Magnesium in PDB 4irc: Polymerase-Dna Complex

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

The structure of Polymerase-Dna Complex, PDB code: 4irc 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)	45.30 / 2.67
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.140, 56.950, 110.810, 90.00, 93.53, 90.00
R / Rfree (%)	22.5 / 27.5

The binding sites of Magnesium atom in the Polymerase-Dna Complex (pdb code 4irc). 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: 4irc:
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:47.6 occ:1.00 O F:MET9 1.9 49.3 1.0 OD1 F:ASP8 2.0 56.7 1.0 O1A F:0KX401 2.2 46.5 1.0 O1G F:0KX401 2.2 51.2 1.0 OD1 F:ASP103 2.4 51.3 1.0 O2B F:0KX401 2.4 48.4 1.0 O F:HOH502 3.0 65.3 1.0 MG F:MG403 3.1 78.8 1.0 CG F:ASP8 3.2 54.5 1.0 C F:MET9 3.2 48.8 1.0 PB F:0KX401 3.4 45.4 1.0 PG F:0KX401 3.5 47.5 1.0 O3B F:0KX401 3.6 46.4 1.0 PA F:0KX401 3.6 44.5 1.0 CG F:ASP103 3.6 47.5 1.0 OD2 F:ASP8 3.8 55.1 1.0 N3A F:0KX401 3.9 46.9 1.0 O3G F:0KX401 3.9 49.0 1.0 C5' F:0KX401 4.0 46.7 1.0 N F:MET9 4.0 44.8 1.0 N F:ASP10 4.0 49.7 1.0 CA F:ASP10 4.1 52.6 1.0 O5' F:0KX401 4.2 43.7 1.0 CA F:MET9 4.2 46.6 1.0 CB F:ASP8 4.2 49.4 1.0 C F:ASP8 4.3 45.4 1.0 OD2 F:ASP103 4.3 42.9 1.0 O F:HOH518 4.5 76.0 1.0 N F:CYS11 4.5 52.1 1.0 C F:ASP10 4.6 50.1 1.0 CA F:ASP8 4.6 46.2 1.0 O F:HOH536 4.7 66.8 1.0 CB F:ASP103 4.7 44.5 1.0 O2G F:0KX401 4.7 47.2 1.0 O1B F:0KX401 4.7 49.0 1.0 CB F:MET9 4.7 48.2 1.0 NZ F:LYS157 4.8 63.0 1.0 O2A F:0KX401 4.8 40.4 1.0 O F:ASP8 4.9 47.6 1.0 CB F:PHE12 5.0 53.1 1.0 N F:PHE12 5.0 55.1 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:78.8 occ:1.00 O1A F:0KX401 2.1 46.5 1.0 O F:HOH518 2.3 76.0 1.0 OE1 F:GLU104 2.7 54.9 1.0 OD1 F:ASP8 2.9 56.7 1.0 PA F:0KX401 3.0 44.5 1.0 OD1 F:ASP103 3.0 51.3 1.0 O F:HOH502 3.1 65.3 1.0 MG F:MG402 3.1 47.6 1.0 OD2 F:ASP103 3.1 42.9 1.0 OD2 F:ASP8 3.2 55.1 1.0 CG F:GLU104 3.3 49.9 1.0 O5' F:0KX401 3.3 43.7 1.0 CD F:GLU104 3.3 52.6 1.0 CG F:ASP8 3.4 54.5 1.0 CG F:ASP103 3.5 47.5 1.0 O2A F:0KX401 3.7 40.4 1.0 C3' H:DC873 3.8 49.4 1.0 C5' F:0KX401 3.9 46.7 1.0 O3' H:DC873 3.9 48.8 1.0 N3A F:0KX401 4.4 46.9 1.0 O1G F:0KX401 4.5 51.2 1.0 