Magnesium in PDB 4dkx: Crystal Structure of the Rab 6A'(Q72L)

The structure of Crystal Structure of the Rab 6A'(Q72L), PDB code: 4dkx was solved by H.H.Park, Y.-C.Shin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.39 / 1.90
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	36.838, 96.780, 109.997, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 25

The binding sites of Magnesium atom in the Crystal Structure of the Rab 6A'(Q72L) (pdb code 4dkx). 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 Rab 6A'(Q72L), PDB code: 4dkx:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Rab 6A'(Q72L)


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 Rab 6A'(Q72L) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:30.0 occ:1.00 O A:HOH518 2.2 30.0 1.0 O A:HOH519 2.3 30.0 1.0 O2B A:GDP301 2.3 28.6 1.0 OG1 A:THR27 2.4 23.5 1.0 O A:HOH520 2.5 30.0 1.0 PB A:GDP301 3.4 24.0 1.0 CB A:THR27 3.4 21.5 1.0 O1B A:GDP301 3.6 26.6 1.0 OD2 A:ASP68 4.1 31.0 1.0 N A:THR27 4.1 19.1 1.0 O2A A:GDP301 4.2 30.6 1.0 O A:HOH443 4.3 43.0 1.0 CA A:THR27 4.4 20.6 1.0 O A:HOH414 4.4 30.3 1.0 O3B A:GDP301 4.4 26.9 1.0 OD1 A:ASP68 4.4 24.8 1.0 O3A A:GDP301 4.4 29.2 1.0 CG2 A:THR27 4.4 22.5 1.0 CG A:ASP68 4.7 30.1 1.0 PA A:GDP301 4.7 24.3 1.0 CB A:ALA70 4.7 38.1 1.0 O A:THR69 4.8 34.4 1.0 O A:HOH454 4.9 42.3 1.0 CA A:ALA70 4.9 38.6 1.0 O1A A:GDP301 4.9 25.0 1.0 N A:ALA70 5.0 37.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Rab 6A'(Q72L)


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 Rab 6A'(Q72L) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:30.0 occ:1.00 O B:HOH525 2.1 30.0 1.0 OG1 B:THR27 2.3 21.1 1.0 O3B B:GDP302 2.3 26.9 1.0 O B:HOH526 2.3 30.0 1.0 O B:HOH527 2.3 30.0 1.0 PB B:GDP302 3.3 24.0 1.0 CB B:THR27 3.4 20.4 1.0 O1B B:GDP302 3.5 26.6 1.0 N B:THR27 4.2 18.3 1.0 O2A B:GDP302 4.2 30.6 1.0 OD2 B:ASP68 4.3 28.1 1.0 O B:HOH439 4.3 37.2 1.0 CA B:THR27 4.4 18.4 1.0 O2B B:GDP302 4.4 28.6 1.0 O3A B:GDP302 4.4 29.2 1.0 O B:THR69 4.4 37.3 1.0 OD1 B:ASP68 4.5 26.5 1.0 CG2 B:THR27 4.5 22.4 1.0 O B:HOH448 4.5 38.8 1.0 O B:HOH450 4.5 52.5 1.0 PA B:GDP302 4.7 24.3 1.0 CG B:ASP68 4.8 26.7 1.0 CB B:ALA70 4.9 38.1 1.0 O B:HOH480 4.9 32.1 1.0 O1A B:GDP302 5.0 25.0 1.0

Y.-C.Shin, J.H.Yoon, T.-H.Jang, S.Y.Kim, W.D.Heo, I.So, J.-H.Jeon, H.H.Park. Crystal Structure of RAB6A'(Q72L) Mutant Reveals Unexpected Gdp/MG2+ Binding with Opened Gtp-Binding Domain Biochem.Biophys.Res.Commun. V. 424 269 2012.
ISSN: ISSN 0006-291X
PubMed: 22750005
DOI: 10.1016/J.BBRC.2012.06.102