Magnesium in PDB 5yux: Dna Polymerase IV - Dna Ternary Complex 8

All present enzymatic activity of Dna Polymerase IV - Dna Ternary Complex 8:
2.7.7.7;

The structure of Dna Polymerase IV - Dna Ternary Complex 8, PDB code: 5yux 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)	44.64 / 2.04
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.070, 57.090, 109.990, 90.00, 94.50, 90.00
R / Rfree (%)	18.5 / 23.7

The binding sites of Magnesium atom in the Dna Polymerase IV - Dna Ternary Complex 8 (pdb code 5yux). 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 8, PDB code: 5yux:
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 8


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 8 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg901 b:27.7 occ:1.00 O1B F:TTP900 1.9 33.3 0.6 OD1 F:ASP8 2.1 33.1 0.5 O1A F:TTP900 2.1 31.0 0.6 OP1 H:DT874 2.2 35.4 0.4 O F:MET9 2.3 31.5 1.0 OD2 F:ASP103 2.3 30.3 1.0 O3G F:TTP900 2.4 44.8 0.6 O1 F:DPO903 2.5 28.1 0.4 O7 F:DPO903 2.5 43.1 0.4 OD1 F:ASP8 2.5 34.1 0.5 PB F:TTP900 3.1 40.7 0.6 MG F:MG902 3.2 50.8 1.0 CG F:ASP8 3.2 34.6 0.5 CG F:ASP8 3.3 34.7 0.5 O2 F:DPO903 3.4 41.9 0.4 CG F:ASP103 3.4 35.0 1.0 P1 F:DPO903 3.4 37.5 0.4 PA F:TTP900 3.4 31.8 0.6 C F:MET9 3.4 23.6 1.0 PG F:TTP900 3.4 47.3 0.6 OD2 F:ASP8 3.5 38.7 0.5 O3A F:TTP900 3.5 43.3 0.6 P H:DT874 3.6 33.9 0.4 O3B F:TTP900 3.7 45.0 0.6 OD2 F:ASP8 3.7 38.8 0.5 P2 F:DPO903 3.8 45.9 0.4 OD1 F:ASP103 3.8 33.9 1.0 O1G F:TTP900 3.9 41.4 0.6 N F:MET9 3.9 27.9 1.0 O4 F:DPO903 4.0 44.4 0.4 C5' F:TTP900 4.0 26.5 0.6 O5' H:DT874 4.1 27.2 0.4 C5' H:DT874 4.1 26.4 0.4 O H:HOH1017 4.2 46.6 1.0 O5' F:TTP900 4.2 27.3 0.6 CA F:MET9 4.2 30.1 1.0 NZ F:LYS157 4.2 32.5 1.0 O3' H:DC873 4.3 36.4 0.6 C F:ASP8 4.3 27.6 1.0 O2B F:TTP900 4.3 32.1 0.6 N F:ASP10 4.5 32.2 1.0 CB F:ASP8 4.5 30.3 0.5 CB F:ASP8 4.5 30.3 0.5 O5 F:DPO903 4.5 48.0 0.4 OP2 H:DT874 4.5 32.7 0.4 O2A F:TTP900 4.5 31.0 0.6 CE F:LYS157 4.6 46.3 1.0 N F:CYS11 4.6 26.0 1.0 CB F:ASP103 4.6 26.3 1.0 O3' H:DC873 4.7 33.1 0.4 CB F:MET9 4.7 26.6 1.0 CA F:ASP10 4.7 27.9 1.0 N F:PHE12 4.7 29.0 1.0 O3 F:DPO903 4.7 33.8 0.4 CB F:PHE12 4.7 24.4 1.0 O2G F:TTP900 4.8 56.0 0.6 CA F:ASP8 4.8 28.1 1.0 O F:ASP8 4.8 28.2 1.0 O6 F:DPO903 4.9 54.5 0.4 C F:ASP10 4.9 26.4 1.0

Magnesium binding site 2 out of 4 in the Dna Polymerase IV - Dna Ternary Complex 8


