Magnesium in PDB 4lhw: Crystal Structure of RAB8 in Its Active Gppnhp-Bound Form

The structure of Crystal Structure of RAB8 in Its Active Gppnhp-Bound Form, PDB code: 4lhw was solved by Z.Guo, X.M.Hou, R.S.Goody, A.Itzen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.89 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	90.381, 96.676, 105.090, 90.00, 90.00, 90.00
R / Rfree (%)	14.4 / 18.3

The binding sites of Magnesium atom in the Crystal Structure of RAB8 in Its Active Gppnhp-Bound Form (pdb code 4lhw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of RAB8 in Its Active Gppnhp-Bound Form, PDB code: 4lhw:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of RAB8 in Its Active Gppnhp-Bound Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of RAB8 in Its Active Gppnhp-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:8.9 occ:1.00 O2G A:GNP302 2.0 9.4 1.0 O2B A:GNP302 2.0 8.7 1.0 OG1 A:THR22 2.0 8.9 1.0 OG1 A:THR40 2.1 8.7 1.0 O A:HOH402 2.1 9.6 1.0 O A:HOH425 2.1 10.4 1.0 CB A:THR22 3.1 8.7 1.0 CB A:THR40 3.2 9.0 1.0 PG A:GNP302 3.2 8.7 1.0 PB A:GNP302 3.3 8.5 1.0 N3B A:GNP302 3.4 8.7 1.0 N A:THR40 3.8 9.3 1.0 O1G A:GNP302 3.9 9.8 1.0 N A:THR22 3.9 8.2 1.0 CA A:THR40 4.0 9.6 1.0 OD1 A:ASP63 4.1 12.6 1.0 CA A:THR22 4.1 7.9 1.0 O2A A:GNP302 4.2 10.4 1.0 CG2 A:THR22 4.2 10.1 1.0 OD2 A:ASP63 4.2 14.2 1.0 O3A A:GNP302 4.2 9.3 1.0 CG2 A:THR40 4.2 9.8 1.0 O A:HOH412 4.3 12.9 1.0 O1B A:GNP302 4.4 9.2 1.0 O3G A:GNP302 4.4 10.6 1.0 CG A:ASP63 4.5 12.3 1.0 PA A:GNP302 4.5 9.0 1.0 O A:ILE38 4.6 10.8 1.0 O1A A:GNP302 4.7 9.3 1.0 C A:SER39 4.8 9.9 1.0 O A:THR64 4.8 13.2 1.0 CB A:LYS21 4.9 9.0 1.0 CA A:SER39 5.0 10.6 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of RAB8 in Its Active Gppnhp-Bound Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of RAB8 in Its Active Gppnhp-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:11.3 occ:1.00 O2G B:GNP202 2.0 12.1 1.0 OG1 B:THR22 2.1 11.1 1.0 O2B B:GNP202 2.1 10.9 1.0 OG1 B:THR40 2.1 11.9 1.0 O B:HOH322 2.1 12.9 1.0 O B:HOH327 2.1 12.9 1.0 CB B:THR40 3.1 9.4 1.0 CB B:THR22 3.2 11.6 1.0 PG B:GNP202 3.2 11.0 1.0 PB B:GNP202 3.3 10.7 1.0 N3B B:GNP202 3.4 10.5 1.0 N B:THR40 3.7 10.3 1.0 O1G B:GNP202 3.9 11.8 1.0 N B:THR22 3.9 11.0 1.0 CA B:THR40 4.0 9.9 1.0 OD1 B:ASP63 4.0 16.3 1.0 CA B:THR22 4.1 11.6 1.0 OD2 B:ASP63 4.2 14.6 1.0 CG2 B:THR22 4.2 13.9 1.0 O2A B:GNP202 4.2 12.7 1.0 O3A B:GNP202 4.2 10.7 1.0 CG2 B:THR40 4.3 10.8 1.0 O B:HOH314 4.3 16.9 1.0 O1B B:GNP202 4.3 12.7 1.0 O3G B:GNP202 4.4 12.5 1.0 CG B:ASP63 4.5 13.8 1.0 PA B:GNP202 4.6 11.6 1.0 O B:ILE38 4.6 11.3 1.0 O1A B:GNP202 4.6 12.3 1.0 C B:SER39 4.7 11.2 1.0 O B:THR64 4.7 13.1 1.0 CB B:LYS21 4.9 11.4 1.0 CA B:SER39 4.9 10.4 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of RAB8 in Its Active Gppnhp-Bound Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of RAB8 in Its Active Gppnhp-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg201 b:11.1 occ:1.00 O2G C:GNP202 2.0 11.0 1.0 O2B C:GNP202 2.0 9.9 1.0 O C:HOH307 2.1 12.6 1.0 OG1 C:THR22 2.1 10.1 1.0 O C:HOH318 2.1 12.2 1.0 OG1 C:THR40 2.1 10.6 1.0 CB C:THR22 3.1 9.2 1.0 PG C:GNP202 3.2 11.7 1.0 CB C:THR40 3.2 11.2 1.0 PB C:GNP202 3.2 10.7 1.0 N3B C:GNP202 3.4 11.1 1.0 N C:THR40 3.7 11.8 1.0 O1G C:GNP202 3.9 13.0 1.0 N C:THR22 3.9 8.8 1.0 CA C:THR40 4.0 12.1 1.0 CA C:THR22 4.1 9.1 1.0 OD1 C:ASP63 4.1 14.1 1.0 O2A C:GNP202 4.2 11.1 1.0 CG2 C:THR22 4.2 10.7 1.0 O3A C:GNP202 4.3 10.3 1.0 OD2 C:ASP63 4.3 12.7 1.0 O1B C:GNP202 4.3 10.2 1.0 CG2 C:THR40 4.3 12.8 1.0 O C:HOH331 4.4 16.5 1.0 O3G C:GNP202 4.4 14.0 1.0 PA C:GNP202 4.5 10.9 1.0 CG C:ASP63 4.6 11.5 1.0 O C:ILE38 4.6 15.6 1.0 O C:THR64 4.6 12.4 1.0 O1A C:GNP202 4.6 10.6 1.0 C C:SER39 4.7 13.3 1.0 CA C:SER39 4.9 14.9 1.0 O C:HOH344 4.9 19.3 1.0 CB C:LYS21 5.0 9.7 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of RAB8 in Its Active Gppnhp-Bound Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of RAB8 in Its Active Gppnhp-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg201 b:12.4 occ:1.00 O2G D:GNP202 2.0 13.8 1.0 O2B D:GNP202 2.0 11.1 1.0 O D:HOH311 2.1 14.8 1.0 OG1 D:THR22 2.1 11.2 1.0 OG1 D:THR40 2.2 13.8 1.0 O D:HOH314 2.2 14.1 1.0 PG D:GNP202 3.1 13.5 1.0 CB D:THR22 3.2 10.5 1.0 CB D:THR40 3.2 15.1 1.0 PB D:GNP202 3.2 12.3 1.0 N3B D:GNP202 3.4 13.5 1.0 N D:THR40 3.7 15.6 1.0 O1G D:GNP202 3.8 14.6 1.0 N D:THR22 3.9 10.2 1.0 CA D:THR40 4.1 15.2 1.0 OD1 D:ASP63 4.1 17.1 1.0 CA D:THR22 4.1 10.8 1.0 O2A D:GNP202 4.1 15.1 1.0 O3A D:GNP202 4.2 12.3 1.0 CG2 D:THR22 4.2 12.9 1.0 OD2 D:ASP63 4.2 15.3 1.0 O1B D:GNP202 4.3 11.8 1.0 CG2 D:THR40 4.3 15.7 1.0 O D:HOH317 4.3 25.0 1.0 O3G D:GNP202 4.4 15.4 1.0 PA D:GNP202 4.5 12.7 1.0 CG D:ASP63 4.6 14.1 1.0 O D:THR64 4.6 17.2 1.0 O1A D:GNP202 4.6 12.3 1.0 O D:ILE38 4.6 20.4 1.0 C D:SER39 4.7 17.5 1.0 CA D:SER39 4.8 18.8 0.7 CA D:SER39 4.9 17.3 0.3

