Magnesium in PDB 5c5j: Poymerase Nucleotide Complex

All present enzymatic activity of Poymerase Nucleotide Complex:
2.7.7.7;

The structure of Poymerase Nucleotide Complex, PDB code: 5c5j was solved by D.T.Nair, J.Kottur, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.91 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.450, 57.380, 110.640, 90.00, 94.51, 90.00
R / Rfree (%)	22.2 / 27.4

The binding sites of Magnesium atom in the Poymerase Nucleotide Complex (pdb code 5c5j). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Poymerase Nucleotide Complex, PDB code: 5c5j:

Magnesium binding site 1 out of 1 in the Poymerase Nucleotide Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Poymerase Nucleotide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:46.5 occ:1.00 OD1 A:ASP8 2.1 55.1 1.0 O A:MET9 2.1 45.7 1.0 O2B A:8GT401 2.3 51.4 1.0 OD2 A:ASP103 2.4 55.3 1.0 O1A A:8GT401 2.6 57.1 1.0 O1G A:8GT401 2.6 58.9 1.0 CG A:ASP8 3.2 53.7 1.0 PB A:8GT401 3.3 57.3 1.0 C A:MET9 3.3 47.3 1.0 O3A A:8GT401 3.5 63.1 1.0 CG A:ASP103 3.5 55.0 1.0 PA A:8GT401 3.5 62.5 1.0 N A:MET9 3.8 47.2 1.0 PG A:8GT401 3.8 62.1 1.0 OD2 A:ASP8 3.8 58.2 1.0 O3B A:8GT401 3.9 61.5 1.0 CA A:MET9 4.0 48.0 1.0 OD1 A:ASP103 4.1 59.1 1.0 C A:ASP8 4.1 46.5 1.0 C5' A:8GT401 4.3 57.5 1.0 OE2 A:GLU104 4.3 57.0 1.0 N A:ASP10 4.4 48.1 1.0 O5' A:8GT401 4.4 58.1 1.0 CB A:ASP8 4.4 49.2 1.0 CB A:MET9 4.5 50.1 1.0 CG A:GLU104 4.5 56.3 1.0 CA A:ASP8 4.5 47.1 1.0 O A:ASP103 4.6 53.6 1.0 NZ A:LYS157 4.6 55.8 1.0 O3G A:8GT401 4.6 62.1 1.0 O A:ASP8 4.6 50.2 1.0 CE A:LYS157 4.6 54.7 1.0 CB A:ASP103 4.6 53.2 1.0 O1B A:8GT401 4.6 52.5 1.0 CA A:ASP10 4.7 46.8 1.0 N A:CYS11 4.7 43.9 1.0 O2A A:8GT401 4.7 63.5 1.0 N A:PHE12 4.8 45.6 1.0 CB A:PHE12 4.8 48.5 1.0 O2G A:8GT401 4.9 63.4 1.0 CD A:GLU104 4.9 58.0 1.0 C A:ASP10 5.0 49.9 1.0

J.Kottur, D.T.Nair. Reactive Oxygen Species Play An Important Role in the Bactericidal Activity of Quinolone Antibiotics Angew.Chem.Int.Ed.Engl. V. 55 2397 2016.
ISSN: ESSN 1521-3773
PubMed: 26757158
DOI: 10.1002/ANIE.201509340