Magnesium in PDB 4ir9: Polymerase-Dna Complex

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

The structure of Polymerase-Dna Complex, PDB code: 4ir9 was solved by A.Sharma, D.T.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.66 / 2.33
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.760, 57.040, 110.700, 90.00, 94.76, 90.00
R / Rfree (%)	21.1 / 27.2

The binding sites of Magnesium atom in the Polymerase-Dna Complex (pdb code 4ir9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Polymerase-Dna Complex, PDB code: 4ir9:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Polymerase-Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Polymerase-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:20.1 occ:1.00 OD1 F:ASP8 2.0 40.5 1.0 O2B F:XG4401 2.0 32.2 1.0 O1G F:XG4401 2.2 37.8 1.0 O F:MET9 2.2 36.6 1.0 OD1 F:ASP103 2.2 35.2 1.0 O1A F:XG4401 2.4 33.6 1.0 CG F:ASP8 3.2 41.1 1.0 PB F:XG4401 3.2 33.9 1.0 O F:HOH549 3.4 57.3 1.0 C F:MET9 3.4 39.9 1.0 CG F:ASP103 3.5 35.7 1.0 PG F:XG4401 3.5 36.2 1.0 PA F:XG4401 3.6 31.9 1.0 N3A F:XG4401 3.7 34.5 1.0 O3B F:XG4401 3.7 34.4 1.0 OD2 F:ASP8 3.9 47.4 1.0 MG F:MG403 3.9 57.0 1.0 O F:HOH508 4.0 43.8 1.0 N F:MET9 4.0 40.5 1.0 C5' F:XG4401 4.1 33.0 1.0 O3G F:XG4401 4.1 36.5 1.0 O F:HOH518 4.2 41.8 1.0 OD2 F:ASP103 4.2 33.1 1.0 CA F:MET9 4.3 39.4 1.0 C F:ASP8 4.3 40.5 1.0 O5' F:XG4401 4.3 33.2 1.0 CB F:ASP8 4.4 42.8 1.0 N F:ASP10 4.4 40.5 1.0 N F:CYS11 4.5 37.8 1.0 O1B F:XG4401 4.5 34.1 1.0 CA F:ASP10 4.6 39.4 1.0 CB F:ASP103 4.6 34.9 1.0 N F:PHE12 4.7 43.8 1.0 CA F:ASP8 4.7 40.9 1.0 CB F:PHE12 4.7 44.8 1.0 O F:ASP8 4.7 43.3 1.0 CB F:MET9 4.7 39.2 1.0 C F:ASP10 4.7 38.6 1.0 O2G F:XG4401 4.7 35.8 1.0 O2A F:XG4401 4.8 34.9 1.0 NZ F:LYS157 4.8 57.0 1.0

Magnesium binding site 2 out of 4 in the Polymerase-Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Polymerase-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg403 b:57.0 occ:1.00 OE1 F:GLU104 1.9 52.0 1.0 O F:HOH518 2.5 41.8 1.0 OD2 F:ASP103 2.5 33.1 1.0 O1A F:XG4401 2.7 33.6 1.0 CD F:GLU104 2.8 47.6 1.0 O3' H:DC873 2.8 41.6 1.0 CG F:GLU104 3.2 45.0 1.0 CG F:ASP103 3.2 35.7 1.0 OD1 F:ASP103 3.3 35.2 1.0 C3' H:DC873 3.3 40.4 1.0 OD2 F:ASP8 3.5 47.4 1.0 OD1 F:ASP8 3.6 40.5 1.0 CB F:GLU104 3.6 40.4 1.0 PA F:XG4401 3.7 31.9 1.0 CG F:ASP8 3.8 41.1 1.0 O5' F:XG4401 3.9 33.2 1.0 OG F:SER101 3.9 40.4 1.0 OE2 F:GLU104 3.9 50.3 1.0 MG F:MG402 3.9 20.1 1.0 C5' F:XG4401 4.0 33.0 1.0 O2A F:XG4401 4.2 34.9 1.0 C4' H:DC873 4.3 41.9 1.0 C5' H:DC873 4.4 44.4 1.0 C2' H:DC873 4.5 40.1 1.0 CB F:ASP103 4.7 34.9 1.0 CA F:GLU104 4.7 35.6 1.0 O5' H:DC873 4.7 48.3 1.0 O F:HOH508 4.7 43.8 1.0 C F:ASP103 4.8 35.8 1.0 N F:GLU104 4.8 35.2 1.0 O2B F:XG4401 4.9 32.2 1.0 CB F:SER101 5.0 38.6 1.0

