Magnesium in PDB 6vij: Crystal Structure of Mouse RABL3 in Complex with Gdp

The structure of Crystal Structure of Mouse RABL3 in Complex with Gdp, PDB code: 6vij was solved by L.Su, D.R.Tomchick, B.Beutler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.02 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.910, 78.203, 118.532, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 22.7

The binding sites of Magnesium atom in the Crystal Structure of Mouse RABL3 in Complex with Gdp (pdb code 6vij). 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 Mouse RABL3 in Complex with Gdp, PDB code: 6vij:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Mouse RABL3 in Complex with Gdp


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 Mouse RABL3 in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:15.1 occ:1.00 O1B B:GDP302 2.0 14.1 1.0 O B:HOH410 2.0 14.0 1.0 O B:HOH423 2.0 17.6 1.0 OG B:SER20 2.1 14.7 1.0 O B:HOH412 2.1 18.2 1.0 OG1 B:THR38 2.2 21.1 1.0 CB B:SER20 3.1 13.9 1.0 CB B:THR38 3.2 28.7 1.0 PB B:GDP302 3.2 15.4 1.0 O3B B:GDP302 3.5 17.9 1.0 N B:SER20 3.9 11.0 1.0 O1A B:GDP302 4.0 18.6 1.0 CA B:SER20 4.1 11.6 1.0 N B:THR38 4.1 31.0 1.0 CG2 B:THR38 4.2 23.5 1.0 OD2 B:ASP66 4.2 18.1 1.0 O2B B:GDP302 4.2 13.2 1.0 O B:SER36 4.2 27.0 1.0 O B:HOH458 4.3 23.7 1.0 CA B:THR38 4.3 32.4 1.0 O3A B:GDP302 4.3 15.0 1.0 O B:HOH465 4.4 36.0 1.0 PA B:GDP302 4.5 18.2 1.0 O2A B:GDP302 4.6 13.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Mouse RABL3 in Complex with Gdp


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 Mouse RABL3 in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:16.9 occ:1.00 O2B A:GDP302 2.0 13.8 1.0 O A:HOH403 2.0 17.2 1.0 OG A:SER20 2.0 14.3 1.0 OG1 A:THR38 2.2 25.7 1.0 O A:HOH405 2.2 24.0 1.0 O A:HOH417 2.3 15.2 1.0 CB A:SER20 3.2 13.9 1.0 PB A:GDP302 3.2 16.2 1.0 CB A:THR38 3.2 24.9 1.0 O3B A:GDP302 3.4 17.4 1.0 N A:SER20 3.9 14.2 1.0 O1A A:GDP302 4.1 15.1 1.0 CA A:SER20 4.1 15.1 1.0 OD2 A:ASP66 4.1 19.5 1.0 CG2 A:THR38 4.2 22.5 1.0 N A:THR38 4.2 41.7 1.0 O1B A:GDP302 4.2 13.6 1.0 O A:HOH436 4.2 18.6 1.0 O3A A:GDP302 4.3 16.7 1.0 CA A:THR38 4.3 36.2 1.0 O A:SER36 4.4 39.6 1.0 O A:HOH442 4.5 34.4 1.0 PA A:GDP302 4.5 15.5 1.0 O2A A:GDP302 4.8 12.1 1.0 NZ A:LYS19 4.9 13.3 1.0 O A:HOH452 4.9 18.8 1.0

X.Zhong, L.Su, Y.Yang, E.Nair-Gill, M.Tang, P.Anderton, X.Li, J.Wang, X.Zhan, D.R.Tomchick, C.A.Brautigam, E.M.Y.Moresco, J.H.Choi, B.Beutler. Genetic and Structural Studies of RABL3 Reveal An Essential Role in Lymphoid Development and Function. Proc.Natl.Acad.Sci.Usa 2020.
ISSN: ESSN 1091-6490
PubMed: 32220963
DOI: 10.1073/PNAS.2000703117