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 8 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg902 b:50.8 occ:1.00 OE1 F:GLU104 1.9 51.2 1.0 OP1 H:DT874 2.2 35.4 0.4 OD1 F:ASP103 2.2 33.9 1.0 O1A F:TTP900 2.2 31.0 0.6 OD1 F:ASP8 2.4 34.1 0.5 O3' H:DC873 2.6 33.1 0.4 O3' H:DC873 2.7 36.4 0.6 P H:DT874 2.9 33.9 0.4 OD2 F:ASP8 2.9 38.8 0.5 CG F:ASP103 3.0 35.0 1.0 CD F:GLU104 3.0 38.7 1.0 OD2 F:ASP103 3.1 30.3 1.0 OD1 F:ASP8 3.2 33.1 0.5 CG F:ASP8 3.2 34.7 0.5 MG F:MG901 3.2 27.7 1.0 CG F:ASP8 3.3 34.6 0.5 PA F:TTP900 3.3 31.8 0.6 OD2 F:ASP8 3.4 38.7 0.5 CB F:GLU104 3.6 30.0 1.0 CG F:GLU104 3.6 32.6 1.0 C3' H:DC873 3.8 32.8 0.6 C4' H:DC873 3.9 34.0 0.6 C3' H:DC873 4.0 32.2 0.4 O2A F:TTP900 4.0 31.0 0.6 O5' F:TTP900 4.0 27.3 0.6 O5' H:DT874 4.0 27.2 0.4 OP2 H:DT874 4.0 32.7 0.4 C5' H:DT874 4.1 26.4 0.4 OG F:SER101 4.1 46.8 1.0 C5' F:TTP900 4.1 26.5 0.6 OE2 F:GLU104 4.1 41.4 1.0 C5' H:DC873 4.2 37.2 0.6 C4' H:DC873 4.4 33.9 0.4 O F:ASP103 4.4 34.8 1.0 C F:ASP103 4.5 31.3 1.0 CB F:ASP103 4.5 26.3 1.0 CB F:ASP8 4.5 30.3 0.5 CB F:ASP8 4.5 30.3 0.5 O1B F:TTP900 4.7 33.3 0.6 O3A F:TTP900 4.7 43.3 0.6 C5' H:DC873 4.7 32.8 0.4 N F:GLU104 4.7 29.1 1.0 O3G F:TTP900 4.7 44.8 0.6 C2' H:DC873 4.7 32.8 0.6 O H:HOH1017 4.7 46.6 1.0 CA F:GLU104 4.8 28.3 1.0 CA F:ASP8 4.9 28.1 1.0 C2' H:DC873 4.9 32.5 0.4 CA F:ASP103 5.0 30.5 1.0

Magnesium binding site 3 out of 4 in the Dna Polymerase IV - Dna Ternary Complex 8


