Magnesium in PDB 2y8e: Crystal Structure of D. Melanogaster RAB6 Gtpase Bound to Gmppnp

The structure of Crystal Structure of D. Melanogaster RAB6 Gtpase Bound to Gmppnp, PDB code: 2y8e was solved by M.Walden, T.A.Edwards, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.40 / 1.39
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.520, 42.710, 86.860, 90.00, 133.12, 90.00
R / Rfree (%)	14.458 / 17.296

The binding sites of Magnesium atom in the Crystal Structure of D. Melanogaster RAB6 Gtpase Bound to Gmppnp (pdb code 2y8e). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of D. Melanogaster RAB6 Gtpase Bound to Gmppnp, PDB code: 2y8e:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of D. Melanogaster RAB6 Gtpase 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 Crystal Structure of D. Melanogaster RAB6 Gtpase Bound to Gmppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1177 b:7.5 occ:1.00 O3G A:GNP1176 2.0 9.1 1.0 O1B A:GNP1176 2.1 6.3 1.0 OG1 A:THR26 2.1 6.6 1.0 O A:HOH2039 2.1 7.7 1.0 O A:HOH2120 2.1 8.1 1.0 OG1 A:THR44 2.1 6.9 1.0 CB A:THR44 3.2 6.6 1.0 CB A:THR26 3.2 5.6 1.0 PB A:GNP1176 3.2 6.5 1.0 PG A:GNP1176 3.2 6.9 1.0 N3B A:GNP1176 3.4 5.4 1.0 N A:THR44 3.8 7.5 1.0 N A:THR26 3.9 6.1 1.0 O A:HOH2030 4.1 12.3 1.0 CA A:THR44 4.1 6.4 1.0 CA A:THR26 4.1 6.1 1.0 O2A A:GNP1176 4.1 7.0 1.0 O1G A:GNP1176 4.1 9.6 1.0 OD2 A:ASP67 4.2 7.0 1.0 OD1 A:ASP67 4.2 7.2 1.0 CG2 A:THR26 4.2 7.7 1.0 O2B A:GNP1176 4.3 7.1 1.0 O3A A:GNP1176 4.3 5.9 1.0 CG2 A:THR44 4.3 7.7 1.0 O2G A:GNP1176 4.3 8.0 1.0 O A:THR68 4.5 7.8 1.0 CG A:ASP67 4.5 7.6 1.0 PA A:GNP1176 4.6 6.7 1.0 O A:GLN42 4.7 8.5 1.0 CB A:LYS25 4.7 6.5 1.0 CE A:LYS25 4.8 9.6 1.0 O1A A:GNP1176 4.8 7.4 1.0 C A:ALA43 4.9 7.2 1.0 O B:HOH2028 4.9 21.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of D. Melanogaster RAB6 Gtpase 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 Crystal Structure of D. Melanogaster RAB6 Gtpase Bound to Gmppnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1177 b:9.8 occ:1.00 O1G B:GNP1176 2.0 11.2 1.0 O2B B:GNP1176 2.0 7.9 1.0 O B:HOH2040 2.1 9.4 1.0 OG1 B:THR26 2.1 7.9 1.0 O B:HOH2105 2.1 8.9 1.0 OG1 B:THR44 2.1 9.4 1.0 CB B:THR44 3.2 9.2 1.0 CB B:THR26 3.2 6.5 1.0 PB B:GNP1176 3.2 8.0 1.0 PG B:GNP1176 3.3 9.5 1.0 N3B B:GNP1176 3.4 7.8 1.0 N B:THR44 3.8 11.0 1.0 N B:THR26 3.9 6.6 1.0 CA B:THR44 4.1 10.6 1.0 O2G B:GNP1176 4.1 10.8 1.0 O2A B:GNP1176 4.1 9.0 1.0 OD1 B:ASP67 4.1 10.2 1.0 OD2 B:ASP67 4.1 9.3 1.0 O B:HOH2025 4.1 18.2 1.0 CA B:THR26 4.1 7.0 1.0 CG2 B:THR44 4.2 9.9 1.0 O1B B:GNP1176 4.3 8.2 1.0 CG2 B:THR26 4.3 8.0 1.0 O3A B:GNP1176 4.3 7.8 1.0 O3G B:GNP1176 4.3 12.0 1.0 O B:HOH2022 4.3 0.7 1.0 CG B:ASP67 4.5 8.0 1.0 O B:THR68 4.5 10.2 1.0 PA B:GNP1176 4.6 8.2 1.0 CE B:LYS25 4.8 10.9 1.0 CB B:LYS25 4.8 6.4 1.0 O1A B:GNP1176 4.8 8.2 1.0 O B:GLN42 4.8 14.2 1.0 C B:ALA43 4.9 12.8 1.0

M.Walden, H.T.Jenkins, T.A.Edwards. Structure of the Drosophila Melanogaster RAB6 Gtpase at 1.4 A Resolution Acta Crystallogr.,Sect.F V. 67 744 2011.
ISSN: ISSN 1744-3091
PubMed: 21795785
DOI: 10.1107/S1744309111017453