Magnesium in PDB 5yv1: Dna Polymerase IV - Dna Ternary Complex 13

All present enzymatic activity of Dna Polymerase IV - Dna Ternary Complex 13:
2.7.7.7;

The structure of Dna Polymerase IV - Dna Ternary Complex 13, PDB code: 5yv1 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)	54.97 / 2.09
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.070, 57.100, 110.300, 90.00, 94.59, 90.00
R / Rfree (%)	19.6 / 25.1

The binding sites of Magnesium atom in the Dna Polymerase IV - Dna Ternary Complex 13 (pdb code 5yv1). 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 13, PDB code: 5yv1:
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 13


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 13 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg901 b:25.3 occ:1.00 OP1 H:DT874 2.2 28.8 1.0 O F:MET9 2.3 25.9 1.0 OD1 F:ASP8 2.3 27.4 0.4 OD2 F:ASP103 2.3 30.4 1.0 O1 F:PO4903 2.4 26.5 1.0 OD1 F:ASP8 2.8 24.8 0.6 O2 F:PO4904 2.9 45.7 0.8 MG F:MG902 3.2 28.1 1.0 CG F:ASP8 3.4 28.2 0.4 CG F:ASP103 3.4 32.1 1.0 CG F:ASP8 3.4 28.5 0.6 C F:MET9 3.5 27.5 1.0 P F:PO4903 3.5 49.1 1.0 O3 F:PO4903 3.5 38.6 1.0 P H:DT874 3.5 30.9 1.0 OD2 F:ASP8 3.6 31.0 0.6 OD2 F:ASP8 3.8 30.7 0.4 OD1 F:ASP103 3.8 33.4 1.0 C5' H:DT874 3.9 22.7 1.0 N F:MET9 4.0 29.1 1.0 P F:PO4904 4.0 44.2 0.8 O5' H:DT874 4.0 27.1 1.0 O1 F:PO4904 4.0 31.2 0.8 O F:HOH1014 4.2 41.5 1.0 CA F:MET9 4.2 31.8 1.0 NZ F:LYS157 4.3 16.7 0.5 C F:ASP8 4.4 27.2 1.0 O4 F:PO4903 4.4 74.5 1.0 N F:ASP10 4.5 29.8 1.0 O F:HOH1008 4.5 74.0 1.0 OP2 H:DT874 4.6 24.8 1.0 O3' H:DC873 4.6 27.8 1.0 CB F:ASP8 4.6 28.8 0.6 CB F:ASP8 4.6 28.9 0.4 CB F:ASP103 4.6 20.6 1.0 O F:HOH1022 4.7 62.6 1.0 N F:CYS11 4.7 22.2 1.0 CB F:PHE12 4.7 26.4 1.0 CB F:MET9 4.7 30.0 1.0 CA F:ASP10 4.7 24.7 1.0 N F:PHE12 4.7 30.8 1.0 O2 F:PO4903 4.7 40.7 1.0 O4 F:PO4904 4.8 59.0 0.8 CA F:ASP8 4.9 32.1 1.0 C F:ASP10 4.9 23.5 1.0 O F:ASP8 4.9 28.0 1.0 CE F:LYS157 5.0 27.0 0.5

Magnesium binding site 2 out of 4 in the Dna Polymerase IV - Dna Ternary Complex 13


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 13 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg902 b:28.1 occ:1.00 OD1 F:ASP103 2.0 33.4 1.0 OE1 F:GLU104 2.0 41.5 1.0 OP1 H:DT874 2.3 28.8 1.0 OD1 F:ASP8 2.3 24.8 0.6 O3' H:DC873 2.7 27.8 1.0 CG F:ASP103 2.8 32.1 1.0 OD2 F:ASP103 2.9 30.4 1.0 P H:DT874 3.0 30.9 1.0 O F:HOH1022 3.1 62.6 1.0 OD1 F:ASP8 3.1 27.4 0.4 CD F:GLU104 3.1 29.7 1.0 OD2 F:ASP8 3.2 30.7 0.4 MG F:MG901 3.2 25.3 1.0 CG F:ASP8 3.2 28.5 0.6 CG F:ASP8 3.3 28.2 0.4 CB F:GLU104 3.5 29.4 1.0 CG F:GLU104 3.5 30.7 1.0 OD2 F:ASP8 3.5 31.0 0.6 C3' H:DC873 4.0 24.6 1.0 OG F:SER101 4.0 44.3 1.0 C5' H:DT874 4.0 22.7 1.0 O5' H:DT874 4.0 27.1 1.0 OP2 H:DT874 4.2 24.8 1.0 OE2 F:GLU104 4.2 34.4 1.0 CB F:ASP103 4.2 20.6 1.0 O F:HOH1108 4.3 43.2 1.0 C4' H:DC873 4.3 26.4 1.0 C F:ASP103 4.3 34.0 1.0 O F:ASP103 4.3 30.4 1.0 N F:GLU104 4.5 28.9 1.0 CB F:ASP8 4.5 28.8 0.6 CB F:ASP8 4.5 28.9 0.4 CA F:GLU104 4.6 27.5 1.0 C5' H:DC873 4.6 30.2 1.0 CA F:ASP103 4.8 29.2 1.0 CA F:ASP8 4.8 32.1 1.0 C2' H:DC873 4.9 23.5 1.0 N F:MET9 5.0 29.1 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 13


