Magnesium in PDB 5yuy: Dna Polymerase IV - Dna Ternary Complex 9

All present enzymatic activity of Dna Polymerase IV - Dna Ternary Complex 9:
2.7.7.7;

The structure of Dna Polymerase IV - Dna Ternary Complex 9, PDB code: 5yuy was solved by J.Kottur, D.T.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.54 / 1.74
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.460, 57.050, 110.170, 90.00, 95.03, 90.00
R / Rfree (%)	18.8 / 21.5

The binding sites of Magnesium atom in the Dna Polymerase IV - Dna Ternary Complex 9 (pdb code 5yuy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Dna Polymerase IV - Dna Ternary Complex 9, PDB code: 5yuy:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Dna Polymerase IV - Dna Ternary Complex 9


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dna Polymerase IV - Dna Ternary Complex 9 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg901 b:17.2 occ:1.00 O2A H:TTP901 2.1 27.9 0.5 OD1 F:ASP8 2.2 24.2 0.5 O2B H:TTP901 2.2 25.7 0.5 O F:MET9 2.3 20.6 1.0 OP1 H:DT874 2.3 22.2 0.5 OD2 F:ASP103 2.4 22.7 1.0 O7 F:DPO903 2.4 24.0 0.5 O2G H:TTP901 2.4 24.9 0.5 OD1 F:ASP8 2.4 21.8 0.5 O3 F:DPO903 2.5 34.7 0.5 PB H:TTP901 3.0 32.7 0.5 O3A H:TTP901 3.0 43.2 0.5 CG F:ASP8 3.1 28.9 0.5 CG F:ASP8 3.2 28.8 0.5 MG F:MG902 3.4 32.9 1.0 CG F:ASP103 3.4 25.9 1.0 P2 F:DPO903 3.4 19.3 0.5 PA H:TTP901 3.5 26.7 0.5 C F:MET9 3.5 22.0 1.0 OD2 F:ASP8 3.5 32.5 0.5 OD2 F:ASP8 3.5 33.5 0.5 PG H:TTP901 3.5 28.9 0.5 O5 F:DPO903 3.7 22.6 0.5 P H:DT874 3.7 26.9 0.5 P1 F:DPO903 3.7 30.6 0.5 O3B H:TTP901 3.7 31.4 0.5 OD1 F:ASP103 3.8 21.4 1.0 N F:MET9 3.9 21.6 1.0 O4 F:DPO903 3.9 33.5 0.5 NZ F:LYS157 4.1 16.7 0.5 O5' H:DT874 4.1 22.7 0.5 C5' H:TTP901 4.1 18.7 0.5 C5' H:DT874 4.1 21.9 0.5 CA F:MET9 4.2 21.3 1.0 O F:HOH1002 4.2 40.3 1.0 O5' H:TTP901 4.2 25.5 0.5 O3G H:TTP901 4.2 28.1 0.5 O F:HOH1099 4.2 46.4 1.0 O2 F:DPO903 4.3 29.7 0.5 C F:ASP8 4.3 22.6 1.0 O3' H:DC873 4.4 33.1 0.5 O1B H:TTP901 4.4 32.4 0.5 CB F:ASP8 4.4 24.4 0.5 CB F:ASP8 4.5 24.6 0.5 OP2 H:DT874 4.5 16.5 0.5 CE F:LYS157 4.5 34.2 0.5 N F:ASP10 4.6 22.6 1.0 O1A H:TTP901 4.6 23.4 0.5 CB F:MET9 4.7 21.5 1.0 O1G H:TTP901 4.7 34.0 0.5 N F:CYS11 4.7 24.1 1.0 CB F:ASP103 4.7 18.2 1.0 CA F:ASP8 4.7 24.6 1.0 O6 F:DPO903 4.7 16.6 0.5 CB F:PHE12 4.7 19.6 1.0 O3' H:DC873 4.7 18.1 0.5 N F:PHE12 4.8 20.8 1.0 CA F:ASP10 4.8 20.5 1.0 O F:ASP8 4.8 23.3 1.0 O1 F:DPO903 4.9 32.1 0.5 C F:ASP10 5.0 22.2 1.0

Magnesium binding site 2 out of 4 in the Dna Polymerase IV - Dna Ternary Complex 9