Magnesium binding site 3 out of 4 in the Polymerase-Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Polymerase-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:30.0 occ:1.00 O1G A:XG4401 2.1 45.2 1.0 O1A A:XG4401 2.1 57.4 1.0 OD1 A:ASP103 2.2 45.5 1.0 O A:MET9 2.3 54.0 1.0 O2B A:XG4401 2.3 51.8 1.0 OD1 A:ASP8 2.5 70.3 1.0 OD2 A:ASP8 2.6 59.5 1.0 CG A:ASP8 2.8 62.1 1.0 MG A:MG403 2.9 0.4 1.0 CG A:ASP103 3.3 53.6 1.0 PA A:XG4401 3.3 48.9 1.0 PB A:XG4401 3.3 47.7 1.0 PG A:XG4401 3.4 48.0 1.0 N3A A:XG4401 3.4 44.6 1.0 C A:MET9 3.4 47.8 1.0 OD2 A:ASP103 3.7 51.6 1.0 O3B A:XG4401 3.9 51.2 1.0 NZ A:LYS157 3.9 63.7 1.0 O3G A:XG4401 4.0 52.5 1.0 N A:MET9 4.0 51.2 1.0 CA A:MET9 4.2 51.9 1.0 CB A:ASP8 4.3 60.0 1.0 C5' A:XG4401 4.3 54.1 1.0 C A:ASP8 4.3 52.9 1.0 O2A A:XG4401 4.4 43.4 1.0 O5' A:XG4401 4.4 54.1 1.0 N A:ASP10 4.5 47.1 1.0 O2G A:XG4401 4.6 47.8 1.0 CB A:ASP103 4.7 56.2 1.0 CB A:MET9 4.7 55.6 1.0 CA A:ASP10 4.7 46.1 1.0 OE2 A:GLU104 4.7 69.7 1.0 CA A:ASP8 4.7 54.8 1.0 O A:ASP103 4.8 53.3 1.0 O1B A:XG4401 4.8 51.6 1.0 CE A:LYS157 4.8 61.3 1.0 O A:ASP8 4.8 51.5 1.0 N A:PHE12 4.9 44.2 1.0 CB A:PHE12 4.9 51.9 1.0 N A:CYS11 4.9 46.0 1.0 C A:ASP10 5.0 44.3 1.0

Magnesium binding site 4 out of 4 in the Polymerase-Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Polymerase-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:0.4 occ:1.00 O1A A:XG4401 1.8 57.4 1.0 OE2 A:GLU104 2.0 69.7 1.0 OD1 A:ASP8 2.1 70.3 1.0 MG A:MG402 2.9 30.0 1.0 PA A:XG4401 2.9 48.9 1.0 OD2 A:ASP103 2.9 51.6 1.0 CD A:GLU104 3.0 69.0 1.0 CG A:ASP8 3.3 62.1 1.0 O2A A:XG4401 3.3 43.4 1.0 OD1 A:ASP103 3.5 45.5 1.0 CG A:GLU104 3.5 66.7 1.0 CG A:ASP103 3.6 53.6 1.0 OD2 A:ASP8 3.9 59.5 1.0 O3' C:DC873 3.9 51.6 1.0 O5' A:XG4401 3.9 54.1 1.0 O1G A:XG4401 3.9 45.2 1.0 C3' C:DC873 4.0 49.3 1.0 OE1 A:GLU104 4.0 70.2 1.0 N3A A:XG4401 4.1 44.6 1.0 C5' A:XG4401 4.2 54.1 1.0 CB A:ASP8 4.4 60.0 1.0 O2B A:XG4401 4.4 51.8 1.0 CB A:GLU104 4.7 65.7 1.0 O A:ASP103 4.9 53.3 1.0 C2' C:DC873 4.9 51.8 1.0 O5' C:DC873 4.9 60.7 1.0 O A:MET9 4.9 54.0 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