Magnesium in PDB 2bcg: Structure of Doubly Prenylated YPT1:Gdi Complex

The structure of Structure of Doubly Prenylated YPT1:Gdi Complex, PDB code: 2bcg was solved by 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)	19.92 / 1.48
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.660, 120.230, 60.550, 90.00, 90.67, 90.00
R / Rfree (%)	16.3 / 19.3

The binding sites of Magnesium atom in the Structure of Doubly Prenylated YPT1:Gdi Complex (pdb code 2bcg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Structure of Doubly Prenylated YPT1:Gdi Complex, PDB code: 2bcg:

Magnesium binding site 1 out of 1 in the Structure of Doubly Prenylated YPT1:Gdi Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Doubly Prenylated YPT1:Gdi Complex within 5.0Å range: probe atom residue distance (Å) B Occ Y:Mg1208 b:9.7 occ:1.00 O Y:HOH3244 2.0 11.0 1.0 O3B Y:GDP1207 2.1 8.4 1.0 O Y:HOH3243 2.1 9.0 1.0 OG Y:SER22 2.1 9.0 1.0 O Y:HOH3246 2.1 10.5 1.0 O Y:HOH3245 2.1 11.1 1.0 CB Y:SER22 3.3 8.7 1.0 PB Y:GDP1207 3.3 9.4 1.0 O1B Y:GDP1207 3.5 10.1 1.0 N Y:SER22 3.9 8.0 1.0 OD1 Y:ASP63 4.0 11.8 1.0 O2A Y:GDP1207 4.1 9.1 1.0 CA Y:SER22 4.1 9.1 1.0 O Y:HOH3183 4.1 31.6 1.0 O Y:HOH3006 4.2 11.8 1.0 O Y:HOH3023 4.3 15.3 1.0 OD2 Y:ASP63 4.3 10.2 1.0 OG1 Y:THR64 4.3 8.9 1.0 O Y:HOH3104 4.3 21.6 1.0 O2B Y:GDP1207 4.3 9.5 1.0 OE1 Y:GLU68 4.3 10.2 1.0 O3A Y:GDP1207 4.4 9.0 1.0 O Y:HOH3017 4.4 13.9 1.0 CG Y:ASP63 4.5 11.7 1.0 PA Y:GDP1207 4.6 9.4 1.0 O1A Y:GDP1207 4.7 10.0 1.0 CB Y:LYS21 4.9 9.1 1.0 N Y:GLY66 4.9 9.0 1.0 C Y:LYS21 5.0 9.1 1.0 NZ Y:LYS21 5.0 9.4 1.0

O.Pylypenko, A.Rak, T.Durek, S.Kushnir, B.E.Dursina, N.H.Thomae, A.T.Constantinescu, L.Brunsveld, A.Watzke, H.Waldmann, R.S.Goody, K.Alexandrov. Structure of Doubly Prenylated YPT1:Gdi Complex and the Mechanism of Gdi-Mediated Rab Recycling Embo J. V. 25 13 2006.
ISSN: ISSN 0261-4189
PubMed: 16395334
DOI: 10.1038/SJ.EMBOJ.7600921