Magnesium in PDB 5ca8: Structures of the Yeast Dynamin-Like Gtpase SEY1P in Complex with Gdp

All present enzymatic activity of Structures of the Yeast Dynamin-Like Gtpase SEY1P in Complex with Gdp:
3.6.5.5;

The structure of Structures of the Yeast Dynamin-Like Gtpase SEY1P in Complex with Gdp, PDB code: 5ca8 was solved by L.Yan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.36 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	228.120, 43.620, 97.560, 90.00, 108.12, 90.00
R / Rfree (%)	23 / 28.5

The binding sites of Magnesium atom in the Structures of the Yeast Dynamin-Like Gtpase SEY1P in Complex with Gdp (pdb code 5ca8). 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 Structures of the Yeast Dynamin-Like Gtpase SEY1P in Complex with Gdp, PDB code: 5ca8:

Magnesium binding site 1 out of 1 in the Structures of the Yeast Dynamin-Like Gtpase SEY1P in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structures of the Yeast Dynamin-Like Gtpase SEY1P in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:59.7 occ:1.00 O A:HOH829 2.0 61.6 1.0 OG A:SER72 2.3 67.3 1.0 O3B A:GDP702 2.7 48.2 1.0 OE2 A:GLU125 2.8 90.9 1.0 OD2 A:ASP123 3.1 62.7 1.0 O1B A:GDP702 3.3 46.8 1.0 CD A:GLU125 3.4 98.0 1.0 O A:HOH850 3.4 48.2 1.0 OE1 A:GLU125 3.5 0.8 1.0 PB A:GDP702 3.6 47.1 1.0 CB A:SER72 3.6 49.8 1.0 CG A:ASP123 3.9 62.3 1.0 OD1 A:ASP123 3.9 61.1 1.0 O A:ASP84 4.0 65.5 1.0 N A:SER72 4.1 44.2 1.0 O2B A:GDP702 4.3 46.9 1.0 CA A:SER72 4.4 31.0 1.0 O A:HOH868 4.6 85.5 1.0 CE A:LYS71 4.6 43.8 1.0 CG A:GLU125 4.7 89.5 1.0 NZ A:LYS71 4.7 48.5 1.0 O1A A:GDP702 4.7 45.9 1.0 CB A:LYS71 4.9 35.8 1.0 O3A A:GDP702 4.9 44.4 1.0

L.Yan, S.Sun, W.Wang, J.Shi, X.Hu, S.Wang, D.Su, Z.Rao, J.Hu, Z.Lou. Structures of the Yeast Dynamin-Like Gtpase SEY1P Provide Insight Into Homotypic Er Fusion J.Cell Biol. V. 210 961 2015.
ISSN: ESSN 1540-8140
PubMed: 26370501
DOI: 10.1083/JCB.201502078