Magnesium in PDB 9fzf: Transcriptional Repressor Nrdr From E. Coli, Adp/Datp Bound State

The structure of Transcriptional Repressor Nrdr From E. Coli, Adp/Datp Bound State, PDB code: 9fzf was solved by O.Bimai, I.Rozman Grinberg, B.M.Sjoberg, D.T.Logan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	127.42 / 2.44
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	147.126, 147.126, 85.805, 90, 90, 120
R / Rfree (%)	21.5 / 28.3

The structure of Transcriptional Repressor Nrdr From E. Coli, Adp/Datp Bound State also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Transcriptional Repressor Nrdr From E. Coli, Adp/Datp Bound State (pdb code 9fzf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Transcriptional Repressor Nrdr From E. Coli, Adp/Datp Bound State, PDB code: 9fzf:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Transcriptional Repressor Nrdr From E. Coli, Adp/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 Transcriptional Repressor Nrdr From E. Coli, Adp/Datp Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:34.1 occ:0.49 O2A A:DTP200 1.9 47.1 1.0 O2B A:DTP200 1.9 46.0 1.0 O A:HOH301 1.9 5.0 1.0 O2G A:DTP200 2.1 46.3 1.0 O3B A:ADP201 2.5 48.4 1.0 O2A A:ADP201 2.6 45.1 1.0 PB A:DTP200 2.9 46.0 1.0 PA A:DTP200 3.0 46.7 1.0 O3A A:DTP200 3.1 46.5 1.0 PB A:ADP201 3.2 48.1 1.0 PG A:DTP200 3.3 46.4 1.0 O3B A:DTP200 3.3 46.0 1.0 O1B A:ADP201 3.3 48.3 1.0 PA A:ADP201 3.5 45.0 1.0 O3A A:ADP201 3.5 46.8 1.0 O5' A:ADP201 4.0 43.8 1.0 NZ A:LYS53 4.0 59.7 1.0 O1A A:DTP200 4.1 46.7 1.0 O5' A:DTP200 4.1 45.9 1.0 O3G A:DTP200 4.2 46.9 1.0 C5' A:DTP200 4.2 45.4 1.0 O1B A:DTP200 4.3 45.9 1.0 O1G A:DTP200 4.4 46.4 1.0 C8 A:ADP201 4.6 40.5 1.0 O2B A:ADP201 4.7 47.9 1.0 O1A A:ADP201 4.9 45.1 1.0 O A:HOH349 5.0 30.4 1.0 CE A:LYS53 5.0 58.0 1.0

Magnesium binding site 2 out of 2 in the Transcriptional Repressor Nrdr From E. Coli, Adp/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 Transcriptional Repressor Nrdr From E. Coli, Adp/Datp Bound State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:19.9 occ:0.49 O B:HOH302 1.9 14.9 1.0 O2B B:DTP200 1.9 29.8 1.0 O1B B:ADP201 1.9 25.1 1.0 O2A B:DTP200 1.9 27.1 1.0 O3G B:DTP200 1.9 29.9 1.0 O2A B:ADP201 2.6 26.1 1.0 PB B:DTP200 2.9 29.3 1.0 PA B:DTP200 3.0 27.5 1.0 O3A B:DTP200 3.0 28.6 1.0 PG B:DTP200 3.2 30.2 1.0 PB B:ADP201 3.2 25.6 1.0 O3B B:DTP200 3.3 29.7 1.0 PA B:ADP201 3.6 25.7 1.0 O3A B:ADP201 3.6 25.6 1.0 O5' B:ADP201 4.0 24.9 1.0 NZ B:LYS53 4.0 42.2 1.0 O5' B:DTP200 4.1 27.3 1.0 O1A B:DTP200 4.1 27.0 1.0 O2B B:ADP201 4.1 26.3 1.0 C5' B:DTP200 4.1 26.9 1.0 O1G B:DTP200 4.2 30.7 1.0 O2G B:DTP200 4.2 30.3 1.0 O1B B:DTP200 4.3 28.9 1.0 O3B B:ADP201 4.3 25.6 1.0 O B:HOH301 4.4 29.9 1.0 C8 B:ADP201 4.6 21.5 1.0 O B:HOH379 4.8 4.7 1.0 O1A B:ADP201 4.9 25.9 1.0 C2' B:ADP201 5.0 20.9 1.0

I.Rozman Grinberg, O.Bimai, S.Shahid, L.Philipp, M.Martinez-Carranza, I.Banerjee, D.Lundin, P.Stenmark, B.M.Sjoberg, D.T.Logan. Bacterial Transcriptional Repressor Nrdr - A Flexible Multifactorial Nucleotide Sensor. Febs J. 2025.
ISSN: ISSN 1742-464X
PubMed: 40029022
DOI: 10.1111/FEBS.70037