Magnesium in PDB 5yv0: Dna Polymerase IV - Dna Ternary Complex 12

All present enzymatic activity of Dna Polymerase IV - Dna Ternary Complex 12:
2.7.7.7;

The structure of Dna Polymerase IV - Dna Ternary Complex 12, PDB code: 5yv0 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)	44.73 / 2.09
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.080, 57.120, 110.210, 90.00, 94.44, 90.00
R / Rfree (%)	19.2 / 24.1

The binding sites of Magnesium atom in the Dna Polymerase IV - Dna Ternary Complex 12 (pdb code 5yv0). 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 12, PDB code: 5yv0:
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 12


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 12 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg901 b:26.1 occ:1.00 OP1 H:DT874 2.1 28.6 1.0 OD1 F:ASP8 2.2 29.0 0.5 O1 F:PO4903 2.3 29.6 1.0 O F:MET9 2.3 25.9 1.0 OD2 F:ASP103 2.4 31.4 1.0 OD1 F:ASP8 2.9 27.6 0.5 MG F:MG902 3.2 32.5 1.0 CG F:ASP8 3.4 28.8 0.5 CG F:ASP8 3.4 29.2 0.5 P F:PO4903 3.4 43.4 1.0 CG F:ASP103 3.4 32.6 1.0 O2 F:PO4904 3.5 86.9 1.0 C F:MET9 3.5 25.1 1.0 P H:DT874 3.5 29.5 1.0 OD2 F:ASP8 3.5 28.8 0.5 O3 F:PO4903 3.6 47.1 1.0 O1 F:PO4904 3.8 38.2 1.0 OD2 F:ASP8 3.8 28.9 0.5 OD1 F:ASP103 3.8 34.7 1.0 C5' H:DT874 4.0 23.8 1.0 O5' H:DT874 4.0 25.1 1.0 N F:MET9 4.0 27.9 1.0 O F:HOH1009 4.1 59.6 1.0 P F:PO4904 4.1 70.8 1.0 CA F:MET9 4.2 33.4 1.0 NZ F:LYS157 4.3 20.1 0.6 O4 F:PO4903 4.3 67.3 1.0 C F:ASP8 4.4 27.2 1.0 O4 F:PO4904 4.5 79.7 1.0 OP2 H:DT874 4.5 23.8 1.0 N F:ASP10 4.5 27.9 1.0 O3' H:DC873 4.5 28.2 1.0 N F:CYS11 4.6 21.7 1.0 CB F:ASP8 4.6 26.4 0.5 CB F:ASP8 4.6 26.6 0.5 O2 F:PO4903 4.6 33.9 1.0 CB F:PHE12 4.7 21.7 1.0 CB F:MET9 4.7 27.8 1.0 N F:PHE12 4.7 23.2 1.0 CA F:ASP10 4.7 23.1 1.0 CB F:ASP103 4.7 26.6 1.0 O F:HOH1017 4.8 52.1 1.0 C F:ASP10 4.9 28.4 1.0 CA F:ASP8 4.9 28.3 1.0 O F:ASP8 4.9 28.0 1.0

Magnesium binding site 2 out of 4 in the Dna Polymerase IV - Dna Ternary Complex 12


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 12 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg902 b:32.5 occ:1.00 OE1 F:GLU104 2.1 45.1 1.0 OD1 F:ASP103 2.1 34.7 1.0 OP1 H:DT874 2.2 28.6 1.0 OD1 F:ASP8 2.3 27.6 0.5 O3' H:DC873 2.6 28.2 1.0 CG F:ASP103 2.9 32.6 1.0 P H:DT874 3.0 29.5 1.0 OD2 F:ASP8 3.0 28.9 0.5 OD2 F:ASP103 3.1 31.4 1.0 O F:HOH1017 3.1 52.1 1.0 CD F:GLU104 3.1 32.7 1.0 OD1 F:ASP8 3.2 29.0 0.5 MG F:MG901 3.2 26.1 1.0 CG F:ASP8 3.2 29.2 0.5 CG F:ASP8 3.3 28.8 0.5 CB F:GLU104 3.5 29.1 1.0 OD2 F:ASP8 3.6 28.8 0.5 CG F:GLU104 3.6 28.6 1.0 C3' H:DC873 3.9 24.1 1.0 O5' H:DT874 4.0 25.1 1.0 OG F:SER101 4.0 45.7 1.0 C5' H:DT874 4.0 23.8 1.0 OP2 H:DT874 4.1 23.8 1.0 OE2 F:GLU104 4.2 38.0 1.0 O F:HOH1063 4.3 44.0 1.0 C4' H:DC873 4.3 28.8 1.0 O F:ASP103 4.3 30.3 1.0 C F:ASP103 4.3 31.4 1.0 CB F:ASP103 4.4 26.6 1.0 N F:GLU104 4.5 24.7 1.0 CB F:ASP8 4.5 26.4 0.5 CB F:ASP8 4.5 26.6 0.5 CA F:GLU104 4.6 27.0 1.0 C5' H:DC873 4.6 26.5 1.0 O F:HOH1009 4.7 59.6 1.0 CA F:ASP103 4.8 31.2 1.0 C2' H:DC873 4.9 24.7 1.0 CA F:ASP8 4.9 28.3 1.0 O1 F:PO4903 4.9 29.6 1.0 O F:MET9 5.0 25.9 1.0

Magnesium binding site 3 out of 4 in the Dna Polymerase IV - Dna Ternary Complex 12