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dna Polymerase IV - Dna Ternary Complex 9 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg902 b:32.9 occ:1.00 OE2 F:GLU104 2.0 40.6 1.0 OP1 H:DT874 2.0 22.2 0.5 O2A H:TTP901 2.1 27.9 0.5 OD1 F:ASP103 2.3 21.4 1.0 O F:HOH1002 2.4 40.3 1.0 O3' H:DC873 2.5 33.1 0.5 O3' H:DC873 2.5 18.1 0.5 OD1 F:ASP8 2.6 21.8 0.5 OD2 F:ASP8 2.6 32.5 0.5 P H:DT874 2.8 26.9 0.5 CD F:GLU104 3.1 33.0 1.0 CG F:ASP103 3.1 25.9 1.0 PA H:TTP901 3.2 26.7 0.5 OD2 F:ASP103 3.3 22.7 1.0 MG F:MG901 3.4 17.2 1.0 CG F:ASP8 3.4 28.9 0.5 CG F:ASP8 3.4 28.8 0.5 CG F:GLU104 3.6 29.9 1.0 CB F:GLU104 3.6 22.7 1.0 C3' H:DC873 3.7 24.8 0.5 OD1 F:ASP8 3.7 24.2 0.5 OD2 F:ASP8 3.7 33.5 0.5 OP2 H:DT874 3.8 16.5 0.5 C3' H:DC873 3.9 23.1 0.5 O5' H:DT874 3.9 22.7 0.5 C4' H:DC873 3.9 25.9 0.5 OG F:SER101 4.0 27.8 1.0 C5' H:DT874 4.0 21.9 0.5 O5' H:TTP901 4.1 25.5 0.5 C5' H:TTP901 4.1 18.7 0.5 OE1 F:GLU104 4.2 31.6 1.0 O1A H:TTP901 4.2 23.4 0.5 O3A H:TTP901 4.2 43.2 0.5 C4' H:DC873 4.2 26.8 0.5 C5' H:DC873 4.3 22.0 0.5 O F:HOH1141 4.4 32.2 1.0 C2' H:DC873 4.5 26.1 0.5 C5' H:DC873 4.5 20.3 0.5 C F:ASP103 4.5 24.7 1.0 O F:ASP103 4.5 20.9 1.0 CB F:ASP103 4.6 18.2 1.0 N F:GLU104 4.6 22.3 1.0 CB F:ASP8 4.6 24.4 0.5 O F:HOH1099 4.6 46.4 1.0 CB F:ASP8 4.7 24.6 0.5 CA F:GLU104 4.7 20.1 1.0 C2' H:DC873 4.9 22.5 0.5 O2B H:TTP901 4.9 25.7 0.5

Magnesium binding site 3 out of 4 in the Dna Polymerase IV - Dna Ternary Complex 9


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Dna Polymerase IV - Dna Ternary Complex 9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:21.9 occ:1.00 O1A C:TTP901 2.1 30.1 0.8 O1B C:TTP901 2.2 31.0 0.8 OP1 C:DT874 2.3 23.7 0.2 O A:MET9 2.3 24.9 1.0 OD2 A:ASP103 2.3 25.9 1.0 O3G C:TTP901 2.4 39.0 0.8 OD2 A:ASP8 2.5 38.8 1.0 O5 A:DPO903 2.6 28.5 0.2 O3 A:DPO903 2.6 37.7 0.2 OD1 A:ASP8 2.7 32.6 1.0 CG A:ASP8 2.9 31.6 1.0 PB C:TTP901 3.2 33.6 0.8 O3A C:TTP901 3.2 44.4 0.8 CG A:ASP103 3.4 29.6 1.0 C A:MET9 3.5 22.6 1.0 MG A:MG902 3.5 56.0 1.0 PA C:TTP901 3.5 33.5 0.8 PG C:TTP901 3.6 34.6 0.8 P C:DT874 3.6 22.8 0.2 P2 A:DPO903 3.7 21.3 0.2 P1 A:DPO903 3.7 33.5 0.2 OD1 A:ASP103 3.8 27.6 1.0 O3B C:TTP901 3.8 30.0 0.8 N A:MET9 3.9 27.6 1.0 O7 A:DPO903 3.9 30.5 0.2 O1G C:TTP901 4.0 29.2 0.8 O1 A:DPO903 4.0 31.7 0.2 O5' C:DT874 4.1 26.3 0.2 C5' C:DT874 4.1 26.7 0.2 O4 A:DPO903 4.1 33.4 0.2 NZ A:LYS157 4.2 27.2 1.0 C5' C:TTP901 4.2 28.7 0.8 O C:HOH1034 4.2 46.8 1.0 CA A:MET9 4.2 23.6 1.0 CB A:ASP8 4.3 25.2 1.0 C A:ASP8 4.4 27.0 1.0 O5' C:TTP901 4.4 28.8 0.8 O3' C:DC873 4.4 35.8 0.8 O2B C:TTP901 4.5 32.6 0.8 N A:ASP10 4.5 22.8 1.0 O A:HOH1075 4.5 55.4 1.0 OP2 C:DT874 4.5 22.0 0.2 O2A C:TTP901 4.6 30.4 0.8 CB A:MET9 4.7 28.4 1.0 N A:CYS11 4.7 27.1 1.0 O3' C:DC873 4.7 21.6 0.2 CB A:ASP103 4.7 27.0 1.0 CB A:PHE12 4.7 24.5 1.0 CA A:ASP10 4.7 25.8 1.0 CA A:ASP8 4.8 23.7 1.0 N A:PHE12 4.8 24.7 1.0 O2G C:TTP901 4.9 36.3 0.8 O A:ASP8 4.9 31.3 1.0 CE A:LYS157 4.9 36.1 1.0 O6 A:DPO903 5.0 20.8 0.2 C A:ASP10 5.0 24.3 1.0

