Magnesium in PDB 5yv3: Dna Polymerase IV - Dna Ternary Complex 7

All present enzymatic activity of Dna Polymerase IV - Dna Ternary Complex 7:
2.7.7.7;

The structure of Dna Polymerase IV - Dna Ternary Complex 7, PDB code: 5yv3 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)	54.80 / 2.03
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.249, 57.038, 109.950, 90.00, 94.55, 90.00
R / Rfree (%)	20.3 / 24.9

The binding sites of Magnesium atom in the Dna Polymerase IV - Dna Ternary Complex 7 (pdb code 5yv3). 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 7, PDB code: 5yv3:
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 7


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 7 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg901 b:22.1 occ:1.00 O1A H:TTP900 1.8 30.5 0.8 O2B H:TTP900 2.2 28.9 0.8 O F:MET9 2.2 31.9 1.0 OD1 F:ASP8 2.2 29.9 0.5 O1G H:TTP900 2.3 32.2 0.8 OD2 F:ASP103 2.3 34.2 1.0 OP1 H:DT874 2.4 28.1 0.2 O2 F:DPO903 2.4 28.9 0.2 O7 F:DPO903 2.4 32.5 0.2 OD1 F:ASP8 2.5 29.7 0.5 PB H:TTP900 3.1 34.9 0.8 O3A H:TTP900 3.3 37.3 0.8 CG F:ASP8 3.3 33.7 0.5 CG F:ASP8 3.3 33.5 0.5 C F:MET9 3.4 27.5 1.0 CG F:ASP103 3.4 35.0 1.0 MG F:MG902 3.4 47.2 1.0 P1 F:DPO903 3.4 26.4 0.2 PA H:TTP900 3.5 37.3 0.8 PG H:TTP900 3.5 36.2 0.8 O1 F:DPO903 3.6 29.4 0.2 OD2 F:ASP8 3.7 34.8 0.5 OD2 F:ASP8 3.7 36.8 0.5 O3B H:TTP900 3.7 33.4 0.8 P2 F:DPO903 3.7 35.8 0.2 P H:DT874 3.8 31.9 0.2 OD1 F:ASP103 3.8 31.8 1.0 N F:MET9 3.9 33.0 1.0 O4 F:DPO903 4.0 36.2 0.2 C5' H:TTP900 4.0 23.2 0.8 O3G H:TTP900 4.1 34.1 0.8 C5' H:DT874 4.1 26.1 0.2 NZ F:LYS157 4.1 20.3 0.6 CA F:MET9 4.1 33.3 1.0 O5' H:DT874 4.2 28.7 0.2 O5' H:TTP900 4.3 34.4 0.8 C F:ASP8 4.3 28.2 1.0 O5 F:DPO903 4.4 38.3 0.2 N F:ASP10 4.5 30.4 1.0 O H:HOH1022 4.5 60.8 1.0 O2A H:TTP900 4.5 34.5 0.8 CE F:LYS157 4.5 33.4 0.6 CB F:ASP8 4.5 30.4 0.5 CB F:ASP8 4.5 30.5 0.5 O3' H:DC873 4.6 40.7 0.8 O1B H:TTP900 4.6 47.0 0.8 CB F:MET9 4.6 28.6 1.0 CA F:ASP10 4.7 24.2 1.0 OP2 H:DT874 4.7 31.3 0.2 O F:HOH1071 4.7 41.4 1.0 N F:CYS11 4.7 28.2 1.0 O2G H:TTP900 4.7 44.0 0.8 CB F:ASP103 4.7 28.6 1.0 O3 F:DPO903 4.7 22.1 0.2 CB F:PHE12 4.7 28.8 1.0 N F:PHE12 4.8 27.0 1.0 O3' H:DC873 4.8 29.0 0.2 CA F:ASP8 4.8 33.3 1.0 O F:ASP8 4.8 31.2 1.0 O6 F:DPO903 4.9 40.9 0.2 C F:ASP10 4.9 27.3 1.0

Magnesium binding site 2 out of 4 in the Dna Polymerase IV - Dna Ternary Complex 7


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 7 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg902 b:47.2 occ:1.00 OE1 F:GLU104 2.0 47.5 1.0 OP1 H:DT874 2.1 28.1 0.2 OD1 F:ASP103 2.2 31.8 1.0 O3' H:DC873 2.5 29.0 0.2 O1A H:TTP900 2.6 30.5 0.8 OD2 F:ASP8 2.6 34.8 0.5 O3' H:DC873 2.7 40.7 0.8 OD1 F:ASP8 2.7 29.7 0.5 P H:DT874 2.8 31.9 0.2 O F:HOH1071 2.9 41.4 1.0 PA H:TTP900 3.0 37.3 0.8 CG F:ASP103 3.1 35.0 1.0 CD F:GLU104 3.1 42.6 1.0 OD2 F:ASP103 3.3 34.2 1.0 CG F:ASP8 3.3 33.5 0.5 CG F:ASP8 3.4 33.7 0.5 OD2 F:ASP8 3.4 36.8 0.5 MG F:MG901 3.4 22.1 1.0 OD1 F:ASP8 3.6 29.9 0.5 CB F:GLU104 3.6 29.2 1.0 CG F:GLU104 3.7 34.9 1.0 O5' H:TTP900 3.7 34.4 0.8 C3' H:DC873 3.8 31.6 0.2 C3' H:DC873 3.9 32.5 0.8 OP2 H:DT874 3.9 31.3 0.2 O5' H:DT874 3.9 28.7 0.2 O2A H:TTP900 4.0 34.5 0.8 C5' H:DT874 4.1 26.1 0.2 C5' H:TTP900 4.1 23.2 0.8 OG F:SER101 4.1 56.1 1.0 OE2 F:GLU104 4.2 43.9 1.0 C4' H:DC873 4.2 33.3 0.2 C4' H:DC873 4.2 33.7 0.8 O3A H:TTP900 4.3 37.3 0.8 C5' H:DC873 4.4 32.5 0.8 O F:ASP103 4.5 35.1 1.0 C F:ASP103 4.5 35.7 1.0 C5' H:DC873 4.5 34.2 0.2 CB F:ASP103 4.5 28.6 1.0 CB F:ASP8 4.6 30.4 0.5 CB F:ASP8 4.7 30.5 0.5 N F:GLU104 4.7 30.0 1.0 CA F:GLU104 4.8 30.8 1.0 C2' H:DC873 4.8 32.1 0.2 C2' H:DC873 4.8 31.1 0.8 O1G H:TTP900 4.9 32.2 0.8 O2B H:TTP900 5.0 28.9 0.8