Magnesium binding site 5 out of 5 in the Crystal Structure of RAB8 in Its Active Gppnhp-Bound Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of RAB8 in Its Active Gppnhp-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg201 b:12.2 occ:1.00 O2G E:GNP202 2.0 11.1 1.0 O2B E:GNP202 2.1 10.0 1.0 O E:HOH309 2.1 13.9 1.0 OG1 E:THR22 2.1 9.8 1.0 OG1 E:THR40 2.1 10.3 1.0 O E:HOH304 2.2 12.4 1.0 PG E:GNP202 3.1 11.9 1.0 CB E:THR22 3.1 9.2 1.0 CB E:THR40 3.2 10.9 1.0 PB E:GNP202 3.2 11.0 1.0 N3B E:GNP202 3.4 11.4 1.0 N E:THR40 3.6 12.0 1.0 O1G E:GNP202 3.8 12.5 1.0 N E:THR22 3.9 8.8 1.0 CA E:THR40 4.0 11.5 1.0 OD1 E:ASP63 4.1 15.7 1.0 CA E:THR22 4.1 9.3 1.0 OD2 E:ASP63 4.1 14.3 1.0 CG2 E:THR22 4.2 10.8 1.0 O2A E:GNP202 4.2 13.0 1.0 O E:HOH325 4.2 22.3 1.0 O3A E:GNP202 4.3 10.1 1.0 O1B E:GNP202 4.3 11.6 1.0 CG2 E:THR40 4.4 12.7 1.0 O3G E:GNP202 4.4 13.5 1.0 O E:THR64 4.5 14.1 1.0 CG E:ASP63 4.5 14.0 1.0 PA E:GNP202 4.6 11.1 1.0 C E:SER39 4.6 12.9 1.0 O E:ILE38 4.6 15.9 1.0 O1A E:GNP202 4.7 12.1 1.0 CA E:SER39 4.8 13.9 1.0 CB E:LYS21 4.9 10.2 1.0 O E:HOH308 5.0 20.0 1.0

Z.Guo, X.Hou, R.S.Goody, A.Itzen. Intermediates in the Guanine Nucleotide Exchange Reaction of RAB8 Protein Catalyzed By Guanine Nucleotide Exchange Factors RABIN8 and Grab. J.Biol.Chem. V. 288 32466 2013.
ISSN: ISSN 0021-9258
PubMed: 24072714
DOI: 10.1074/JBC.M113.498329