Magnesium in PDB 5yuz: Dna Polymerase IV - Dna Ternary Complex 11

All present enzymatic activity of Dna Polymerase IV - Dna Ternary Complex 11:
2.7.7.7;

The structure of Dna Polymerase IV - Dna Ternary Complex 11, PDB code: 5yuz 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)	44.80 / 1.83
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.090, 57.130, 110.300, 90.00, 94.33, 90.00
R / Rfree (%)	19.8 / 23.3

The binding sites of Magnesium atom in the Dna Polymerase IV - Dna Ternary Complex 11 (pdb code 5yuz). 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 11, PDB code: 5yuz:
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 11


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 11 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg901 b:25.8 occ:1.00 OP1 H:DT874 2.2 33.1 1.0 OD2 F:ASP103 2.2 28.1 1.0 OD1 F:ASP8 2.3 28.5 0.5 O1 F:DPO903 2.3 30.2 1.0 O F:MET9 2.4 31.9 1.0 OD1 F:ASP8 2.4 25.7 0.5 O7 F:DPO903 2.5 44.8 1.0 CG F:ASP8 3.2 33.8 0.5 CG F:ASP8 3.3 33.6 0.5 CG F:ASP103 3.4 30.4 1.0 MG F:MG902 3.4 35.0 1.0 P1 F:DPO903 3.4 38.4 1.0 OD2 F:ASP8 3.5 35.7 0.5 C F:MET9 3.5 29.6 1.0 O2 F:DPO903 3.6 44.2 1.0 P H:DT874 3.6 32.5 1.0 P2 F:DPO903 3.7 43.3 1.0 OD2 F:ASP8 3.7 34.9 0.5 OD1 F:ASP103 3.8 29.8 1.0 N F:MET9 3.9 28.0 1.0 O4 F:DPO903 3.9 51.2 1.0 C5' H:DT874 4.0 24.4 1.0 O5' H:DT874 4.1 32.5 1.0 NZ F:LYS157 4.1 34.9 1.0 CA F:MET9 4.2 29.3 1.0 O5 F:DPO903 4.2 36.7 1.0 C F:ASP8 4.3 28.2 1.0 CB F:ASP8 4.5 34.2 0.5 O F:HOH1015 4.5 47.3 1.0 OP2 H:DT874 4.5 27.9 1.0 CB F:ASP8 4.5 34.3 0.5 O3' H:DC873 4.6 30.9 1.0 N F:ASP10 4.6 32.2 1.0 CB F:ASP103 4.6 27.6 1.0 CB F:MET9 4.6 29.9 1.0 CE F:LYS157 4.7 48.2 1.0 N F:CYS11 4.7 29.9 1.0 O3 F:DPO903 4.7 36.2 1.0 N F:PHE12 4.7 28.3 1.0 CB F:PHE12 4.7 30.2 1.0 CA F:ASP8 4.8 32.1 1.0 CA F:ASP10 4.8 30.7 1.0 O F:ASP8 4.9 31.6 1.0 O6 F:DPO903 4.9 48.3 1.0 C F:ASP10 5.0 32.1 1.0

Magnesium binding site 2 out of 4 in the Dna Polymerase IV - Dna Ternary Complex 11


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 11 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg902 b:35.0 occ:1.00 OE2 F:GLU104 2.1 40.2 1.0 OP1 H:DT874 2.2 33.1 1.0 OD1 F:ASP103 2.3 29.8 1.0 OD2 F:ASP8 2.4 35.7 0.5 O3' H:DC873 2.5 30.9 1.0 O F:HOH1015 2.5 47.3 1.0 OD1 F:ASP8 2.7 25.7 0.5 P H:DT874 2.9 32.5 1.0 CG F:ASP103 3.1 30.4 1.0 CD F:GLU104 3.2 34.9 1.0 CG F:ASP8 3.3 33.6 0.5 OD2 F:ASP103 3.3 28.1 1.0 CG F:ASP8 3.3 33.8 0.5 MG F:MG901 3.4 25.8 1.0 OD2 F:ASP8 3.4 34.9 0.5 CB F:GLU104 3.6 29.7 1.0 CG F:GLU104 3.7 29.8 1.0 OD1 F:ASP8 3.7 28.5 0.5 C3' H:DC873 3.8 31.4 1.0 OG F:SER101 4.0 40.4 1.0 OP2 H:DT874 4.0 27.9 1.0 O5' H:DT874 4.0 32.5 1.0 C4' H:DC873 4.1 31.4 1.0 C5' H:DT874 4.1 24.4 1.0 OE1 F:GLU104 4.2 38.1 1.0 C5' H:DC873 4.4 29.4 1.0 O F:HOH1088 4.5 39.8 1.0 O F:ASP103 4.5 30.0 1.0 CB F:ASP8 4.5 34.2 0.5 C F:ASP103 4.5 34.0 1.0 CB F:ASP8 4.6 34.3 0.5 CB F:ASP103 4.6 27.6 1.0 N F:GLU104 4.7 26.4 1.0 CA F:GLU104 4.7 26.8 1.0 C2' H:DC873 4.8 29.8 1.0 O7 F:DPO903 5.0 44.8 1.0 CA F:ASP8 5.0 32.1 1.0

Magnesium binding site 3 out of 4 in the Dna Polymerase IV - Dna Ternary Complex 11


