Magnesium in PDB 2gil: Structure of the Extremely Slow Gtpase RAB6A in the Gtp Bound Form at 1.8 Resolution

The structure of Structure of the Extremely Slow Gtpase RAB6A in the Gtp Bound Form at 1.8 Resolution, PDB code: 2gil was solved by T.Bergbrede, O.Pylypenko, A.Rak, K.Alexandrov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.05 / 1.82
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.008, 124.853, 66.162, 90.00, 107.57, 90.00
R / Rfree (%)	20.5 / 27.7

The binding sites of Magnesium atom in the Structure of the Extremely Slow Gtpase RAB6A in the Gtp Bound Form at 1.8 Resolution (pdb code 2gil). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of the Extremely Slow Gtpase RAB6A in the Gtp Bound Form at 1.8 Resolution, PDB code: 2gil:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of the Extremely Slow Gtpase RAB6A in the Gtp Bound Form at 1.8 Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Extremely Slow Gtpase RAB6A in the Gtp Bound Form at 1.8 Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1201 b:16.1 occ:1.00 O2G A:GTP1200 1.9 24.0 1.0 O2B A:GTP1200 2.0 14.2 1.0 OG1 A:THR27 2.0 16.2 1.0 O A:HOH1304 2.1 15.6 1.0 O A:HOH1305 2.1 25.1 1.0 OG1 A:THR45 2.2 21.7 1.0 PG A:GTP1200 3.1 25.7 1.0 CB A:THR27 3.1 14.8 1.0 CB A:THR45 3.2 24.9 1.0 PB A:GTP1200 3.3 17.8 1.0 O3B A:GTP1200 3.5 19.9 1.0 O3G A:GTP1200 3.8 28.2 1.0 N A:THR27 3.9 15.5 1.0 N A:THR45 3.9 25.6 1.0 OD2 A:ASP68 4.0 22.5 1.0 OD1 A:ASP68 4.0 21.5 1.0 CA A:THR27 4.1 15.3 1.0 CA A:THR45 4.1 24.8 1.0 O1B A:GTP1200 4.2 16.7 1.0 CG2 A:THR27 4.2 16.7 1.0 O2A A:GTP1200 4.2 20.6 1.0 O1G A:GTP1200 4.3 26.2 1.0 CG2 A:THR45 4.3 21.5 1.0 CG A:ASP68 4.4 22.2 1.0 O3A A:GTP1200 4.4 19.4 1.0 O A:THR69 4.5 27.3 1.0 PA A:GTP1200 4.6 19.8 1.0 CB A:LYS26 4.7 16.6 1.0 O A:HOH1240 4.7 34.1 1.0 O A:GLN43 4.7 30.8 1.0 O1A A:GTP1200 4.7 19.2 1.0 NZ A:LYS26 4.8 18.1 1.0 C A:ALA44 4.9 26.5 1.0 C A:LYS26 4.9 15.8 1.0

Magnesium binding site 2 out of 4 in the Structure of the Extremely Slow Gtpase RAB6A in the Gtp Bound Form at 1.8 Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Extremely Slow Gtpase RAB6A in the Gtp Bound Form at 1.8 Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2201 b:16.1 occ:1.00 O2G B:GTP2200 2.0 14.4 1.0 O B:HOH2336 2.0 13.9 1.0 O2B B:GTP2200 2.1 16.0 1.0 OG1 B:THR27 2.1 13.5 1.0 O B:HOH2335 2.1 16.1 1.0 OG1 B:THR45 2.1 14.9 1.0 CB B:THR45 3.2 15.9 1.0 CB B:THR27 3.2 14.1 1.0 PB B:GTP2200 3.2 15.7 1.0 PG B:GTP2200 3.2 13.7 1.0 O3B B:GTP2200 3.4 13.2 1.0 N B:THR45 3.8 15.6 1.0 N B:THR27 3.9 13.4 1.0 CA B:THR45 4.0 15.9 1.0 CA B:THR27 4.1 13.1 1.0 O2A B:GTP2200 4.1 16.0 1.0 O3G B:GTP2200 4.1 16.7 1.0 O B:HOH2299 4.2 24.1 1.0 OD2 B:ASP68 4.2 19.2 1.0 O1G B:GTP2200 4.2 16.1 1.0 OD1 B:ASP68 4.3 18.2 1.0 CG2 B:THR27 4.3 12.1 1.0 O1B B:GTP2200 4.3 14.2 1.0 CG2 B:THR45 4.3 15.7 1.0 O3A B:GTP2200 4.3 16.4 1.0 O B:GLN43 4.5 17.8 1.0 O B:THR69 4.5 20.3 1.0 PA B:GTP2200 4.6 15.3 1.0 CG B:ASP68 4.6 20.2 1.0 CE B:LYS26 4.7 16.1 1.0 O1A B:GTP2200 4.7 15.6 1.0 CB B:LYS26 4.8 14.0 1.0 C B:ALA44 4.8 16.1 1.0

