Magnesium in PDB 3wnc: Crystal Structure of Ef-Pyl in Complex with Gdp

The structure of Crystal Structure of Ef-Pyl in Complex with Gdp, PDB code: 3wnc was solved by T.Yanagisawa, R.Ishii, R.Fukunaga, T.Sengoku, S.Yokoyama, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.49 / 1.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	62.020, 108.700, 58.390, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 21.7

The binding sites of Magnesium atom in the Crystal Structure of Ef-Pyl in Complex with Gdp (pdb code 3wnc). 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 Ef-Pyl in Complex with Gdp, PDB code: 3wnc:

Magnesium binding site 1 out of 1 in the Crystal Structure of Ef-Pyl 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 Crystal Structure of Ef-Pyl in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:36.4 occ:1.00 O A:HOH875 2.3 49.1 1.0 OG1 A:THR15 2.9 19.8 1.0 O3B A:GDP401 2.9 44.3 1.0 OD1 A:ASP46 3.3 20.6 1.0 CZ A:ARG14 3.3 32.2 1.0 NH2 A:ARG14 3.3 38.8 1.0 O A:HOH506 3.5 32.3 1.0 CA A:HIS48 3.6 21.1 1.0 NE A:ARG14 3.6 32.5 1.0 CB A:HIS48 3.7 21.9 1.0 NH1 A:ARG14 3.8 34.9 1.0 OD2 A:ASP46 3.9 18.7 1.0 CG A:ASP46 4.0 27.5 1.0 PB A:GDP401 4.0 52.0 1.0 CB A:ARG14 4.1 16.8 1.0 N A:THR15 4.1 17.8 1.0 CB A:THR15 4.2 19.5 1.0 O1B A:GDP401 4.2 38.2 1.0 O A:HOH876 4.3 31.5 1.0 O2B A:GDP401 4.3 55.8 1.0 O A:HIS48 4.4 20.1 1.0 CD A:ARG14 4.4 31.0 1.0 N A:HIS48 4.4 23.2 1.0 C A:HIS48 4.5 21.6 1.0 CA A:THR15 4.6 17.0 1.0 O A:ALA47 4.7 17.5 1.0 O A:HOH880 4.7 31.0 1.0 C A:ALA47 4.8 20.1 1.0 CG A:ARG14 4.9 21.0 1.0 C A:ARG14 4.9 13.8 1.0

T.Yanagisawa, R.Ishii, R.Fukunaga, T.Sengoku, S.Yokoyama. Crystal Structures of Ef-Pyl, An Ef-Tu/Selb/AIF2GAMMA-Like Translation Factor From Methanosarcina Mazei, in the Gtp-Bound, Gdp-Bound, and Apo Forms To Be Published.