Magnesium in PDB 8p2s: Cryo-Em Structure of the Anaerobic Ribonucleotide Reductase From Prevotella Copri in Its Dimeric, Atp/Dttp/Gtp-Bound State

The structure of Cryo-Em Structure of the Anaerobic Ribonucleotide Reductase From Prevotella Copri in Its Dimeric, Atp/Dttp/Gtp-Bound State also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Magnesium atom in the Cryo-Em Structure of the Anaerobic Ribonucleotide Reductase From Prevotella Copri in Its Dimeric, Atp/Dttp/Gtp-Bound State (pdb code 8p2s). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Cryo-Em Structure of the Anaerobic Ribonucleotide Reductase From Prevotella Copri in Its Dimeric, Atp/Dttp/Gtp-Bound State, PDB code: 8p2s:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Cryo-Em Structure of the Anaerobic Ribonucleotide Reductase From Prevotella Copri in Its Dimeric, Atp/Dttp/Gtp-Bound State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of the Anaerobic Ribonucleotide Reductase From Prevotella Copri in Its Dimeric, Atp/Dttp/Gtp-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:29.6 occ:1.00 OE1 A:GLN290 2.2 29.0 1.0 O3A B:TTP802 2.4 29.7 1.0 OE1 A:GLU293 2.8 29.5 1.0 CD A:GLN290 2.9 29.0 1.0 O1G B:TTP802 2.9 29.7 1.0 O2B B:TTP802 3.0 29.7 1.0 NE2 A:GLN290 3.0 29.0 1.0 PB B:TTP802 3.1 29.7 1.0 O3B B:TTP802 3.5 29.7 1.0 NH1 B:ARG196 3.5 28.2 1.0 PA B:TTP802 3.7 29.7 1.0 CD A:GLU293 3.8 29.5 1.0 PG B:TTP802 3.8 29.7 1.0 O2A B:TTP802 3.9 29.7 1.0 OE2 A:GLU293 4.1 29.5 1.0 O5' B:TTP802 4.2 29.7 1.0 CG A:GLN290 4.4 29.0 1.0 CZ B:ARG196 4.5 28.2 1.0 O1B B:TTP802 4.5 29.7 1.0 NH2 B:ARG196 4.6 28.2 1.0 NH2 B:ARG192 4.7 29.7 1.0 O3G B:TTP802 4.7 29.7 1.0 O1A B:TTP802 4.9 29.7 1.0 CA A:GLN290 4.9 29.0 1.0 CB A:GLN290 4.9 29.0 1.0 CG A:GLU293 4.9 29.5 1.0 O2G B:TTP802 5.0 29.7 1.0

Magnesium binding site 2 out of 2 in the Cryo-Em Structure of the Anaerobic Ribonucleotide Reductase From Prevotella Copri in Its Dimeric, Atp/Dttp/Gtp-Bound State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of the Anaerobic Ribonucleotide Reductase From Prevotella Copri in Its Dimeric, Atp/Dttp/Gtp-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg801 b:25.5 occ:1.00 O3G A:TTP801 2.1 27.2 1.0 O2B A:TTP801 2.3 27.2 1.0 O2A A:TTP801 2.6 27.2 1.0 OE1 B:GLU293 2.8 29.4 1.0 OE1 B:GLN290 2.9 28.5 1.0 CD B:GLN290 3.4 28.5 1.0 NH2 A:ARG196 3.4 28.1 1.0 PG A:TTP801 3.4 27.2 1.0 CG B:GLN290 3.4 28.5 1.0 PB A:TTP801 3.5 27.2 1.0 O3B A:TTP801 3.7 27.2 1.0 CD B:GLU293 3.7 29.4 1.0 PA A:TTP801 3.9 27.2 1.0 OE2 B:GLU293 3.9 29.4 1.0 O1G A:TTP801 4.0 27.2 1.0 O3A A:TTP801 4.2 27.2 1.0 NE2 B:GLN290 4.4 28.5 1.0 O2G A:TTP801 4.5 27.2 1.0 CZ A:ARG196 4.6 28.1 1.0 CD2 B:HIS289 4.6 28.7 1.0 CB B:GLN290 4.6 28.5 1.0 O1B A:TTP801 4.7 27.2 1.0 CA B:GLN290 4.7 28.5 1.0 O1A A:TTP801 4.8 27.2 1.0 NE2 B:HIS289 4.9 28.7 1.0

O.Bimai, I.Banerjee, I.Rozman Grinberg, P.Huang, D.Lundin, B.M.Sjoberg, D.T.Logan. Activity Modulation in Anaerobic Ribonucleotide Reductase: Nucleotide Binding to the Atp-Cone Mediates Long-Range Order-Disorder Transitions in the Active Site Elife 2023.
ISSN: ESSN 2050-084X