Magnesium in PDB 6pdt: Cryoem Structure of Yeast Glucokinase Filament

All present enzymatic activity of Cryoem Structure of Yeast Glucokinase Filament:
2.7.1.2;

The binding sites of Magnesium atom in the Cryoem Structure of Yeast Glucokinase Filament (pdb code 6pdt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Cryoem Structure of Yeast Glucokinase Filament, PDB code: 6pdt:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Cryoem Structure of Yeast Glucokinase Filament


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryoem Structure of Yeast Glucokinase Filament within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:39.7 occ:1.00 O1G A:ATP603 1.8 39.7 1.0 OD2 A:ASP218 1.8 39.7 1.0 O2B A:ATP603 1.8 39.7 1.0 PB A:ATP603 3.0 39.7 1.0 PG A:ATP603 3.0 39.7 1.0 CG A:ASP218 3.1 39.7 1.0 O3B A:ATP603 3.3 39.7 1.0 O1B A:ATP603 3.3 39.7 1.0 HG23 A:ILE249 3.5 39.7 1.0 HD12 A:ILE249 3.5 39.7 1.0 HG A:SER164 3.6 39.7 1.0 O3G A:ATP603 3.6 39.7 1.0 HG21 A:ILE249 3.7 39.7 1.0 HH22 A:ARG92 3.8 39.7 1.0 OD1 A:ASP218 3.8 39.7 1.0 HH21 A:ARG92 3.9 39.7 1.0 CG2 A:ILE249 4.1 39.7 1.0 CB A:ASP218 4.1 39.7 1.0 HB3 A:ASP218 4.1 39.7 1.0 O2G A:ATP603 4.2 39.7 1.0 NH2 A:ARG92 4.2 39.7 1.0 HB2 A:ASP218 4.2 39.7 1.0 OG A:SER164 4.3 39.7 1.0 O3A A:ATP603 4.3 39.7 1.0 HO6 A:GLC601 4.4 39.7 1.0 HB3 A:SER489 4.5 39.7 1.0 CD1 A:ILE249 4.6 39.7 1.0 HG22 A:ILE249 4.7 39.7 1.0 OD2 A:ASP85 4.7 39.7 1.0 O2A A:ATP603 4.8 39.7 1.0 HA2 A:GLY450 4.8 39.7 1.0 O6 A:GLC601 4.8 39.7 1.0 OD1 A:ASP85 4.8 39.7 1.0 HG13 A:ILE249 4.9 39.7 1.0 HA3 A:GLY251 4.9 39.7 1.0 HD11 A:ILE249 5.0 39.7 1.0

Magnesium binding site 2 out of 4 in the Cryoem Structure of Yeast Glucokinase Filament


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryoem Structure of Yeast Glucokinase Filament within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:39.7 occ:1.00 O1G B:ATP603 1.8 39.7 1.0 OD2 B:ASP218 1.8 39.7 1.0 O2B B:ATP603 1.8 39.7 1.0 PB B:ATP603 3.0 39.7 1.0 PG B:ATP603 3.0 39.7 1.0 CG B:ASP218 3.1 39.7 1.0 O3B B:ATP603 3.3 39.7 1.0 O1B B:ATP603 3.3 39.7 1.0 HG23 B:ILE249 3.5 39.7 1.0 HD12 B:ILE249 3.5 39.7 1.0 HG B:SER164 3.6 39.7 1.0 O3G B:ATP603 3.6 39.7 1.0 HG21 B:ILE249 3.7 39.7 1.0 HH22 B:ARG92 3.8 39.7 1.0 OD1 B:ASP218 3.8 39.7 1.0 HH21 B:ARG92 3.9 39.7 1.0 CG2 B:ILE249 4.1 39.7 1.0 CB B:ASP218 4.1 39.7 1.0 HB3 B:ASP218 4.1 39.7 1.0 O2G B:ATP603 4.2 39.7 1.0 NH2 B:ARG92 4.2 39.7 1.0 HB2 B:ASP218 4.2 39.7 1.0 OG B:SER164 4.3 39.7 1.0 O3A B:ATP603 4.3 39.7 1.0 HO6 B:GLC601 4.4 39.7 1.0 HB3 B:SER489 4.5 39.7 1.0 CD1 B:ILE249 4.6 39.7 1.0 HG22 B:ILE249 4.7 39.7 1.0 OD2 B:ASP85 4.7 39.7 1.0 HA2 B:GLY450 4.8 39.7 1.0 O2A B:ATP603 4.8 39.7 1.0 O6 B:GLC601 4.8 39.7 1.0 OD1 B:ASP85 4.8 39.7 1.0 HG13 B:ILE249 4.9 39.7 1.0 HA3 B:GLY251 4.9 39.7 1.0 HD11 B:ILE249 5.0 39.7 1.0