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 11 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:37.6 occ:1.00 O2B C:TTP901 2.1 44.6 0.5 O2A C:TTP901 2.1 44.7 0.5 OP1 C:DT874 2.2 42.8 0.5 O A:MET9 2.3 35.9 1.0 OD2 A:ASP103 2.3 35.2 1.0 O2 A:DPO903 2.4 36.9 0.5 O3G C:TTP901 2.5 51.1 0.5 O6 A:DPO903 2.6 60.1 0.5 OD2 A:ASP8 2.7 60.6 1.0 OD1 A:ASP8 2.8 51.5 1.0 PB C:TTP901 3.0 45.0 0.5 CG A:ASP8 3.0 51.3 1.0 O3A C:TTP901 3.1 46.4 0.5 MG A:MG902 3.3 67.7 1.0 CG A:ASP103 3.4 41.4 1.0 PA C:TTP901 3.4 44.2 0.5 C A:MET9 3.5 35.9 1.0 P C:DT874 3.5 43.5 0.5 PG C:TTP901 3.6 56.6 0.5 P1 A:DPO903 3.6 36.1 0.5 O3B C:TTP901 3.7 42.8 0.5 P2 A:DPO903 3.8 56.5 0.5 OD1 A:ASP103 3.8 37.6 1.0 O3 A:DPO903 3.8 40.8 0.5 N A:MET9 4.0 40.0 1.0 O5' C:DT874 4.0 38.2 0.5 C5' C:TTP901 4.0 40.9 0.5 O2G C:TTP901 4.0 60.2 0.5 O4 A:DPO903 4.1 46.9 0.5 NZ A:LYS157 4.1 37.0 1.0 C5' C:DT874 4.1 42.2 0.5 O7 A:DPO903 4.2 52.5 0.5 O5' C:TTP901 4.2 43.6 0.5 CA A:MET9 4.2 36.4 1.0 O1B C:TTP901 4.3 39.7 0.5 C A:ASP8 4.4 38.9 1.0 O3' C:DC873 4.4 50.5 0.5 CB A:ASP8 4.4 40.4 1.0 OP2 C:DT874 4.5 38.9 0.5 N A:ASP10 4.5 37.4 1.0 O1A C:TTP901 4.5 39.5 0.5 O3' C:DC873 4.6 42.9 0.5 N A:CYS11 4.7 37.6 1.0 CB A:ASP103 4.7 41.2 1.0 CB A:MET9 4.7 44.0 1.0 CA A:ASP10 4.7 39.1 1.0 N A:PHE12 4.8 38.0 1.0 CB A:PHE12 4.8 43.8 1.0 CA A:ASP8 4.8 38.8 1.0 O1 A:DPO903 4.8 34.2 0.5 CE A:LYS157 4.8 52.9 1.0 O1G C:TTP901 4.9 58.6 0.5 O A:ASP8 4.9 39.8 1.0 C A:ASP10 5.0 38.8 1.0

Magnesium binding site 4 out of 4 in the Dna Polymerase IV - Dna Ternary Complex 11


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 11 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:67.7 occ:1.00 OE1 A:GLU104 1.9 68.8 1.0 OD1 A:ASP8 2.1 51.5 1.0 O2A C:TTP901 2.1 44.7 0.5 OP1 C:DT874 2.3 42.8 0.5 OD1 A:ASP103 2.3 37.6 1.0 O3' C:DC873 2.6 50.5 0.5 O3' C:DC873 2.6 42.9 0.5 CD A:GLU104 3.0 54.4 1.0 P C:DT874 3.0 43.5 0.5 CG A:ASP103 3.1 41.4 1.0 PA C:TTP901 3.3 44.2 0.5 OD2 A:ASP103 3.3 35.2 1.0 CG A:ASP8 3.3 51.3 1.0 MG A:MG901 3.3 37.6 1.0 CG A:GLU104 3.5 46.3 1.0 CB A:GLU104 3.5 40.7 1.0 C3' C:DC873 3.9 44.5 0.5 C3' C:DC873 4.0 42.4 0.5 OG A:SER101 4.0 55.2 1.0 OD2 A:ASP8 4.0 60.6 1.0 OE2 A:GLU104 4.1 49.4 1.0 OP2 C:DT874 4.1 38.9 0.5 O5' C:DT874 4.1 38.2 0.5 O5' C:TTP901 4.2 43.6 0.5 C5' C:TTP901 4.2 40.9 0.5 O1A C:TTP901 4.2 39.5 0.5 C5' C:DT874 4.2 42.2 0.5 C4' C:DC873 4.3 43.0 0.5 C4' C:DC873 4.3 44.5 0.5 O A:ASP103 4.3 37.0 1.0 CB A:ASP8 4.4 40.4 1.0 O3A C:TTP901 4.4 46.4 0.5 C A:ASP103 4.4 38.2 1.0 CB A:ASP103 4.5 41.2 1.0 C5' C:DC873 4.5 44.4 0.5 C5' C:DC873 4.6 41.2 0.5 N A:GLU104 4.6 37.0 1.0 CA A:GLU104 4.6 36.4 1.0 C2' C:DC873 4.7 40.8 0.5 CA A:ASP8 4.8 38.8 1.0 O3G C:TTP901 4.9 51.1 0.5 O2B C:TTP901 4.9 44.6 0.5 C2' C:DC873 4.9 39.6 0.5 CA A:ASP103 4.9 42.7 1.0

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