Magnesium in PDB 1z0d: Gdp-Bound RAB5C Gtpase

The structure of Gdp-Bound RAB5C Gtpase, PDB code: 1z0d 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)	8.00 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.401, 70.931, 137.610, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 24.7

The binding sites of Magnesium atom in the Gdp-Bound RAB5C Gtpase (pdb code 1z0d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Gdp-Bound RAB5C Gtpase, PDB code: 1z0d:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Gdp-Bound RAB5C Gtpase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Gdp-Bound RAB5C Gtpase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:18.9 occ:1.00 OG A:SER35 2.2 16.0 1.0 O2B A:GDP700 2.2 15.1 1.0 O A:HOH724 2.2 28.1 1.0 O A:HOH706 2.2 16.0 1.0 O A:HOH718 2.2 20.6 1.0 O A:HOH709 2.2 14.0 1.0 CB A:SER35 3.3 16.0 1.0 PB A:GDP700 3.4 16.4 1.0 O3B A:GDP700 3.5 14.9 1.0 O2A A:GDP700 4.0 19.9 1.0 N A:SER35 4.1 15.9 1.0 OD2 A:ASP76 4.2 24.5 1.0 CA A:SER35 4.3 16.2 1.0 OD1 A:ASP76 4.4 24.4 1.0 O A:HOH734 4.4 25.9 1.0 O1B A:GDP700 4.4 14.7 1.0 O4 A:PO4600 4.4 51.2 1.0 O3A A:GDP700 4.4 17.0 1.0 O A:HOH768 4.5 36.5 1.0 O A:THR77 4.5 24.6 1.0 O A:GLU51 4.5 27.3 1.0 PA A:GDP700 4.6 18.1 1.0 CB A:ALA78 4.6 24.2 1.0 O A:HOH907 4.7 52.6 1.0 CG A:ASP76 4.7 24.2 1.0 O1A A:GDP700 4.7 20.1 1.0 O A:HOH863 4.8 54.5 1.0 CA A:SER52 4.9 25.6 1.0

Magnesium binding site 2 out of 2 in the Gdp-Bound RAB5C Gtpase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Gdp-Bound RAB5C Gtpase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg800 b:26.6 occ:1.00 O C:HOH923 2.0 25.0 1.0 O C:HOH916 2.0 30.2 1.0 O C:HOH907 2.0 16.4 1.0 O C:HOH913 2.1 26.4 1.0 O2B C:GDP900 2.1 20.8 1.0 OG C:SER35 2.3 19.1 1.0 PB C:GDP900 3.3 21.3 1.0 O3B C:GDP900 3.4 21.3 1.0 CB C:SER35 3.4 18.6 1.0 O C:SER52 4.0 41.6 1.0 N C:SER35 4.1 18.1 1.0 O C:THR77 4.2 23.2 1.0 O2A C:GDP900 4.2 21.6 1.0 OD2 C:ASP76 4.2 21.7 1.0 O1B C:GDP900 4.3 21.3 1.0 O C:HOH906 4.3 30.3 1.0 OD1 C:ASP76 4.3 21.6 1.0 CA C:SER35 4.3 18.6 1.0 O C:ALA78 4.4 26.0 1.0 O3A C:GDP900 4.4 21.6 1.0 O C:HOH1029 4.5 35.3 1.0 CB C:SER52 4.6 41.8 1.0 PA C:GDP900 4.7 21.5 1.0 CG C:ASP76 4.7 21.8 1.0 CA C:ALA78 4.8 25.2 1.0 O1A C:GDP900 4.8 21.6 1.0 CE C:LYS34 4.9 16.9 1.0 C C:SER52 4.9 41.6 1.0 O C:HOH925 4.9 24.8 1.0 C C:ALA78 5.0 25.7 1.0 NZ C:LYS34 5.0 17.0 1.0 CB C:LYS34 5.0 18.0 1.0 C C:THR77 5.0 23.4 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