4.4 10.1 1.0 PA B:GNP201 4.5 11.0 1.0 CG B:ASP57 4.5 12.0 1.0 O B:ASP33 4.5 16.4 1.0 O2A B:GNP201 4.6 10.6 1.0 CB B:LYS16 4.7 9.6 1.0 C B:PRO34 4.8 14.0 1.0 C B:LYS16 4.9 9.0 1.0 CE B:LYS16 5.0 10.4 1.0 NZ B:LYS16 5.0 11.0 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