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 12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:32.6 occ:1.00 O2A C:TTP901 2.0 50.4 0.3 O2B C:TTP901 2.1 45.4 0.3 OP1 C:DT874 2.2 43.4 0.7 O2 A:DPO903 2.3 38.8 0.7 O A:MET9 2.4 30.7 1.0 OD1 A:ASP8 2.4 49.5 1.0 OD2 A:ASP103 2.4 36.2 1.0 O3G C:TTP901 2.5 69.0 0.3 O5 A:DPO903 2.9 72.9 0.7 PB C:TTP901 3.1 47.7 0.3 O3A C:TTP901 3.1 47.4 0.3 MG A:MG902 3.2 48.1 1.0 CG A:ASP8 3.3 56.6 1.0 CG A:ASP103 3.4 38.7 1.0 PA C:TTP901 3.5 49.5 0.3 P1 A:DPO903 3.5 40.5 0.7 C A:MET9 3.5 40.9 1.0 PG C:TTP901 3.6 67.0 0.3 P C:DT874 3.6 42.5 0.7 OD2 A:ASP8 3.7 68.0 1.0 O3B C:TTP901 3.8 52.8 0.3 OD1 A:ASP103 3.8 37.1 1.0 O3 A:DPO903 3.8 45.1 0.7 P2 A:DPO903 3.9 69.0 0.7 NZ A:LYS157 3.9 54.4 1.0 N A:MET9 4.0 38.2 1.0 O2G C:TTP901 4.0 73.4 0.3 O7 A:DPO903 4.0 64.9 0.7 C5' C:TTP901 4.1 42.8 0.3 C5' C:DT874 4.1 42.1 0.7 O4 A:DPO903 4.1 59.2 0.7 O5' C:DT874 4.1 40.3 0.7 O5' C:TTP901 4.3 47.5 0.3 CA A:MET9 4.3 43.8 1.0 O3' C:DC873 4.3 49.4 0.3 O1B C:TTP901 4.4 42.0 0.3 C A:ASP8 4.4 43.0 1.0 CE A:LYS157 4.4 63.3 1.0 O3' C:DC873 4.5 48.1 0.7 CB A:ASP8 4.5 48.4 1.0 O1A C:TTP901 4.5 52.0 0.3 N A:ASP10 4.6 37.9 1.0 OP2 C:DT874 4.6 37.1 0.7 OE2 A:GLU104 4.7 66.6 1.0 CB A:MET9 4.7 42.6 1.0 N A:CYS11 4.8 35.4 1.0 CA A:ASP8 4.8 41.2 1.0 O1 A:DPO903 4.8 41.2 0.7 CB A:ASP103 4.8 44.1 1.0 CA A:ASP10 4.8 36.6 1.0 CB A:PHE12 4.8 37.6 1.0 N A:PHE12 4.8 34.0 1.0 O1G C:TTP901 4.9 68.9 0.3 O A:ASP8 4.9 38.0 1.0

Magnesium binding site 4 out of 4 in the Dna Polymerase IV - Dna Ternary Complex 12


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 12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:48.1 occ:1.00 OD1 A:ASP103 2.1 37.1 1.0 OE2 A:GLU104 2.1 66.6 1.0 O2A C:TTP901 2.1 50.4 0.3 CG A:GLU104 2.5 57.3 1.0 CD A:GLU104 2.5 60.0 1.0 OD1 A:ASP8 2.6 49.5 1.0 OP1 C:DT874 2.6 43.4 0.7 O3' C:DC873 2.7 48.1 0.7 CG A:ASP103 2.9 38.7 1.0 O3' C:DC873 3.0 49.4 0.3 OD2 A:ASP103 3.1 36.2 1.0 MG A:MG901 3.2 32.6 1.0 P C:DT874 3.3 42.5 0.7 PA C:TTP901 3.3 49.5 0.3 CG A:ASP8 3.4 56.6 1.0 CB A:GLU104 3.5 44.1 1.0 OD2 A:ASP8 3.7 68.0 1.0 OE1 A:GLU104 3.7 39.8 1.0 OG A:SER101 3.9 42.1 1.0 C3' C:DC873 4.0 43.9 0.7 C4' C:DC873 4.1 42.6 0.3 C5' C:TTP901 4.1 42.8 0.3 C5' C:DC873 4.1 43.8 0.3 C5' C:DT874 4.1 42.1 0.7 C3' C:DC873 4.1 44.9 0.3 O5' C:TTP901 4.1 47.5 0.3 O A:ASP103 4.2 38.3 1.0 O5' C:DT874 4.2 40.3 0.7 C A:ASP103 4.2 40.3 1.0 C4' C:DC873 4.2 42.1 0.7 O1A C:TTP901 4.3 52.0 0.3 CB A:ASP103 4.4 44.1 1.0 O3A C:TTP901 4.4 47.4 0.3 CA A:GLU104 4.4 35.9 1.0 OP2 C:DT874 4.5 37.1 0.7 N A:GLU104 4.5 32.2 1.0 C5' C:DC873 4.6 41.6 0.7 CB A:ASP8 4.6 48.4 1.0 O A:HOH1071 4.7 47.8 1.0 CA A:ASP103 4.8 45.7 1.0 C2' C:DC873 4.9 44.1 0.7 O2B C:TTP901 4.9 45.4 0.3 CA A:ASP8 4.9 41.2 1.0 C2' C:DC873 4.9 44.5 0.3 O3G C:TTP901 5.0 69.0 0.3

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