Magnesium in PDB 3v2u: Crystal Structure of the Yeast Gal Regulon Complex of the Repressor, GAL80P, and the Transducer, GAL3P, with Galactose and Atp

The structure of Crystal Structure of the Yeast Gal Regulon Complex of the Repressor, GAL80P, and the Transducer, GAL3P, with Galactose and Atp, PDB code: 3v2u was solved by T.Lavy, P.R.Kumar, H.He, L.Joshua-Tor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.63 / 2.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	82.186, 83.221, 92.629, 114.04, 92.88, 90.37
R / Rfree (%)	15 / 19.7

The binding sites of Magnesium atom in the Crystal Structure of the Yeast Gal Regulon Complex of the Repressor, GAL80P, and the Transducer, GAL3P, with Galactose and Atp (pdb code 3v2u). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Yeast Gal Regulon Complex of the Repressor, GAL80P, and the Transducer, GAL3P, with Galactose and Atp, PDB code: 3v2u:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Yeast Gal Regulon Complex of the Repressor, GAL80P, and the Transducer, GAL3P, with Galactose and Atp


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 Yeast Gal Regulon Complex of the Repressor, GAL80P, and the Transducer, GAL3P, with Galactose and Atp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg521 b:29.9 occ:1.00 O2B C:ATP523 2.2 24.5 1.0 O2A C:ATP523 2.2 24.0 1.0 OG C:SER163 2.2 23.2 1.0 O2G C:ATP523 2.2 24.8 1.0 O C:HOH594 2.3 20.9 1.0 O C:HOH595 2.5 22.5 1.0 PB C:ATP523 3.1 24.1 1.0 CB C:SER163 3.2 27.8 1.0 PG C:ATP523 3.3 25.5 1.0 O3B C:ATP523 3.4 24.9 1.0 PA C:ATP523 3.4 25.4 1.0 O3A C:ATP523 3.6 24.9 1.0 N C:SER163 3.8 25.4 1.0 CA C:SER163 4.0 22.3 1.0 O C:HOH878 4.0 31.5 1.0 O3G C:ATP523 4.1 27.6 1.0 NZ C:LYS258 4.1 49.0 1.0 O1 C:GLA522 4.1 24.3 1.0 OE1 C:GLU198 4.1 35.2 1.0 OE2 C:GLU198 4.2 40.2 1.0 N C:SER164 4.3 22.5 1.0 O2 C:GLA522 4.3 24.4 1.0 O5' C:ATP523 4.3 26.8 1.0 OD2 C:ASP209 4.4 23.5 1.0 CA C:GLY161 4.4 24.3 1.0 OG C:SER164 4.4 33.3 1.0 O1A C:ATP523 4.4 26.0 1.0 O1G C:ATP523 4.4 24.5 1.0 O1B C:ATP523 4.4 23.2 1.0 C C:GLY161 4.5 24.0 1.0 CE C:LYS258 4.6 41.1 1.0 C C:SER163 4.6 23.2 1.0 CD C:GLU198 4.6 0.6 1.0 N C:LEU162 4.7 24.2 1.0 C C:LEU162 5.0 31.4 1.0 O C:GLY161 5.0 29.0 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Yeast Gal Regulon Complex of the Repressor, GAL80P, and the Transducer, GAL3P, with Galactose and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Yeast Gal Regulon Complex of the Repressor, GAL80P, and the Transducer, GAL3P, with Galactose and Atp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg521 b:31.6 occ:1.00 O2B D:ATP523 2.2 30.6 1.0 OG D:SER163 2.2 29.1 1.0 O1G D:ATP523 2.2 29.5 1.0 O2A D:ATP523 2.3 29.6 1.0 O D:HOH596 2.3 25.6 1.0 O D:HOH533 2.4 33.8 1.0 PB D:ATP523 3.1 30.2 1.0 CB D:SER163 3.2 26.9 1.0 NZ D:LYS258 3.2 90.5 1.0 PG D:ATP523 3.3 30.6 1.0 O3B D:ATP523 3.4 30.9 1.0 PA D:ATP523 3.5 30.1 1.0 O3A D:ATP523 3.7 30.0 1.0 N D:SER163 3.9 31.6 1.0 O2G D:ATP523 3.9 31.4 1.0 O1 D:GLA522 3.9 27.6 1.0 OE1 D:GLU198 4.0 41.3 1.0 CA D:SER163 4.0 26.5 1.0 O2 D:GLA522 4.1 27.5 1.0 O D:HOH879 4.1 26.5 1.0 OE2 D:GLU198 4.3 36.4 1.0 N D:SER164 4.3 27.4 1.0 CA D:GLY161 4.3 31.0 1.0 OD2 D:ASP209 4.3 35.0 1.0 O5' D:ATP523 4.4 31.3 1.0 OG D:SER164 4.4 37.1 1.0 O1A D:ATP523 4.5 29.8 1.0 O1B D:ATP523 4.5 30.4 1.0 C D:GLY161 4.5 33.8 1.0 O3G D:ATP523 4.5 29.5 1.0 CD D:GLU198 4.5 48.6 1.0 CE D:LYS258 4.5 37.8 1.0 O D:HOH874 4.6 56.9 1.0 C D:SER163 4.6 31.1 1.0 N D:LEU162 4.8 29.7 1.0 O D:GLY161 4.9 33.2 1.0

T.Lavy, P.R.Kumar, H.He, L.Joshua-Tor. The GAL3P Transducer of the Gal Regulon Interacts with the GAL80P Repressor in Its Ligand-Induced Closed Conformation. Genes Dev. V. 26 294 2012.
ISSN: ISSN 0890-9369
PubMed: 22302941
DOI: 10.1101/GAD.182691.111