Magnesium in PDB 1z0a: Gdp-Bound RAB2A Gtpase

The structure of Gdp-Bound RAB2A Gtpase, PDB code: 1z0a 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)	10.00 / 2.12
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	98.773, 128.473, 68.236, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 27.9

The binding sites of Magnesium atom in the Gdp-Bound RAB2A Gtpase (pdb code 1z0a). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Gdp-Bound RAB2A Gtpase, PDB code: 1z0a:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Gdp-Bound RAB2A 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 RAB2A Gtpase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1201 b:83.1 occ:1.00 OG A:SER20 2.0 37.3 1.0 O2B A:GDP1200 2.3 35.8 1.0 O A:HOH1217 2.9 50.2 1.0 CB A:ALA63 3.0 36.8 1.0 OD2 A:ASP61 3.0 41.7 1.0 CB A:SER20 3.3 31.2 1.0 OD1 A:ASP61 3.5 35.1 1.0 PB A:GDP1200 3.5 35.6 1.0 CG A:ASP61 3.7 37.3 1.0 O3B A:GDP1200 3.7 32.3 1.0 N A:SER20 3.8 30.4 1.0 O D:HOH4251 4.0 63.9 1.0 O A:HOH1372 4.0 81.5 1.0 CD1 A:LEU37 4.0 71.5 1.0 O A:HOH1357 4.0 66.5 1.0 CA A:SER20 4.1 32.3 1.0 CA A:ALA63 4.2 36.9 1.0 O1B A:GDP1200 4.3 31.5 1.0 O2A A:GDP1200 4.5 36.1 1.0 CE A:LYS19 4.6 27.4 1.0 CB A:LYS19 4.6 30.1 1.0 O3A A:GDP1200 4.6 34.5 1.0 N A:ALA63 4.6 34.7 1.0 CD2 A:LEU37 4.7 60.8 1.0 CG A:LEU37 4.7 60.6 1.0 C A:LYS19 4.8 30.3 1.0 PA A:GDP1200 4.9 34.8 1.0 O1A A:GDP1200 4.9 36.5 1.0 NZ A:LYS19 5.0 27.5 1.0

Magnesium binding site 2 out of 4 in the Gdp-Bound RAB2A 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 RAB2A Gtpase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2201 b:66.6 occ:1.00 O B:HOH2209 2.0 44.8 1.0 OG B:SER20 2.2 39.8 1.0 O B:HOH2256 2.3 62.1 1.0 O B:HOH2283 2.4 74.5 1.0 O2B B:GDP2200 2.4 41.9 1.0 CB B:SER20 3.5 35.0 1.0 PB B:GDP2200 3.6 43.4 1.0 O3B B:GDP2200 3.6 41.3 1.0 O B:HOH2279 3.8 68.5 1.0 OD2 B:ASP61 3.9 46.1 1.0 O B:HOH2276 4.2 57.5 1.0 N B:SER20 4.2 33.3 1.0 O2A B:GDP2200 4.4 43.0 1.0 OD1 B:ASP61 4.4 39.7 1.0 N B:GLY64 4.4 55.1 1.0 O B:THR62 4.5 42.0 1.0 CA B:SER20 4.5 34.3 1.0 O1B B:GDP2200 4.5 41.8 1.0 O B:HOH2266 4.5 77.1 1.0 CA B:ALA63 4.6 48.8 1.0 CG B:ASP61 4.6 37.8 1.0 O3A B:GDP2200 4.7 40.6 1.0 OD1 B:ASP36 4.8 64.6 1.0 PA B:GDP2200 4.9 38.3 1.0 CE B:LYS19 4.9 33.6 1.0

Magnesium binding site 3 out of 4 in the Gdp-Bound RAB2A Gtpase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Gdp-Bound RAB2A Gtpase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg3201 b:51.3 occ:1.00 O2B C:GDP3200 2.4 30.2 1.0 OD2 C:ASP61 2.7 35.3 1.0 CB C:ALA63 3.0 34.1 1.0 O C:HOH3227 3.1 41.7 1.0 OD1 C:ASP61 3.2 35.3 1.0 CG C:ASP61 3.3 29.8 1.0 PB C:GDP3200 3.5 33.6 1.0 O3B C:GDP3200 3.5 26.5 1.0 CD2 C:LEU37 3.8 52.8 1.0 CE C:LYS19 3.8 26.4 1.0 NZ C:LYS19 4.0 22.8 1.0 CB C:SER20 4.0 32.2 1.0 O1B C:GDP3200 4.0 29.8 1.0 CD1 C:LEU37 4.0 53.8 1.0 N C:SER20 4.1 28.0 1.0 CB C:LYS19 4.1 25.8 1.0 CA C:ALA63 4.4 36.6 1.0 OE2 C:GLU66 4.5 42.2 1.0 CG C:LEU37 4.5 50.2 1.0 CA C:SER20 4.5 29.0 1.0 O C:HOH3377 4.6 76.5 1.0 N C:ALA63 4.7 33.2 1.0 CB C:ASP61 4.8 27.0 1.0 C C:LYS19 4.8 26.9 1.0 O3A C:GDP3200 4.9 30.7 1.0 CD C:LYS19 4.9 19.9 1.0 CG C:LYS19 4.9 22.0 1.0 CA C:LYS19 5.0 24.0 1.0

Magnesium binding site 4 out of 4 in the Gdp-Bound RAB2A Gtpase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Gdp-Bound RAB2A Gtpase within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg4201 b:83.1 occ:1.00 O2B D:GDP4200 2.1 35.8 1.0 O D:HOH4292 2.1 80.5 1.0 PB D:GDP4200 3.3 35.6 1.0 CB D:SER20 3.4 48.6 1.0 O3B D:GDP4200 3.5 32.3 1.0 OD2 D:ASP61 3.7 42.1 1.0 O2A D:GDP4200 4.1 36.1 1.0 O D:HOH4230 4.1 60.3 1.0 OG D:SER20 4.2 54.9 1.0 N D:SER20 4.2 46.3 1.0 O1B D:GDP4200 4.2 31.5 1.0 CA D:SER20 4.3 48.2 1.0 O3A D:GDP4200 4.4 34.5 1.0 CG D:ASP61 4.6 41.6 1.0 OD1 D:ASP61 4.6 42.0 1.0 PA D:GDP4200 4.7 34.8 1.0 CA D:ALA63 4.7 53.1 1.0 O1A D:GDP4200 4.9 36.5 1.0 O D:THR62 5.0 46.9 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