Magnesium in PDB 4rkf: Drosophila Melanogaster RAB3 Bound to Gmppnp

The structure of Drosophila Melanogaster RAB3 Bound to Gmppnp, PDB code: 4rkf was solved by J.A.Lardong, J.H.Driller, H.Depner, C.Weise, A.Petzoldt, M.C.Wahl, S.J.Sigrist, B.Loll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.27 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.230, 80.470, 123.940, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 19.4

The binding sites of Magnesium atom in the Drosophila Melanogaster RAB3 Bound to Gmppnp (pdb code 4rkf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Drosophila Melanogaster RAB3 Bound to Gmppnp, PDB code: 4rkf:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Drosophila Melanogaster RAB3 Bound to Gmppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Drosophila Melanogaster RAB3 Bound to Gmppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:9.3 occ:1.00 O2G A:GNP201 2.0 8.8 1.0 OG1 A:THR35 2.0 8.3 1.0 OG1 A:THR53 2.1 9.0 1.0 O2B A:GNP201 2.1 8.0 1.0 O A:HOH302 2.1 8.4 1.0 O A:HOH301 2.1 8.3 1.0 CB A:THR35 3.1 6.9 1.0 CB A:THR53 3.2 8.6 1.0 PG A:GNP201 3.2 9.8 1.0 PB A:GNP201 3.3 8.3 1.0 N3B A:GNP201 3.4 6.5 1.0 N A:THR53 3.7 8.9 1.0 N A:THR35 3.9 8.4 1.0 O3G A:GNP201 3.9 9.6 1.0 CA A:THR53 4.0 9.3 1.0 CA A:THR35 4.1 7.7 1.0 OD2 A:ASP76 4.1 10.0 1.0 OD1 A:ASP76 4.2 9.3 1.0 CG2 A:THR35 4.2 7.7 1.0 O2A A:GNP201 4.2 9.2 1.0 O A:HOH306 4.2 14.8 1.0 CG2 A:THR53 4.3 11.4 1.0 O3A A:GNP201 4.3 8.6 1.0 O1B A:GNP201 4.4 7.9 1.0 O1G A:GNP201 4.5 9.1 1.0 CG A:ASP76 4.5 9.0 1.0 PA A:GNP201 4.6 8.7 1.0 O A:VAL51 4.6 11.1 1.0 C A:SER52 4.7 10.9 1.0 O A:THR77 4.7 9.6 1.0 O1A A:GNP201 4.7 8.5 1.0 CA A:SER52 4.9 9.8 1.0 CB A:LYS34 5.0 7.3 1.0 C A:LYS34 5.0 8.0 1.0

Magnesium binding site 2 out of 2 in the Drosophila Melanogaster RAB3 Bound to Gmppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Drosophila Melanogaster RAB3 Bound to Gmppnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:8.9 occ:1.00 O2G B:GNP201 2.0 9.4 1.0 OG1 B:THR35 2.1 8.4 1.0 O1B B:GNP201 2.1 7.4 1.0 O B:HOH302 2.1 8.8 1.0 OG1 B:THR53 2.1 9.4 1.0 O B:HOH450 2.1 8.4 1.0 CB B:THR53 3.1 9.1 1.0 CB B:THR35 3.2 7.6 1.0 PG B:GNP201 3.2 9.3 1.0 PB B:GNP201 3.3 7.8 1.0 N3B B:GNP201 3.5 7.2 1.0 N B:THR53 3.7 9.4 1.0 N B:THR35 3.9 7.1 1.0 O1G B:GNP201 4.0 9.4 1.0 CA B:THR53 4.0 9.1 1.0 OD2 B:ASP76 4.0 13.1 1.0 CA B:THR35 4.1 7.9 1.0 OD1 B:ASP76 4.1 10.5 1.0 O2A B:GNP201 4.2 9.3 1.0 CG2 B:THR35 4.2 8.3 1.0 CG2 B:THR53 4.3 11.7 1.0 O B:HOH318 4.3 17.8 1.0 O3A B:GNP201 4.3 8.0 1.0 O2B B:GNP201 4.3 8.4 1.0 O3G B:GNP201 4.4 10.0 1.0 CG B:ASP76 4.5 12.2 1.0 PA B:GNP201 4.6 8.3 1.0 O B:THR77 4.6 8.8 1.0 C B:SER52 4.6 11.0 1.0 O B:VAL51 4.7 11.3 1.0 O1A B:GNP201 4.7 7.6 1.0 CB B:LYS34 4.9 7.2 1.0 CA B:SER52 5.0 10.6 0.4 CA B:SER52 5.0 10.2 0.6 C B:LYS34 5.0 6.4 1.0

J.A.Lardong, J.H.Driller, H.Depner, C.Weise, A.Petzoldt, M.C.Wahl, S.J.Sigrist, B.Loll. Crystal Structure of Drosophila Melanogaster RAB2 and RAB3 Bound to Gmppnp To Be Published.