Magnesium binding site 3 out of 4 in the Dna Polymerase IV - Dna Ternary Complex 7


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 7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:40.0 occ:1.00 O1A C:TTP900 1.8 63.4 1.0 O2B C:TTP900 2.0 42.7 1.0 O A:MET9 2.3 48.6 1.0 OD2 A:ASP103 2.3 35.9 1.0 OD1 A:ASP8 2.4 54.4 1.0 O1G C:TTP900 2.5 60.3 1.0 PB C:TTP900 3.2 45.5 1.0 MG A:MG902 3.2 68.4 1.0 CG A:ASP103 3.4 39.4 1.0 PA C:TTP900 3.4 50.8 1.0 C A:MET9 3.4 47.3 1.0 CG A:ASP8 3.4 61.4 1.0 O3A C:TTP900 3.5 62.3 1.0 PG C:TTP900 3.6 54.6 1.0 OD1 A:ASP103 3.8 36.8 1.0 O3B C:TTP900 3.8 46.1 1.0 N A:MET9 3.8 41.1 1.0 C5' C:TTP900 4.0 48.4 1.0 OD2 A:ASP8 4.0 75.8 1.0 O3G C:TTP900 4.1 50.0 1.0 O5' C:TTP900 4.2 58.9 1.0 CA A:MET9 4.2 45.0 1.0 NZ A:LYS157 4.3 47.0 1.0 C A:ASP8 4.3 44.3 1.0 O C:HOH1025 4.4 57.8 1.0 O2A C:TTP900 4.4 52.5 1.0 CB A:ASP8 4.4 49.8 1.0 N A:ASP10 4.5 43.4 1.0 O3' C:DC873 4.6 68.1 1.0 O1B C:TTP900 4.6 51.5 1.0 CE A:LYS157 4.6 57.4 1.0 N A:CYS11 4.7 43.3 1.0 CB A:ASP103 4.7 42.4 1.0 CB A:MET9 4.7 44.7 1.0 CA A:ASP10 4.7 38.8 1.0 CA A:ASP8 4.7 41.8 1.0 N A:PHE12 4.8 39.4 1.0 CB A:PHE12 4.8 42.0 1.0 O A:ASP8 4.8 46.0 1.0 O2G C:TTP900 4.9 55.9 1.0 C A:ASP10 4.9 43.9 1.0

Magnesium binding site 4 out of 4 in the Dna Polymerase IV - Dna Ternary Complex 7


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 7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:68.4 occ:1.00 OE2 A:GLU104 2.0 65.4 1.0 OD1 A:ASP103 2.2 36.8 1.0 OD1 A:ASP8 2.4 54.4 1.0 O1A C:TTP900 2.5 63.4 1.0 CD A:GLU104 3.0 56.5 1.0 CG A:ASP103 3.0 39.4 1.0 O3' C:DC873 3.1 68.1 1.0 CG A:ASP8 3.1 61.4 1.0 OD2 A:ASP103 3.2 35.9 1.0 PA C:TTP900 3.2 50.8 1.0 MG A:MG901 3.2 40.0 1.0 OD2 A:ASP8 3.2 75.8 1.0 CG A:GLU104 3.5 49.7 1.0 O5' C:TTP900 3.6 58.9 1.0 CB A:GLU104 3.7 42.9 1.0 O2A C:TTP900 4.0 52.5 1.0 C3' C:DC873 4.0 52.8 1.0 OG A:SER101 4.1 52.8 1.0 OE1 A:GLU104 4.1 51.9 1.0 C5' C:DC873 4.1 56.5 1.0 C4' C:DC873 4.1 57.2 1.0 C5' C:TTP900 4.2 48.4 1.0 CB A:ASP103 4.5 42.4 1.0 C A:ASP103 4.5 42.6 1.0 O3A C:TTP900 4.5 62.3 1.0 CB A:ASP8 4.5 49.8 1.0 O A:ASP103 4.5 42.7 1.0 N A:GLU104 4.6 37.0 1.0 O2B C:TTP900 4.7 42.7 1.0 CA A:GLU104 4.7 34.8 1.0 O C:HOH1025 4.8 57.8 1.0 O1G C:TTP900 4.8 60.3 1.0 CA A:ASP8 4.9 41.8 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