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 8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:38.3 occ:1.00 OP1 C:DT874 2.2 46.4 0.1 O2B A:TTP900 2.2 39.9 0.9 O2A A:TTP900 2.2 40.9 0.9 OD2 A:ASP103 2.4 32.5 1.0 O A:MET9 2.4 30.6 1.0 OD1 A:ASP8 2.4 50.8 1.0 O2 A:DPO903 2.5 42.0 0.1 O7 A:DPO903 2.5 63.6 0.1 O2G A:TTP900 2.6 68.4 0.9 NZ A:LYS157 2.9 59.9 1.0 PB A:TTP900 3.2 42.5 0.9 MG A:MG902 3.3 65.6 1.0 PA A:TTP900 3.4 44.9 0.9 CG A:ASP8 3.4 50.4 1.0 CG A:ASP103 3.4 39.2 1.0 PG A:TTP900 3.5 59.3 0.9 P C:DT874 3.5 46.8 0.1 O3A A:TTP900 3.5 49.9 0.9 C A:MET9 3.6 35.8 1.0 P1 A:DPO903 3.6 43.5 0.1 O3G A:TTP900 3.7 53.9 0.9 O3B A:TTP900 3.7 50.6 0.9 P2 A:DPO903 3.8 57.6 0.1 OD1 A:ASP103 3.8 40.1 1.0 OD2 A:ASP8 3.8 66.4 1.0 O5' C:DT874 3.9 44.5 0.1 C5' C:DT874 3.9 41.1 0.1 O3 A:DPO903 3.9 45.7 0.1 N A:MET9 4.0 39.1 1.0 O C:HOH1007 4.0 54.1 1.0 O4 A:DPO903 4.1 52.2 0.1 C5' A:TTP900 4.1 36.5 0.9 O5' A:TTP900 4.3 41.7 0.9 O3' C:DC873 4.3 51.1 0.9 CA A:MET9 4.3 38.4 1.0 O6 A:DPO903 4.3 59.2 0.1 C A:ASP8 4.4 41.5 1.0 CE A:LYS157 4.4 45.8 1.0 OP2 C:DT874 4.4 48.4 0.1 O1A A:TTP900 4.5 43.9 0.9 O1B A:TTP900 4.5 34.7 0.9 O3' C:DC873 4.5 48.5 0.1 CB A:ASP8 4.5 40.2 1.0 N A:ASP10 4.6 35.9 1.0 N A:CYS11 4.6 36.1 1.0 CB A:ASP103 4.7 39.3 1.0 N A:PHE12 4.7 37.8 1.0 CB A:PHE12 4.8 38.9 1.0 CB A:MET9 4.8 39.2 1.0 CA A:ASP10 4.8 35.1 1.0 CA A:ASP8 4.8 39.0 1.0 O1G A:TTP900 4.9 62.6 0.9 O1 A:DPO903 4.9 38.3 0.1 O A:ASP8 4.9 39.3 1.0 O5 A:DPO903 5.0 61.7 0.1 C A:ASP10 5.0 34.2 1.0

Magnesium binding site 4 out of 4 in the Dna Polymerase IV - Dna Ternary Complex 8


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 8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:65.6 occ:1.00 OE2 A:GLU104 1.9 62.5 1.0 OP1 C:DT874 2.1 46.4 0.1 O2A A:TTP900 2.3 40.9 0.9 OD1 A:ASP103 2.3 40.1 1.0 OD1 A:ASP8 2.5 50.8 1.0 O3' C:DC873 2.6 48.5 0.1 P C:DT874 2.9 46.8 0.1 CD A:GLU104 2.9 53.4 1.0 O3' C:DC873 3.0 51.1 0.9 CG A:ASP103 3.1 39.2 1.0 OD2 A:ASP103 3.2 32.5 1.0 CG A:ASP8 3.2 50.4 1.0 MG A:MG901 3.3 38.3 1.0 CG A:GLU104 3.4 47.5 1.0 OD2 A:ASP8 3.5 66.4 1.0 PA A:TTP900 3.5 44.9 0.9 CB A:GLU104 3.6 42.8 1.0 C3' C:DC873 3.9 46.6 0.1 O5' C:DT874 4.0 44.5 0.1 OP2 C:DT874 4.0 48.4 0.1 C4' C:DC873 4.0 47.0 0.9 OE1 A:GLU104 4.0 41.9 1.0 C5' C:DT874 4.0 41.1 0.1 C3' C:DC873 4.1 44.4 0.9 O1A A:TTP900 4.1 43.9 0.9 OG A:SER101 4.1 48.7 1.0 C5' C:DC873 4.1 48.8 0.9 O5' A:TTP900 4.2 41.7 0.9 C4' C:DC873 4.3 46.7 0.1 C5' A:TTP900 4.3 36.5 0.9 C5' C:DC873 4.5 49.6 0.1 O A:ASP103 4.5 38.8 1.0 C A:ASP103 4.5 42.2 1.0 CB A:ASP8 4.5 40.2 1.0 O C:HOH1007 4.5 54.1 1.0 CB A:ASP103 4.6 39.3 1.0 N A:GLU104 4.6 39.5 1.0 CA A:GLU104 4.7 37.2 1.0 CA A:ASP8 4.8 39.0 1.0 O3A A:TTP900 4.9 49.9 0.9 O2G A:TTP900 4.9 68.4 0.9 C2' C:DC873 4.9 44.4 0.1 O2B A:TTP900 4.9 39.9 0.9

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