Magnesium in PDB 4ird: Structure of Polymerase-Dna Complex

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

The structure of Structure of Polymerase-Dna Complex, PDB code: 4ird 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)	43.28 / 2.48
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.690, 56.880, 110.930, 90.00, 93.99, 90.00
R / Rfree (%)	21.3 / 27.7

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

Magnesium binding site 1 out of 4 in the Structure of 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 Structure of Polymerase-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg903 b:23.2 occ:1.00 OD1 F:ASP8 2.0 60.6 1.0 O1G F:DZ4876 2.1 34.4 1.0 O1A F:DZ4876 2.2 28.1 1.0 O F:MET9 2.2 39.7 1.0 O1B F:DZ4876 2.2 33.0 1.0 OD1 F:ASP103 2.3 30.5 1.0 CG F:ASP8 3.1 55.6 1.0 PB F:DZ4876 3.3 31.4 1.0 MG F:MG904 3.4 47.7 1.0 C F:MET9 3.4 37.6 1.0 O F:HOH1005 3.4 71.1 1.0 OD2 F:ASP8 3.5 55.5 1.0 PG F:DZ4876 3.5 32.8 1.0 PA F:DZ4876 3.5 31.8 1.0 CG F:ASP103 3.5 33.5 1.0 N3A F:DZ4876 3.7 31.3 1.0 N F:MET9 3.9 38.0 1.0 O3B F:DZ4876 3.9 28.6 1.0 O F:HOH1017 4.1 55.3 1.0 OD2 F:ASP103 4.2 32.1 1.0 O3G F:DZ4876 4.2 33.9 1.0 CA F:MET9 4.2 37.9 1.0 C F:ASP8 4.2 38.1 1.0 C5' F:DZ4876 4.3 36.0 1.0 CB F:ASP8 4.3 48.9 1.0 N F:CYS11 4.4 35.7 1.0 O5' F:DZ4876 4.4 30.2 1.0 N F:ASP10 4.4 34.6 1.0 CA F:ASP10 4.6 36.8 1.0 NZ F:LYS157 4.6 54.9 1.0 O2G F:DZ4876 4.6 30.6 1.0 CA F:ASP8 4.6 41.4 1.0 O2B F:DZ4876 4.7 31.6 1.0 CB F:MET9 4.7 38.3 1.0 CB F:ASP103 4.7 32.3 1.0 C F:ASP10 4.8 35.4 1.0 CE F:LYS157 4.8 60.2 1.0 N F:PHE12 4.8 42.6 1.0 O2A F:DZ4876 4.8 28.7 1.0 CB F:PHE12 4.8 40.1 1.0 O F:ASP8 4.8 39.0 1.0

Magnesium binding site 2 out of 4 in the Structure of 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 Structure of Polymerase-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg904 b:47.7 occ:1.00 OE1 F:GLU104 2.1 46.7 1.0 O1A F:DZ4876 2.2 28.1 1.0 OD2 F:ASP103 2.7 32.1 1.0 O F:HOH1005 2.8 71.1 1.0 CD F:GLU104 2.9 49.6 1.0 CG F:GLU104 3.1 41.7 1.0 OD1 F:ASP103 3.1 30.5 1.0 PA F:DZ4876 3.1 31.8 1.0 OD1 F:ASP8 3.2 60.6 1.0 CG F:ASP103 3.3 33.5 1.0 O F:HOH1079 3.3 41.1 1.0 OD2 F:ASP8 3.3 55.5 1.0 O3' H:DC873 3.4 47.9 1.0 MG F:MG903 3.4 23.2 1.0 C3' H:DC873 3.4 45.5 1.0 O5' F:DZ4876 3.5 30.2 1.0 CG F:ASP8 3.6 55.6 1.0 O2A F:DZ4876 3.7 28.7 1.0 C5' F:DZ4876 3.9 36.0 1.0 OE2 F:GLU104 4.0 39.3 1.0 C2' H:DC873 4.4 44.9 1.0 CB F:GLU104 4.4 32.2 1.0 OG F:SER101 4.5 38.2 1.0 N3A F:DZ4876 4.5 31.3 1.0 C4' H:DC873 4.6 45.7 1.0 O1B F:DZ4876 4.6 33.0 1.0 O1G F:DZ4876 4.6 34.4 1.0 O F:HOH1017 4.8 55.3 1.0 CB F:ASP103 4.8 32.3 1.0 C5' H:DC873 4.8 48.0 1.0 CB F:ASP8 4.9 48.9 1.0