Magnesium binding site 4 out of 4 in the Dna Polymerase IV - Dna Ternary Complex 9


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Dna Polymerase IV - Dna Ternary Complex 9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:56.0 occ:1.00 OE2 A:GLU104 2.1 55.5 1.0 OD1 A:ASP8 2.2 32.6 1.0 OP1 C:DT874 2.2 23.7 0.2 O1A C:TTP901 2.3 30.1 0.8 O A:HOH1075 2.3 55.4 1.0 OD1 A:ASP103 2.4 27.6 1.0 O3' C:DC873 2.6 35.8 0.8 O3' C:DC873 2.6 21.6 0.2 P C:DT874 2.9 22.8 0.2 CD A:GLU104 3.0 41.8 1.0 PA C:TTP901 3.3 33.5 0.8 CG A:ASP103 3.3 29.6 1.0 CG A:ASP8 3.4 31.6 1.0 MG A:MG901 3.5 21.9 1.0 OD2 A:ASP103 3.5 25.9 1.0 CG A:GLU104 3.6 30.5 1.0 CB A:GLU104 3.6 28.3 1.0 C3' C:DC873 3.8 28.2 0.8 OE1 A:GLU104 3.8 32.7 1.0 C3' C:DC873 3.9 27.5 0.2 OP2 C:DT874 3.9 22.0 0.2 OG A:SER101 4.0 41.2 1.0 O5' C:DT874 4.1 26.3 0.2 C4' C:DC873 4.1 27.6 0.2 OD2 A:ASP8 4.1 38.8 1.0 C4' C:DC873 4.1 28.7 0.8 O2A C:TTP901 4.2 30.4 0.8 C5' C:DT874 4.2 26.7 0.2 C5' C:DC873 4.3 25.9 0.8 C5' C:DC873 4.3 28.0 0.2 O5' C:TTP901 4.3 28.8 0.8 C5' C:TTP901 4.4 28.7 0.8 O3A C:TTP901 4.4 44.4 0.8 CB A:ASP8 4.4 25.2 1.0 O A:HOH1052 4.5 42.1 1.0 O A:ASP103 4.6 26.8 1.0 C A:ASP103 4.6 28.7 1.0 C2' C:DC873 4.7 25.0 0.8 N A:GLU104 4.7 25.9 1.0 O C:HOH1034 4.7 46.8 1.0 CA A:GLU104 4.7 26.1 1.0 CB A:ASP103 4.7 27.0 1.0 C2' C:DC873 4.9 24.6 0.2 O5' C:DC873 5.0 29.5 0.8 O3G C:TTP901 5.0 39.0 0.8

J.Kottur, D.T.Nair. Pyrophosphate Hydrolysis Is An Intrinsic and Critical Step of the Dna Synthesis Reaction Nucleic Acids Res. V. 46 5875 2018.
ISSN: ESSN 1362-4962
PubMed: 29850882
DOI: 10.1093/NAR/GKY402