Magnesium in PDB 1yzu: Gppnhp-Bound RAB21 Gtpase at 2.50 A Resolution

The structure of Gppnhp-Bound RAB21 Gtpase at 2.50 A Resolution, PDB code: 1yzu 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)	16.00 / 2.50
Space group	I 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	77.834, 99.719, 105.760, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 29.3

The binding sites of Magnesium atom in the Gppnhp-Bound RAB21 Gtpase at 2.50 A Resolution (pdb code 1yzu). 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 2.50 A Resolution, PDB code: 1yzu:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Gppnhp-Bound RAB21 Gtpase at 2.50 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 2.50 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg300 b:41.4 occ:1.00 O2G A:GNP301 1.8 29.9 1.0 O2B A:GNP301 1.9 33.0 1.0 O A:HOH305 2.0 25.8 1.0 O A:HOH320 2.1 30.6 1.0 OG1 A:THR51 2.1 39.3 1.0 OG1 A:THR33 2.2 29.1 1.0 PG A:GNP301 3.0 34.5 1.0 CB A:THR51 3.2 41.4 1.0 PB A:GNP301 3.2 31.3 1.0 CB A:THR33 3.2 30.3 1.0 N3B A:GNP301 3.3 32.6 1.0 O3G A:GNP301 3.9 34.7 1.0 N A:THR51 4.0 40.5 1.0 O A:HOH332 4.0 39.7 1.0 OD2 A:ASP74 4.0 30.4 1.0 N A:THR33 4.1 30.7 1.0 CG2 A:THR51 4.2 41.6 1.0 O3A A:GNP301 4.2 31.0 1.0 CA A:THR51 4.2 41.2 1.0 O1G A:GNP301 4.2 29.7 1.0 CG2 A:THR33 4.2 29.4 1.0 O1B A:GNP301 4.2 30.0 1.0 CA A:THR33 4.2 30.2 1.0 O2A A:GNP301 4.2 32.0 1.0 OD1 A:ASP74 4.3 35.9 1.0 O A:ILE49 4.4 35.7 1.0 PA A:GNP301 4.5 30.1 1.0 CG A:ASP74 4.6 35.5 1.0 O1A A:GNP301 4.6 27.6 1.0 CE A:LYS32 4.7 31.2 1.0 O A:HOH375 4.8 41.8 1.0 O A:THR75 4.8 43.0 1.0 C A:THR50 4.9 39.2 1.0 CA A:THR50 4.9 37.7 1.0 CB A:LYS32 5.0 31.8 1.0

Magnesium binding site 2 out of 2 in the Gppnhp-Bound RAB21 Gtpase at 2.50 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 2.50 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg400 b:34.4 occ:1.00 O2G B:GNP401 1.8 36.5 1.0 OG1 B:THR51 1.9 45.4 1.0 OG1 B:THR33 2.0 27.6 1.0 O2B B:GNP401 2.0 34.8 1.0 O B:HOH407 2.1 19.6 1.0 O B:HOH404 2.2 21.1 1.0 CB B:THR51 3.0 45.1 1.0 CB B:THR33 3.1 29.7 1.0 PG B:GNP401 3.1 39.5 1.0 PB B:GNP401 3.2 31.6 1.0 N3B B:GNP401 3.5 36.2 1.0 N B:THR51 3.5 44.2 1.0 CA B:THR51 3.8 44.9 1.0 OD2 B:ASP74 3.9 41.9 1.0 N B:THR33 4.0 29.5 1.0 CG2 B:THR33 4.1 29.0 1.0 O3G B:GNP401 4.1 40.1 1.0 CA B:THR33 4.1 29.6 1.0 O B:HOH425 4.1 37.5 1.0 CG2 B:THR51 4.1 44.9 1.0 O2A B:GNP401 4.2 26.5 1.0 OD1 B:ASP74 4.2 38.9 1.0 O B:ILE49 4.2 40.2 1.0 O3A B:GNP401 4.2 30.5 1.0 O1G B:GNP401 4.2 39.5 1.0 O1B B:GNP401 4.3 35.0 1.0 C B:THR50 4.4 43.1 1.0 CG B:ASP74 4.5 41.1 1.0 PA B:GNP401 4.5 28.8 1.0 CA B:THR50 4.7 42.0 1.0 O1A B:GNP401 4.7 26.9 1.0 CE B:LYS32 4.9 26.8 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