Magnesium binding site 3 out of 4 in the Structure of 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 Structure of Polymerase-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:38.1 occ:1.00 OD1 A:ASP8 2.0 74.3 1.0 O1A A:DZ4875 2.0 57.4 1.0 OD1 A:ASP103 2.0 52.7 1.0 O1B A:DZ4875 2.1 57.5 1.0 O A:MET9 2.3 51.4 1.0 O1G A:DZ4875 2.4 43.9 1.0 MG A:MG902 2.6 0.7 1.0 CG A:ASP8 3.1 75.2 1.0 CG A:ASP103 3.1 60.4 1.0 PA A:DZ4875 3.2 51.1 1.0 PB A:DZ4875 3.3 53.0 1.0 OD2 A:ASP8 3.4 84.3 1.0 OD2 A:ASP103 3.4 61.3 1.0 C A:MET9 3.5 55.0 1.0 N3A A:DZ4875 3.6 51.8 1.0 PG A:DZ4875 3.6 47.9 1.0 C5' A:DZ4875 3.8 50.9 1.0 O5' A:DZ4875 3.8 51.9 1.0 O3B A:DZ4875 3.9 55.7 1.0 N A:MET9 4.1 54.4 1.0 O3G A:DZ4875 4.2 51.4 1.0 CA A:MET9 4.2 53.3 1.0 NZ A:LYS157 4.3 61.0 1.0 C A:ASP8 4.4 59.0 1.0 CB A:ASP103 4.4 59.2 1.0 CB A:ASP8 4.4 74.8 1.0 CB A:MET9 4.5 60.5 1.0 O2A A:DZ4875 4.6 52.2 1.0 O A:ASP103 4.6 60.1 1.0 N A:ASP10 4.6 55.0 1.0 O2B A:DZ4875 4.7 52.8 1.0 OE2 A:GLU104 4.8 0.3 1.0 CA A:ASP8 4.8 62.9 1.0 CB A:PHE12 4.8 66.3 1.0 N A:CYS11 4.8 58.5 1.0 N A:PHE12 4.9 60.4 1.0 O A:ASP8 4.9 58.2 1.0 CA A:ASP10 4.9 56.0 1.0 O2G A:DZ4875 4.9 42.0 1.0 CE A:LYS157 4.9 57.3 1.0

Magnesium binding site 4 out of 4 in the Structure of 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 Structure of Polymerase-Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:0.7 occ:1.00 O1A A:DZ4875 2.0 57.4 1.0 OE2 A:GLU104 2.3 0.3 1.0 OD2 A:ASP103 2.6 61.3 1.0 MG A:MG901 2.6 38.1 1.0 OD1 A:ASP8 2.7 74.3 1.0 CD A:GLU104 3.0 98.0 1.0 PA A:DZ4875 3.1 51.1 1.0 OD1 A:ASP103 3.2 52.7 1.0 O3' C:DC873 3.3 66.9 1.0 CG A:ASP103 3.3 60.4 1.0 CG A:GLU104 3.3 87.6 1.0 O5' A:DZ4875 3.4 51.9 1.0 CG A:ASP8 3.5 75.2 1.0 C3' C:DC873 3.7 62.9 1.0 O2A A:DZ4875 3.8 52.2 1.0 OD2 A:ASP8 3.9 84.3 1.0 C5' A:DZ4875 4.1 50.9 1.0 OE1 A:GLU104 4.1 91.2 1.0 O1G A:DZ4875 4.1 43.9 1.0 O1B A:DZ4875 4.3 57.5 1.0 CB A:GLU104 4.4 73.0 1.0 N3A A:DZ4875 4.4 51.8 1.0 O A:ASP103 4.4 60.1 1.0 CB A:ASP8 4.6 74.8 1.0 C2' C:DC873 4.7 65.5 1.0 OG A:SER101 4.8 52.2 1.0 O A:MET9 4.8 51.4 1.0 CB A:ASP103 4.8 59.2 1.0 C A:ASP103 4.8 60.9 1.0 C4' C:DC873 4.8 64.7 1.0 O5' C:DC873 5.0 65.8 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