Magnesium in PDB 8p2c: Cryo-Em Structure of the Anaerobic Ribonucleotide Reductase From Prevotella Copri in Its Tetrameric State Produced in the Presence of Datp and Ctp

The binding sites of Magnesium atom in the Cryo-Em Structure of the Anaerobic Ribonucleotide Reductase From Prevotella Copri in Its Tetrameric State Produced in the Presence of Datp and Ctp (pdb code 8p2c). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Cryo-Em Structure of the Anaerobic Ribonucleotide Reductase From Prevotella Copri in Its Tetrameric State Produced in the Presence of Datp and Ctp, PDB code: 8p2c:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Cryo-Em Structure of the Anaerobic Ribonucleotide Reductase From Prevotella Copri in Its Tetrameric State Produced in the Presence of Datp and Ctp


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 Tetrameric State Produced in the Presence of Datp and Ctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg804 b:34.6 occ:1.00 O2A B:DTP801 2.3 36.8 1.0 O3G B:DTP801 2.5 36.9 1.0 OE1 A:GLN290 2.6 36.8 1.0 O3B B:DTP801 2.7 31.7 1.0 NE2 A:GLN290 2.9 32.8 1.0 CD A:GLN290 3.1 30.8 1.0 PG B:DTP801 3.2 27.8 1.0 OE2 A:GLU293 3.3 44.6 1.0 OE1 A:GLU293 3.4 44.0 1.0 O2B B:DTP801 3.5 40.4 1.0 PB B:DTP801 3.6 26.7 1.0 PA B:DTP801 3.6 29.4 1.0 CD A:GLU293 3.7 40.7 1.0 O3A B:DTP801 3.7 23.9 1.0 NH1 B:ARG196 4.1 38.8 1.0 O1G B:DTP801 4.2 33.7 1.0 O2G B:DTP801 4.3 36.6 1.0 O1A B:DTP801 4.4 45.0 1.0 NH2 B:ARG196 4.5 40.4 1.0 CG A:GLN290 4.6 31.4 1.0 O5' B:DTP801 4.7 31.1 1.0 CE1 A:HIS289 4.8 37.1 1.0 CZ B:ARG196 4.8 31.9 1.0 C5' B:DTP801 4.8 33.9 1.0 O1B B:DTP801 4.9 36.0 1.0 ND1 A:HIS289 5.0 31.8 1.0

Magnesium binding site 2 out of 4 in the Cryo-Em Structure of the Anaerobic Ribonucleotide Reductase From Prevotella Copri in Its Tetrameric State Produced in the Presence of Datp and Ctp


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 Tetrameric State Produced in the Presence of Datp and Ctp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg804 b:37.8 occ:1.00 O2A A:DTP801 2.0 40.6 1.0 O3B A:DTP801 2.0 53.6 1.0 O3G A:DTP801 2.5 61.2 1.0 OE1 B:GLU293 2.8 56.2 1.0 PG A:DTP801 2.8 60.8 1.0 PB A:DTP801 2.9 56.7 1.0 O2B A:DTP801 3.0 55.0 1.0 PA A:DTP801 3.2 44.5 1.0 O3A A:DTP801 3.2 54.4 1.0 NE2 B:GLN290 3.2 48.3 1.0 OE1 B:GLN290 3.3 42.6 1.0 O2G A:DTP801 3.6 62.7 1.0 CD B:GLU293 3.6 56.6 1.0 CD B:GLN290 3.6 45.7 1.0 OE2 B:GLU293 3.7 61.1 1.0 O5' A:DTP801 4.0 54.3 1.0 O1G A:DTP801 4.1 57.4 1.0 NH2 A:ARG196 4.1 50.3 1.0 O1B A:DTP801 4.3 51.4 1.0 O1A A:DTP801 4.3 45.2 1.0 NH2 A:ARG192 4.7 31.4 1.0 CG B:GLU293 4.9 48.0 1.0 C3' A:DTP801 5.0 42.0 1.0

Magnesium binding site 3 out of 4 in the Cryo-Em Structure of the Anaerobic Ribonucleotide Reductase From Prevotella Copri in Its Tetrameric State Produced in the Presence of Datp and Ctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of the Anaerobic Ribonucleotide Reductase From Prevotella Copri in Its Tetrameric State Produced in the Presence of Datp and Ctp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg804 b:34.1 occ:1.00 O3G D:DTP801 2.0 33.6 1.0 OE1 C:GLN290 2.2 37.5 1.0 OE2 C:GLU293 2.3 41.6 1.0 O2B D:DTP801 2.5 32.2 1.0 O2A D:DTP801 2.5 34.1 1.0 CD C:GLN290 2.8 32.8 1.0 NE2 C:GLN290 2.9 38.9 1.0 PG D:DTP801 3.3 27.5 1.0 CD C:GLU293 3.4 41.9 1.0 O3B D:DTP801 3.4 31.2 1.0 PB D:DTP801 3.4 21.8 1.0 PA D:DTP801 3.8 25.9 1.0 O3A D:DTP801 3.8 21.2 1.0 OE1 C:GLU293 3.9 43.3 1.0 NH1 D:ARG196 4.2 38.0 1.0 O1G D:DTP801 4.2 33.6 1.0 O2G D:DTP801 4.3 35.2 1.0 CG C:GLN290 4.3 32.3 1.0 O5' D:DTP801 4.5 37.2 1.0 CG C:GLU293 4.5 36.5 1.0 NH2 D:ARG196 4.7 37.7 1.0 O1B D:DTP801 4.8 29.1 1.0 CB C:GLN290 4.8 31.9 1.0 O1A D:DTP801 4.9 36.5 1.0 CZ D:ARG196 4.9 30.9 1.0 NH1 D:ARG192 5.0 19.1 1.0 CA C:GLN290 5.0 28.7 1.0 CD2 C:HIS289 5.0 33.3 1.0

Magnesium binding site 4 out of 4 in the Cryo-Em Structure of the Anaerobic Ribonucleotide Reductase From Prevotella Copri in Its Tetrameric State Produced in the Presence of Datp and Ctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of the Anaerobic Ribonucleotide Reductase From Prevotella Copri in Its Tetrameric State Produced in the Presence of Datp and Ctp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg804 b:36.0 occ:1.00 O3B C:DTP801 1.9 50.5 1.0 O2A C:DTP801 2.0 34.0 1.0 O2B C:DTP801 2.3 50.5 1.0 O3G C:DTP801 2.4 54.7 1.0 PB C:DTP801 2.5 54.7 1.0 PG C:DTP801 2.7 53.1 1.0 O3A C:DTP801 2.9 50.9 1.0 PA C:DTP801 3.0 40.3 1.0 OE1 D:GLU293 3.0 52.4 1.0 O2G C:DTP801 3.3 54.6 1.0 OE2 D:GLU293 3.7 50.5 1.0 OE1 D:GLN290 3.7 35.1 1.0 CD D:GLU293 3.7 51.2 1.0 NE2 D:GLN290 3.7 42.7 1.0 O5' C:DTP801 3.9 53.2 1.0 O1B C:DTP801 3.9 53.4 1.0 O1G C:DTP801 4.0 51.1 1.0 CD D:GLN290 4.1 39.3 1.0 NH2 C:ARG196 4.2 48.8 1.0 O1A C:DTP801 4.2 41.3 1.0 NH2 C:ARG192 4.3 36.8 1.0 C3' C:DTP801 4.8 37.9 1.0 C5' C:DTP801 5.0 47.2 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