Magnesium in PDB 3cpj: Crystal Structure of YPT31 in Complex with Yeast Rab-Gdi

The structure of Crystal Structure of YPT31 in Complex with Yeast Rab-Gdi, PDB code: 3cpj was solved by S.Kravchenko, A.Ignatev, R.S.Goody, A.Rak, O.Pylypenko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.79 / 2.35
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.940, 61.430, 92.750, 90.00, 103.68, 90.00
R / Rfree (%)	19.9 / 25.5

The structure of Crystal Structure of YPT31 in Complex with Yeast Rab-Gdi also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of YPT31 in Complex with Yeast Rab-Gdi (pdb code 3cpj). 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 Crystal Structure of YPT31 in Complex with Yeast Rab-Gdi, PDB code: 3cpj:

Magnesium binding site 1 out of 1 in the Crystal Structure of YPT31 in Complex with Yeast Rab-Gdi


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 YPT31 in Complex with Yeast Rab-Gdi within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1208 b:42.5 occ:1.00 O3B B:GDP1207 2.0 56.2 1.0 O B:HOH4388 2.0 31.3 1.0 OG B:SER27 2.1 55.3 1.0 O B:HOH4390 2.2 33.0 1.0 O B:HOH4389 2.2 37.5 1.0 O B:HOH4387 2.5 36.7 1.0 PB B:GDP1207 3.2 56.8 1.0 CB B:SER27 3.4 55.7 1.0 O1B B:GDP1207 3.4 56.5 1.0 O2A B:GDP1207 3.8 59.5 1.0 N B:SER27 4.1 55.5 1.0 O2B B:GDP1207 4.2 54.6 1.0 CA B:SER27 4.3 55.9 1.0 O3A B:GDP1207 4.3 58.3 1.0 O B:HOH4386 4.4 43.0 1.0 OD2 B:ASP68 4.4 44.3 1.0 OE2 B:GLU73 4.4 41.9 1.0 OD1 B:ASP68 4.5 42.2 1.0 OG1 B:THR69 4.5 41.3 1.0 PA B:GDP1207 4.5 60.1 1.0 CG B:ASP68 4.8 43.2 1.0 O1A B:GDP1207 4.8 59.2 1.0

A.Ignatev, S.Kravchenko, A.Rak, R.S.Goody, O.Pylypenko. A Structural Model of the Gdp Dissociation Inhibitor Rab Membrane Extraction Mechanism. J.Biol.Chem. V. 283 18377 2008.
ISSN: ISSN 0021-9258
PubMed: 18426803
DOI: 10.1074/JBC.M709718200