Magnesium in PDB 4ir1: Polymerase-Dna Complex

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

The structure of Polymerase-Dna Complex, PDB code: 4ir1 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 / 2.38
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	85.750, 57.250, 111.301, 90.00, 90.44, 90.00
R / Rfree (%)	21.4 / 26.9

The binding sites of Magnesium atom in the Polymerase-Dna Complex (pdb code 4ir1). 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: 4ir1:
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:Mg903 b:40.8 occ:1.00 OD1 F:ASP8 2.1 39.6 1.0 O1A F:1FZ876 2.2 40.9 1.0 O2B F:1FZ876 2.2 40.8 1.0 O1G F:1FZ876 2.3 40.4 1.0 O F:MET9 2.3 40.3 1.0 OD1 F:ASP103 2.3 39.7 1.0 PB F:1FZ876 3.3 40.6 1.0 CG F:ASP8 3.3 39.4 1.0 PA F:1FZ876 3.4 40.8 1.0 CG F:ASP103 3.5 39.6 1.0 PG F:1FZ876 3.5 40.3 1.0 O F:HOH609 3.5 43.5 1.0 C F:MET9 3.5 40.5 1.0 N3A F:1FZ876 3.6 40.7 1.0 O3B F:1FZ876 3.8 40.4 1.0 O F:HOH576 3.8 29.7 1.0 MG F:MG904 3.9 44.5 1.0 N F:MET9 3.9 39.9 1.0 OD2 F:ASP8 4.0 39.4 1.0 O F:HOH526 4.0 38.4 1.0 OD2 F:ASP103 4.0 39.5 1.0 C5' F:1FZ876 4.1 41.3 1.0 O3G F:1FZ876 4.1 40.2 1.0 O5' F:1FZ876 4.1 41.1 1.0 CA F:MET9 4.3 40.3 1.0 C F:ASP8 4.3 39.9 1.0 CB F:ASP8 4.5 39.5 1.0 N F:ASP10 4.6 41.0 1.0 O2A F:1FZ876 4.6 40.9 1.0 O1B F:1FZ876 4.6 40.8 1.0 N F:CYS11 4.7 42.8 1.0 O2G F:1FZ876 4.7 40.3 1.0 NZ F:LYS157 4.7 47.6 1.0 CB F:ASP103 4.7 39.8 1.0 O F:ASP8 4.7 40.2 1.0 CA F:ASP8 4.7 39.5 1.0 CB F:MET9 4.7 40.3 1.0 CA F:ASP10 4.8 41.4 1.0 N F:PHE12 4.8 41.6 1.0 CB F:PHE12 4.8 41.5 1.0 C F:ASP10 4.9 42.3 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:Mg904 b:44.5 occ:1.00 OE1 F:GLU104 1.9 41.2 1.0 CD F:GLU104 2.3 40.6 1.0 CG F:GLU104 2.6 39.6 1.0 O F:HOH576 2.7 29.7 1.0 O1A F:1FZ876 2.7 40.9 1.0 OD2 F:ASP103 2.7 39.5 1.0 O3' H:DC873 3.3 41.6 1.0 C3' H:DC873 3.3 41.5 1.0 OD2 F:ASP8 3.3 39.4 1.0 OE2 F:GLU104 3.4 41.1 1.0 OD1 F:ASP8 3.6 39.6 1.0 CG F:ASP103 3.6 39.6 1.0 PA F:1FZ876 3.7 40.8 1.0 OD1 F:ASP103 3.7 39.7 1.0 CG F:ASP8 3.7 39.4 1.0 CB F:GLU104 3.8 39.0 1.0 MG F:MG903 3.9 40.8 1.0 O5' F:1FZ876 4.0 41.1 1.0 O2A F:1FZ876 4.0 40.9 1.0 O5' H:DC873 4.0 41.5 1.0 OG F:SER101 4.2 39.6 1.0 C4' H:DC873 4.3 41.7 1.0 C5' H:DC873 