Magnesium binding site 3 out of 4 in the Cryoem Structure of Yeast Glucokinase Filament


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryoem Structure of Yeast Glucokinase Filament within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg602 b:39.7 occ:1.00 O1G C:ATP603 1.8 39.7 1.0 OD2 C:ASP218 1.8 39.7 1.0 O2B C:ATP603 1.8 39.7 1.0 PB C:ATP603 3.0 39.7 1.0 PG C:ATP603 3.0 39.7 1.0 CG C:ASP218 3.1 39.7 1.0 O3B C:ATP603 3.3 39.7 1.0 O1B C:ATP603 3.3 39.7 1.0 HG23 C:ILE249 3.5 39.7 1.0 HD12 C:ILE249 3.5 39.7 1.0 HG C:SER164 3.6 39.7 1.0 O3G C:ATP603 3.6 39.7 1.0 HG21 C:ILE249 3.7 39.7 1.0 HH22 C:ARG92 3.8 39.7 1.0 OD1 C:ASP218 3.8 39.7 1.0 HH21 C:ARG92 3.9 39.7 1.0 CG2 C:ILE249 4.1 39.7 1.0 CB C:ASP218 4.1 39.7 1.0 HB3 C:ASP218 4.1 39.7 1.0 O2G C:ATP603 4.2 39.7 1.0 NH2 C:ARG92 4.2 39.7 1.0 HB2 C:ASP218 4.2 39.7 1.0 OG C:SER164 4.3 39.7 1.0 O3A C:ATP603 4.3 39.7 1.0 HO6 C:GLC601 4.4 39.7 1.0 HB3 C:SER489 4.5 39.7 1.0 CD1 C:ILE249 4.6 39.7 1.0 HG22 C:ILE249 4.7 39.7 1.0 OD2 C:ASP85 4.7 39.7 1.0 HA2 C:GLY450 4.8 39.7 1.0 O2A C:ATP603 4.8 39.7 1.0 O6 C:GLC601 4.8 39.7 1.0 OD1 C:ASP85 4.8 39.7 1.0 HG13 C:ILE249 4.9 39.7 1.0 HA3 C:GLY251 4.9 39.7 1.0 HD11 C:ILE249 5.0 39.7 1.0

Magnesium binding site 4 out of 4 in the Cryoem Structure of Yeast Glucokinase Filament


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryoem Structure of Yeast Glucokinase Filament within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg602 b:39.7 occ:1.00 O1G D:ATP603 1.8 39.7 1.0 OD2 D:ASP218 1.8 39.7 1.0 O2B D:ATP603 1.8 39.7 1.0 PB D:ATP603 3.0 39.7 1.0 PG D:ATP603 3.0 39.7 1.0 CG D:ASP218 3.1 39.7 1.0 O3B D:ATP603 3.3 39.7 1.0 O1B D:ATP603 3.3 39.7 1.0 HG23 D:ILE249 3.5 39.7 1.0 HD12 D:ILE249 3.5 39.7 1.0 HG D:SER164 3.6 39.7 1.0 O3G D:ATP603 3.6 39.7 1.0 HG21 D:ILE249 3.7 39.7 1.0 HH22 D:ARG92 3.8 39.7 1.0 OD1 D:ASP218 3.8 39.7 1.0 HH21 D:ARG92 3.9 39.7 1.0 CG2 D:ILE249 4.1 39.7 1.0 CB D:ASP218 4.1 39.7 1.0 HB3 D:ASP218 4.1 39.7 1.0 O2G D:ATP603 4.2 39.7 1.0 NH2 D:ARG92 4.2 39.7 1.0 HB2 D:ASP218 4.2 39.7 1.0 OG D:SER164 4.3 39.7 1.0 O3A D:ATP603 4.3 39.7 1.0 HO6 D:GLC601 4.4 39.7 1.0 HB3 D:SER489 4.5 39.7 1.0 CD1 D:ILE249 4.6 39.7 1.0 HG22 D:ILE249 4.7 39.7 1.0 OD2 D:ASP85 4.7 39.7 1.0 HA2 D:GLY450 4.8 39.7 1.0 O2A D:ATP603 4.8 39.7 1.0 O6 D:GLC601 4.8 39.7 1.0 OD1 D:ASP85 4.8 39.7 1.0 HG13 D:ILE249 4.9 39.7 1.0 HA3 D:GLY251 4.9 39.7 1.0 HD11 D:ILE249 5.0 39.7 1.0

P.R.Stoddard, E.M.Lynch, D.P.Farrell, A.M.Dosey, F.Dimaio, T.A.Williams, J.M.Kollman, A.W.Murray, E.C.Garner. Polymerization in the Actin Atpase Clan Regulates Hexokinase Activity in Yeast. Science V. 367 1039 2020.
ISSN: ESSN 1095-9203
PubMed: 32108112
DOI: 10.1126/SCIENCE.AAY5359