Magnesium binding site 3 out of 4 in the Structure of the Extremely Slow Gtpase RAB6A in the Gtp Bound Form at 1.8 Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Extremely Slow Gtpase RAB6A in the Gtp Bound Form at 1.8 Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg3201 b:19.6 occ:1.00 O2G C:GTP3200 1.9 22.4 1.0 O C:HOH3332 2.0 21.7 1.0 OG1 C:THR27 2.0 12.1 1.0 O2B C:GTP3200 2.1 16.0 1.0 OG1 C:THR45 2.2 22.2 1.0 O C:HOH3331 2.2 16.8 1.0 PG C:GTP3200 3.1 24.4 1.0 CB C:THR27 3.2 13.2 1.0 CB C:THR45 3.2 25.0 1.0 PB C:GTP3200 3.3 17.0 1.0 O3B C:GTP3200 3.5 20.6 1.0 N C:THR45 3.8 26.3 1.0 O3G C:GTP3200 3.9 26.6 1.0 N C:THR27 3.9 13.3 1.0 OD2 C:ASP68 4.0 17.7 1.0 CA C:THR45 4.1 25.1 1.0 OD1 C:ASP68 4.1 19.5 1.0 CA C:THR27 4.1 14.1 1.0 CG2 C:THR27 4.2 16.6 1.0 O2A C:GTP3200 4.2 16.8 1.0 O1G C:GTP3200 4.2 26.9 1.0 O C:HOH3210 4.3 28.9 1.0 CG2 C:THR45 4.3 22.5 1.0 O1B C:GTP3200 4.3 17.7 1.0 O3A C:GTP3200 4.4 17.8 1.0 CG C:ASP68 4.4 21.5 1.0 O C:THR69 4.6 26.9 1.0 PA C:GTP3200 4.6 17.8 1.0 O C:GLN43 4.6 30.4 1.0 O1A C:GTP3200 4.8 16.4 1.0 C C:ALA44 4.8 27.5 1.0 CB C:LYS26 4.8 15.6 1.0 NZ C:LYS26 5.0 16.8 1.0

Magnesium binding site 4 out of 4 in the Structure of the Extremely Slow Gtpase RAB6A in the Gtp Bound Form at 1.8 Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Extremely Slow Gtpase RAB6A in the Gtp Bound Form at 1.8 Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg4201 b:16.8 occ:1.00 O2G D:GTP4200 2.0 17.4 1.0 O2B D:GTP4200 2.0 16.8 1.0 O D:HOH4330 2.1 15.0 1.0 OG1 D:THR45 2.1 17.4 1.0 O D:HOH4329 2.1 16.3 1.0 OG1 D:THR27 2.1 14.7 1.0 CB D:THR45 3.1 18.4 1.0 PG D:GTP4200 3.2 17.8 1.0 CB D:THR27 3.2 15.9 1.0 PB D:GTP4200 3.3 15.9 1.0 O3B D:GTP4200 3.5 18.3 1.0 N D:THR45 3.8 18.1 1.0 N D:THR27 3.9 15.1 1.0 O3G D:GTP4200 4.0 18.6 1.0 CA D:THR45 4.0 18.3 1.0 O D:HOH4234 4.1 20.3 1.0 CA D:THR27 4.2 14.5 1.0 O2A D:GTP4200 4.2 14.6 1.0 O D:THR69 4.2 19.4 1.0 O1G D:GTP4200 4.2 15.2 1.0 OD2 D:ASP68 4.2 17.1 1.0 CG2 D:THR27 4.2 12.5 1.0 O1B D:GTP4200 4.2 13.8 1.0 CG2 D:THR45 4.3 16.8 1.0 OD1 D:ASP68 4.3 20.5 1.0 O3A D:GTP4200 4.3 13.8 1.0 CG D:ASP68 4.6 19.6 1.0 PA D:GTP4200 4.6 15.9 1.0 O D:GLN43 4.6 17.3 1.0 CB D:LYS26 4.7 13.7 1.0 O1A D:GTP4200 4.7 11.2 1.0 CE D:LYS26 4.8 17.4 1.0 C D:ALA44 4.8 18.1 1.0

T.Bergbrede, O.Pylypenko, A.Rak, A.Alexandrov. Structure of the Extremely Slow Gtpase RAB6A in the Gtp Bound Form at 1.8 Resolution J.Struct.Biol. V. 152 235 2005.
ISSN: ISSN 1047-8477
PubMed: 16332443
DOI: 10.1016/J.JSB.2005.10.001