4.3 41.8 1.0 C5' F:1FZ876 4.4 41.3 1.0 C2' H:DC873 4.4 41.4 1.0 OP1 H:DC873 4.7 41.9 1.0 O F:HOH526 4.7 38.4 1.0 NZ F:LYS150 4.8 39.1 1.0 CA F:GLU104 4.8 39.1 1.0 P H:DC873 4.9 41.7 1.0 N F:GLU104 5.0 39.3 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:Mg901 b:49.2 occ:1.00 O1A A:1FZ875 2.0 52.9 1.0 O1G A:1FZ875 2.2 51.9 1.0 OD1 A:ASP8 2.2 52.3 1.0 O A:MET9 2.3 57.3 1.0 O2B A:1FZ875 2.3 51.5 1.0 OD1 A:ASP103 2.4 60.5 1.0 PB A:1FZ875 3.3 50.7 1.0 CG A:ASP8 3.3 53.6 1.0 MG A:MG902 3.4 76.2 1.0 PG A:1FZ875 3.4 51.8 1.0 PA A:1FZ875 3.4 51.7 1.0 C A:MET9 3.4 54.7 1.0 CG A:ASP103 3.5 59.9 1.0 N3A A:1FZ875 3.7 50.7 1.0 O3B A:1FZ875 3.8 51.3 1.0 N A:MET9 3.8 54.7 1.0 O A:HOH518 3.8 67.8 1.0 O3G A:1FZ875 3.8 52.3 1.0 NZ A:LYS157 3.9 53.2 1.0 OD2 A:ASP8 4.0 54.2 1.0 OD2 A:ASP103 4.1 57.8 1.0 C5' A:1FZ875 4.1 51.0 1.0 CA A:MET9 4.1 55.0 1.0 C A:ASP8 4.2 56.1 1.0 O5' A:1FZ875 4.3 51.1 1.0 CB A:ASP8 4.4 54.5 1.0 N A:ASP10 4.5 54.4 1.0 O2A A:1FZ875 4.6 51.5 1.0 CB A:MET9 4.6 55.8 1.0 N A:CYS11 4.6 56.5 1.0 CA A:ASP8 4.6 55.5 1.0 O1B A:1FZ875 4.7 50.3 1.0 CA A:ASP10 4.7 53.6 1.0 N A:PHE12 4.7 54.2 1.0 O2G A:1FZ875 4.7 52.1 1.0 CB A:ASP103 4.7 61.0 1.0 O A:ASP103 4.8 59.8 1.0 CE A:LYS157 4.9 53.3 1.0 O A:ASP8 4.9 57.7 1.0 CB A:PHE12 4.9 56.0 1.0 C A:ASP10 4.9 53.0 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:Mg902 b:76.2 occ:1.00 O A:HOH518 1.8 67.8 1.0 OE2 A:GLU104 2.0 60.9 1.0 O1A A:1FZ875 2.2 52.9 1.0 CD A:GLU104 2.8 62.4 1.0 OD1 A:ASP8 2.8 52.3 1.0 OD2 A:ASP8 3.0 54.2 1.0 PA A:1FZ875 3.1 51.7 1.0 O2A A:1FZ875 3.2 51.5 1.0 CG A:ASP8 3.2 53.6 1.0 CG A:GLU104 3.3 61.5 1.0 MG A:MG901 3.4 49.2 1.0 OE1 A:GLU104 3.6 66.6 1.0 C3' C:DC873 3.7 50.2 1.0 OD2 A:ASP103 3.8 57.8 1.0 O5' A:1FZ875 3.8 51.1 1.0 O3' C:DC873 3.8 50.6 1.0 O1G A:1FZ875 4.0 51.9 1.0 OD1 A:ASP103 4.0 60.5 1.0 O5' C:DC873 4.1 51.2 1.0 CG A:ASP103 4.3 59.9 1.0 C5' A:1FZ875 4.3 51.0 1.0 N3A A:1FZ875 4.4 50.7 1.0 C2' C:DC873 4.6 49.2 1.0 CB A:GLU104 4.7 60.6 1.0 CB A:ASP8 4.7 54.5 1.0 OP1 C:DC873 4.8 53.2 1.0 P C:DC873 4.8 51.8 1.0 OP2 C:DC873 4.8 51.6 1.0 C5' C:DC873 4.8 51.2 1.0 O A:HOH522 4.9 50.0 1.0 C4' C:DC873 4.9 50.4 1.0 O2B A:1FZ875 4.9 51.5 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