Magnesium in PDB 4irk: Structure of Polymerase-Dna Complex, Dna

All present enzymatic activity of Structure of Polymerase-Dna Complex, Dna:
2.7.7.7;

The structure of Structure of Polymerase-Dna Complex, Dna, PDB code: 4irk was solved by D.T.Nair, A.Sharma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.18 / 2.32
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.650, 57.080, 110.230, 90.00, 94.92, 90.00
R / Rfree (%)	20.9 / 26.2

The binding sites of Magnesium atom in the Structure of Polymerase-Dna Complex, Dna (pdb code 4irk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Polymerase-Dna Complex, Dna, PDB code: 4irk:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Polymerase-Dna Complex, Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Polymerase-Dna Complex, Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:46.8 occ:1.00 OD1 B:ASP8 2.0 43.4 1.0 O1A B:DCP401 2.5 73.8 1.0 O1G B:DCP401 2.5 81.1 1.0 OD2 B:ASP103 2.6 59.5 1.0 O2B B:DCP401 2.6 72.3 1.0 O B:MET9 2.9 32.9 1.0 CG B:ASP8 3.1 40.8 1.0 OD2 B:ASP8 3.5 43.2 1.0 PB B:DCP401 3.5 74.0 1.0 OE2 B:GLU104 3.6 48.4 1.0 PA B:DCP401 3.6 83.1 1.0 O3A B:DCP401 3.7 79.7 1.0 PG B:DCP401 3.7 80.1 1.0 CG B:ASP103 3.7 49.8 1.0 O3B B:DCP401 4.0 82.1 1.0 C5' B:DCP401 4.0 69.9 1.0 C B:MET9 4.0 30.8 1.0 NZ B:LYS157 4.1 37.7 1.0 CG B:GLU104 4.2 43.2 1.0 N B:MET9 4.2 32.4 1.0 O5' B:DCP401 4.2 74.7 1.0 O3G B:DCP401 4.3 75.6 1.0 CB B:ASP103 4.3 43.4 1.0 CB B:ASP8 4.4 33.4 1.0 CD B:GLU104 4.4 46.9 1.0 C B:ASP8 4.5 31.5 1.0 O B:ASP103 4.6 36.7 1.0 CA B:MET9 4.6 31.6 1.0 CA B:ASP8 4.6 30.9 1.0 OD1 B:ASP103 4.7 50.3 1.0 O B:HOH551 4.8 60.5 1.0 O1B B:DCP401 4.9 75.1 1.0 O2A B:DCP401 5.0 75.2 1.0 O2G B:DCP401 5.0 82.2 1.0

Magnesium binding site 2 out of 2 in the Structure of Polymerase-Dna Complex, Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Polymerase-Dna Complex, Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:73.4 occ:1.00 O2B A:DCP401 1.9 65.1 1.0 O A:MET9 2.1 25.0 1.0 OD2 A:ASP103 2.6 31.4 1.0 OD1 A:ASP8 2.6 32.2 1.0 O1G A:DCP401 2.9 58.1 1.0 C A:MET9 3.2 25.3 1.0 O1A A:DCP401 3.2 61.9 1.0 PB A:DCP401 3.2 69.0 1.0 CG A:ASP103 3.5 32.1 1.0 CB A:ASP103 3.8 29.3 1.0 PG A:DCP401 3.8 62.2 1.0 O3B A:DCP401 3.8 71.2 1.0 N A:MET9 3.8 24.7 1.0 CG A:ASP8 3.8 29.7 1.0 C5' A:DCP401 3.9 55.2 1.0 CA A:MET9 3.9 25.2 1.0 O3A A:DCP401 3.9 72.4 1.0 O3G A:DCP401 4.1 59.3 1.0 N A:CYS11 4.1 26.8 1.0 PA A:DCP401 4.1 74.3 1.0 N A:PHE12 4.2 28.2 1.0 CB A:MET9 4.2 25.4 1.0 N A:ASP10 4.2 24.1 1.0 O A:HOH514 4.2 29.5 1.0 CB A:PHE12 4.2 29.2 1.0 C A:ASP8 4.3 26.0 1.0 CA A:ASP10 4.4 23.8 1.0 O1B A:DCP401 4.4 68.5 1.0 C A:ASP10 4.4 23.4 1.0 O A:ASP103 4.5 33.3 1.0 OD1 A:ASP103 4.5 33.6 1.0 O5' A:DCP401 4.6 58.7 1.0 OD2 A:ASP8 4.6 29.7 1.0 CA A:CYS11 4.7 29.5 1.0 O A:ASP8 4.8 27.7 1.0 CA A:ASP8 4.8 26.1 1.0 CB A:ASP8 4.8 28.0 1.0 CA A:PHE12 4.8 29.3 1.0 C4' A:DCP401 5.0 54.1 1.0 C A:ASP103 5.0 29.4 1.0

A.Sharma, J.Kottur, N.Narayanan, D.T.Nair. A Strategically Located Serine Residue Is Critical For the Mutator Activity of Dna Polymerase IV From Escherichia Coli. Nucleic Acids Res. V. 41 5104 2013.
ISSN: ISSN 0305-1048
PubMed: 23525461
DOI: 10.1093/NAR/GKT146