Magnesium in PDB 1yzt: Gppnhp-Bound RAB21 Gtpase at 2.05 A Resolution

The structure of Gppnhp-Bound RAB21 Gtpase at 2.05 A Resolution, PDB code: 1yzt was solved by S.Eathiraj, X.Pan, C.Ritacco, D.G.Lambright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	12.00 / 2.05
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	130.357, 36.567, 86.666, 90.00, 113.40, 90.00
R / Rfree (%)	21 / 28.6

The binding sites of Magnesium atom in the Gppnhp-Bound RAB21 Gtpase at 2.05 A Resolution (pdb code 1yzt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Gppnhp-Bound RAB21 Gtpase at 2.05 A Resolution, PDB code: 1yzt:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Gppnhp-Bound RAB21 Gtpase at 2.05 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Gppnhp-Bound RAB21 Gtpase at 2.05 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg700 b:26.1 occ:1.00 O2B A:GNP701 2.0 20.4 1.0 OG1 A:THR51 2.0 22.6 1.0 O A:HOH704 2.0 16.2 1.0 O A:HOH716 2.0 20.8 1.0 OG1 A:THR33 2.0 18.8 1.0 O2G A:GNP701 2.1 19.1 1.0 CB A:THR51 3.1 25.4 1.0 CB A:THR33 3.2 19.0 1.0 PB A:GNP701 3.3 21.6 1.0 PG A:GNP701 3.3 21.9 1.0 N3B A:GNP701 3.6 19.5 1.0 N A:THR51 3.8 26.4 1.0 N A:THR33 3.9 18.9 1.0 OD2 A:ASP74 4.0 21.2 1.0 O A:HOH767 4.0 29.1 1.0 CA A:THR51 4.1 26.3 1.0 CA A:THR33 4.1 18.8 1.0 OD1 A:ASP74 4.1 19.9 1.0 CG2 A:THR51 4.2 25.2 1.0 CG2 A:THR33 4.2 19.5 1.0 O3G A:GNP701 4.2 19.9 1.0 O2A A:GNP701 4.3 19.0 1.0 O3A A:GNP701 4.3 19.5 1.0 O1B A:GNP701 4.3 16.9 1.0 O1G A:GNP701 4.4 22.9 1.0 O A:THR75 4.4 25.8 1.0 O A:ILE49 4.4 28.9 1.0 CG A:ASP74 4.5 22.1 1.0 PA A:GNP701 4.6 20.6 1.0 O1A A:GNP701 4.8 20.4 1.0 CE A:LYS32 4.8 17.0 1.0 C A:THR50 4.8 28.3 1.0 CB A:LYS32 4.9 19.6 1.0

Magnesium binding site 2 out of 2 in the Gppnhp-Bound RAB21 Gtpase at 2.05 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Gppnhp-Bound RAB21 Gtpase at 2.05 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg800 b:24.1 occ:1.00 O2G B:GNP801 1.9 19.5 1.0 O B:HOH803 2.0 15.6 1.0 O B:HOH870 2.1 21.4 1.0 OG1 B:THR33 2.1 19.3 1.0 O2B B:GNP801 2.1 22.7 1.0 OG1 B:THR51 2.1 24.8 1.0 CB B:THR51 3.1 27.0 1.0 CB B:THR33 3.2 19.9 1.0 PG B:GNP801 3.2 22.3 1.0 PB B:GNP801 3.3 22.3 1.0 N3B B:GNP801 3.5 19.9 1.0 N B:THR51 3.8 28.3 1.0 OD2 B:ASP74 3.9 22.2 1.0 N B:THR33 3.9 20.0 1.0 CA B:THR51 4.0 27.7 1.0 O B:HOH902 4.1 35.9 1.0 O3G B:GNP801 4.1 20.6 1.0 CA B:THR33 4.1 20.1 1.0 OD1 B:ASP74 4.1 22.3 1.0 CG2 B:THR33 4.2 20.5 1.0 CG2 B:THR51 4.2 27.6 1.0 O B:THR75 4.3 23.8 1.0 O1B B:GNP801 4.3 18.9 1.0 O1G B:GNP801 4.4 21.3 1.0 O2A B:GNP801 4.4 23.5 1.0 O3A B:GNP801 4.4 20.2 1.0 CG B:ASP74 4.4 22.8 1.0 O B:ILE49 4.5 30.1 1.0 PA B:GNP801 4.7 23.1 1.0 CE B:LYS32 4.8 19.7 1.0 C B:THR50 4.8 29.2 1.0 CB B:LYS32 4.9 20.1 1.0 O1A B:GNP801 4.9 21.4 1.0

S.Eathiraj, X.Pan, C.Ritacco, D.G.Lambright. Structural Basis of Family-Wide Rab Gtpase Recognition By Rabenosyn-5. Nature V. 436 415 2005.
ISSN: ISSN 0028-0836
PubMed: 16034420
DOI: 10.1038/NATURE03798