OE2 F:GLU104 4.5 55.0 1.0 O2B F:0KX401 4.6 48.4 1.0 C2' H:DC873 4.7 50.3 1.0 CB F:GLU104 4.7 44.9 1.0 O F:HOH536 4.7 66.8 1.0 O F:MET9 4.8 49.3 1.0 CB F:ASP8 4.8 49.4 1.0 O5' H:DC873 4.9 55.5 1.0 C5' H:DC873 4.9 53.5 1.0 C4' H:DC873 4.9 50.8 1.0 OG F:SER101 5.0 44.2 1.0 CB F:ASP103 5.0 44.5 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:50.2 occ:1.00 OD1 A:ASP8 1.9 67.6 1.0 O1A A:0KX401 1.9 73.4 1.0 OD1 A:ASP103 2.0 66.0 1.0 O2B A:0KX401 2.1 69.2 1.0 O1G A:0KX401 2.4 80.9 1.0 O A:MET9 2.7 61.9 1.0 CG A:ASP8 2.9 75.5 1.0 PA A:0KX401 3.1 69.6 1.0 MG A:MG403 3.1 0.6 1.0 PB A:0KX401 3.1 67.1 1.0 CG A:ASP103 3.2 68.9 1.0 OD2 A:ASP8 3.3 86.3 1.0 N3A A:0KX401 3.4 72.3 1.0 PG A:0KX401 3.5 65.8 1.0 O3B A:0KX401 3.5 82.2 1.0 C5' A:0KX401 3.6 65.5 1.0 O5' A:0KX401 3.7 76.0 1.0 C A:MET9 3.8 60.1 1.0 N A:MET9 3.8 62.5 1.0 OD2 A:ASP103 3.8 73.9 1.0 O3G A:0KX401 4.0 80.0 1.0 CB A:ASP8 4.3 73.7 1.0 CA A:MET9 4.3 61.3 1.0 CB A:ASP103 4.4 68.1 1.0 O2A A:0KX401 4.4 63.5 1.0 O A:HOH517 4.4 83.1 1.0 O1B A:0KX401 4.5 69.0 1.0 NZ A:LYS157 4.6 64.1 1.0 CB A:PHE12 4.6 66.1 1.0 C A:ASP8 4.6 65.8 1.0 CB A:MET9 4.6 64.9 1.0 CA A:ASP8 4.7 68.8 1.0 N A:PHE12 4.8 63.3 1.0 O2G A:0KX401 4.8 84.2 1.0 O A:ASP103 4.8 71.5 1.0 N A:ASP10 4.8 63.8 1.0 N A:CYS11 4.9 71.2 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:0.6 occ:1.00 O1A A:0KX401 2.1 73.4 1.0 OE2 A:GLU104 2.2 84.7 1.0 OD2 A:ASP8 2.2 86.3 1.0 CG A:ASP8 3.0 75.5 1.0 MG A:MG402 3.1 50.2 1.0 PA A:0KX401 3.1 69.6 1.0 CD A:GLU104 3.2 79.3 1.0 OD1 A:ASP8 3.2 67.6 1.0 O2A A:0KX401 3.6 63.5 1.0 CG A:GLU104 3.6 76.2 1.0 OD1 A:ASP103 3.6 66.0 1.0 O A:HOH517 3.7 83.1 1.0 OD2 A:ASP103 3.7 73.9 1.0 O5' A:0KX401 3.7 76.0 1.0 O3' C:DC873 3.7 66.7 1.0 C3' C:DC873 3.9 64.9 1.0 O1G A:0KX401 4.0 80.9 1.0 CG A:ASP103 4.1 68.9 1.0 OE1 A:GLU104 4.3 74.7 1.0 CB A:ASP8 4.3 73.7 1.0 O5' C:DC873 4.4 65.1 1.0 C5' A:0KX401 4.5 65.5 1.0 N3A A:0KX401 4.6 72.3 1.0 OP1 C:DC873 4.6 72.6 1.0 CB A:GLU104 4.6 69.0 1.0 O2B A:0KX401 4.8 69.2 1.0 C5' C:DC873 4.8 60.8 1.0 P C:DC873 4.8 73.1 1.0 C2' C:DC873 4.9 67.4 1.0 C4' C:DC873 4.9 65.0 1.0 OP2 C:DC873 4.9 66.0 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