Magnesium in PDB 8p28: Cryo-Em Structure of the Anaerobic Ribonucleotide Reductase From Prevotella Copri in Its Tetrameric, Datp-Bound State

The binding sites of Magnesium atom in the Cryo-Em Structure of the Anaerobic Ribonucleotide Reductase From Prevotella Copri in Its Tetrameric, Datp-Bound State (pdb code 8p28). 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, Datp-Bound State, PDB code: 8p28:
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, Datp-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 Tetrameric, Datp-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg804 b:56.2 occ:1.00 O2B B:DTP801 1.8 57.7 1.0 OE2 A:GLU293 2.2 57.6 1.0 PB B:DTP801 2.3 57.7 1.0 O3B B:DTP801 2.3 57.7 1.0 O3A B:DTP801 2.6 57.7 1.0 OE1 A:GLN290 2.7 57.3 1.0 O3G B:DTP801 3.2 57.7 1.0 CD A:GLU293 3.4 57.6 1.0 PG B:DTP801 3.4 57.7 1.0 CD A:GLN290 3.7 57.3 1.0 O1B B:DTP801 3.8 57.7 1.0 PA B:DTP801 3.9 57.7 1.0 OE1 A:GLU293 4.0 57.6 1.0 NE2 A:GLN290 4.0 57.3 1.0 O2A B:DTP801 4.0 57.7 1.0 NH1 B:ARG196 4.2 58.4 1.0 O5' B:DTP801 4.3 57.7 1.0 O2G B:DTP801 4.3 57.7 1.0 O1G B:DTP801 4.5 57.7 1.0 NH2 B:ARG192 4.5 57.2 1.0 CG A:GLU293 4.6 57.6 1.0 C3' B:DTP801 4.7 57.7 1.0 C2' B:DTP801 4.9 57.7 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, Datp-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 Tetrameric, Datp-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg804 b:66.9 occ:1.00 O2B A:DTP801 1.8 62.8 1.0 O2A A:DTP801 2.1 62.8 1.0 OE1 B:GLN290 2.3 62.8 1.0 OE2 B:GLU293 2.4 64.6 1.0 NE2 B:GLN290 2.5 62.8 1.0 CD B:GLN290 2.7 62.8 1.0 PB A:DTP801 3.0 62.8 1.0 PA A:DTP801 3.3 62.8 1.0 O3G A:DTP801 3.3 62.8 1.0 O3A A:DTP801 3.4 62.8 1.0 O3B A:DTP801 3.5 62.8 1.0 CD B:GLU293 3.5 64.6 1.0 PG A:DTP801 3.9 62.8 1.0 NH2 A:ARG196 3.9 61.1 1.0 OE1 B:GLU293 4.1 64.6 1.0 CG B:GLN290 4.1 62.8 1.0 O1G A:DTP801 4.1 62.8 1.0 O5' A:DTP801 4.2 62.8 1.0 O1B A:DTP801 4.3 62.8 1.0 O1A A:DTP801 4.4 62.8 1.0 CG B:GLU293 4.7 64.6 1.0 CB B:GLN290 4.7 62.8 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, Datp-Bound State


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, Datp-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg804 b:60.9 occ:1.00 O3A C:DTP801 1.8 61.5 1.0 O3B C:DTP801 2.0 61.5 1.0 O2A C:DTP801 2.0 61.5 1.0 PB C:DTP801 2.3 61.5 1.0 PA C:DTP801 2.3 61.5 1.0 O2B C:DTP801 2.8 61.5 1.0 PG C:DTP801 3.3 61.5 1.0 O1A C:DTP801 3.4 61.5 1.0 NH2 C:ARG196 3.5 59.6 1.0 OE1 D:GLN290 3.5 60.8 1.0 O5' C:DTP801 3.5 61.5 1.0 NE2 D:GLN290 3.6 60.8 1.0 O3G C:DTP801 3.6 61.5 1.0 O1B C:DTP801 3.6 61.5 1.0 O1G C:DTP801 3.9 61.5 1.0 CD D:GLN290 3.9 60.8 1.0 OE1 D:GLU293 4.4 62.1 1.0 O2G C:DTP801 4.4 61.5 1.0 NH2 C:ARG192 4.5 61.5 1.0 C5' C:DTP801 4.6 61.5 1.0 CZ C:ARG196 4.6 59.6 1.0 C3' C:DTP801 4.7 61.5 1.0 NH1 C:ARG196 5.0 59.6 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, Datp-Bound State


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, Datp-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg805 b:55.8 occ:1.00 OE2 C:GLU293 1.9 57.5 1.0 O2B D:DTP801 1.9 56.8 1.0 OE1 C:GLN290 2.7 57.1 1.0 PB D:DTP801 2.9 56.8 1.0 CD C:GLU293 3.1 57.5 1.0 O3B D:DTP801 3.2 56.8 1.0 O3A D:DTP801 3.3 56.8 1.0 O2A D:DTP801 3.3 56.8 1.0 O3G D:DTP801 3.4 56.8 1.0 CD C:GLN290 3.6 57.1 1.0 PA D:DTP801 3.9 56.8 1.0 NE2 C:GLN290 3.9 57.1 1.0 OE1 C:GLU293 4.0 57.5 1.0 CG C:GLU293 4.0 57.5 1.0 PG D:DTP801 4.0 56.8 1.0 O1B D:DTP801 4.3 56.8 1.0 O5' D:DTP801 4.4 56.8 1.0 NH1 D:ARG196 4.5 57.5 1.0 NH1 D:ARG192 4.5 56.9 1.0 C2' D:DTP801 4.6 56.8 1.0 C3' D:DTP801 4.7 56.8 1.0 O2G D:DTP801 4.8 56.8 1.0 CG C:GLN290 5.0 57.1 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 To Be Published.