Magnesium in PDB 4zkd: Crystal Structure of the S. Cerevisiae SKI7 Gtpase-Like Domain, Bound to Gdp and Inorganic Phosphate.

The structure of Crystal Structure of the S. Cerevisiae SKI7 Gtpase-Like Domain, Bound to Gdp and Inorganic Phosphate., PDB code: 4zkd was solved by E.Kowalinski, E.Conti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	73.72 / 2.18
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	93.136, 120.617, 105.269, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 24.6

The binding sites of Magnesium atom in the Crystal Structure of the S. Cerevisiae SKI7 Gtpase-Like Domain, Bound to Gdp and Inorganic Phosphate. (pdb code 4zkd). 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 the S. Cerevisiae SKI7 Gtpase-Like Domain, Bound to Gdp and Inorganic Phosphate., PDB code: 4zkd:

Magnesium binding site 1 out of 1 in the Crystal Structure of the S. Cerevisiae SKI7 Gtpase-Like Domain, Bound to Gdp and Inorganic Phosphate.


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 the S. Cerevisiae SKI7 Gtpase-Like Domain, Bound to Gdp and Inorganic Phosphate. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg803 b:59.0 occ:1.00 O1 A:PO4801 2.0 61.6 1.0 O A:HOH902 2.0 47.9 1.0 OG A:SER333 2.1 54.0 1.0 O1B A:GDP802 2.1 57.0 1.0 OG A:SER281 2.2 49.5 1.0 O A:HOH903 2.2 50.1 1.0 HB2 A:SER333 2.9 67.2 1.0 CB A:SER333 3.0 56.0 1.0 H A:SER333 3.1 70.0 1.0 HB2 A:SER281 3.3 56.0 1.0 H A:SER281 3.3 68.6 1.0 CB A:SER281 3.3 46.6 1.0 P A:PO4801 3.4 61.1 1.0 PB A:GDP802 3.4 60.4 1.0 HB3 A:SER333 3.7 67.2 1.0 HB2 A:LYS280 3.7 62.1 1.0 O3B A:GDP802 3.8 56.0 1.0 O4 A:PO4801 3.8 60.8 1.0 OD2 A:ASP356 3.8 59.9 1.0 N A:SER333 3.9 58.3 1.0 N A:SER281 3.9 57.1 1.0 HE2 A:LYS280 4.0 67.9 1.0 HB3 A:SER281 4.0 56.0 1.0 CA A:SER333 4.0 58.7 1.0 CA A:SER281 4.1 53.8 1.0 OD1 A:ASP356 4.2 65.9 1.0 HZ1 A:LYS280 4.2 64.0 1.0 O1A A:GDP802 4.2 51.6 1.0 O2B A:GDP802 4.2 62.3 1.0 OD1 A:ASP322 4.2 60.1 1.0 O2 A:PO4801 4.3 55.7 1.0 HZ3 A:LYS280 4.3 64.0 1.0 O3 A:PO4801 4.3 52.6 1.0 HA A:SER281 4.4 64.5 1.0 HA A:PRO358 4.4 75.2 1.0 CG A:ASP356 4.4 72.8 1.0 O A:THR357 4.5 53.7 1.0 O3A A:GDP802 4.5 62.7 1.0 NZ A:LYS280 4.6 53.3 1.0 HA A:SER333 4.6 70.5 1.0 OD2 A:ASP322 4.6 65.1 1.0 CB A:LYS280 4.7 51.7 1.0 CE A:LYS280 4.7 56.6 1.0 HA A:PHE332 4.8 77.1 1.0 PA A:GDP802 4.8 60.4 1.0 CG A:ASP322 4.9 67.8 1.0 C A:LYS280 4.9 58.5 1.0 H A:LYS280 4.9 62.5 1.0 H A:GLY359 4.9 63.5 1.0

E.Kowalinski, A.Schuller, R.Green, E.Conti. Saccharomyces Cerevisiae SKI7 Is A Gtp-Binding Protein Adopting the Characteristic Conformation of Active Translational Gtpases. Structure V. 23 1336 2015.
ISSN: ISSN 0969-2126
PubMed: 26051716
DOI: 10.1016/J.STR.2015.04.018