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 13 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:36.2 occ:1.00 O A:HOH1001 1.8 57.1 1.0 OP1 C:DT874 2.0 35.9 1.0 O2 A:DPO903 2.3 46.4 1.0 OD2 A:ASP103 2.3 34.2 1.0 OD1 A:ASP8 2.3 49.0 1.0 O A:MET9 2.3 32.5 1.0 O7 A:DPO903 2.9 85.2 1.0 MG A:MG902 3.1 48.8 1.0 CG A:ASP103 3.3 39.0 1.0 CG A:ASP8 3.4 49.9 1.0 P1 A:DPO903 3.4 52.7 1.0 P C:DT874 3.4 45.0 1.0 C A:MET9 3.5 38.5 1.0 OD1 A:ASP103 3.7 39.6 1.0 O1 A:DPO903 3.8 46.2 1.0 P2 A:DPO903 3.9 83.3 1.0 C5' C:DT874 3.9 37.6 1.0 N A:MET9 3.9 35.9 1.0 O5' C:DT874 3.9 41.8 1.0 OD2 A:ASP8 4.0 61.8 1.0 O4 A:DPO903 4.0 73.0 1.0 CA A:MET9 4.2 41.7 1.0 NZ A:LYS157 4.2 54.2 1.0 O5 A:DPO903 4.3 76.6 1.0 O3' C:DC873 4.4 45.0 1.0 C A:ASP8 4.4 38.7 1.0 OP2 C:DT874 4.5 45.7 1.0 CB A:ASP8 4.6 41.6 1.0 N A:ASP10 4.6 39.8 1.0 CB A:ASP103 4.6 39.9 1.0 O3 A:DPO903 4.7 52.1 1.0 CB A:MET9 4.7 45.3 1.0 CB A:PHE12 4.7 35.5 1.0 N A:CYS11 4.8 36.2 1.0 CE A:LYS157 4.8 63.5 1.0 N A:PHE12 4.8 35.9 1.0 CA A:ASP10 4.8 37.1 1.0 CA A:ASP8 4.8 37.1 1.0 OE2 A:GLU104 4.8 52.5 1.0 O A:ASP8 5.0 37.8 1.0

Magnesium binding site 4 out of 4 in the Dna Polymerase IV - Dna Ternary Complex 13


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 13 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:48.8 occ:1.00 OE2 A:GLU104 2.0 52.5 1.0 OD1 A:ASP103 2.0 39.6 1.0 OP1 C:DT874 2.4 35.9 1.0 OD1 A:ASP8 2.5 49.0 1.0 O3' C:DC873 2.7 45.0 1.0 CG A:ASP103 2.8 39.0 1.0 CD A:GLU104 2.9 49.2 1.0 OD2 A:ASP103 3.0 34.2 1.0 MG A:MG901 3.1 36.2 1.0 P C:DT874 3.1 45.0 1.0 CG A:ASP8 3.2 49.9 1.0 OD2 A:ASP8 3.2 61.8 1.0 CG A:GLU104 3.3 45.1 1.0 CB A:GLU104 3.6 38.7 1.0 C3' C:DC873 4.0 37.0 1.0 OG A:SER101 4.0 47.4 1.0 OE1 A:GLU104 4.0 43.6 1.0 C5' C:DT874 4.1 37.6 1.0 O5' C:DT874 4.1 41.8 1.0 O A:HOH1001 4.1 57.1 1.0 CB A:ASP103 4.3 39.9 1.0 OP2 C:DT874 4.3 45.7 1.0 C4' C:DC873 4.3 38.4 1.0 C A:ASP103 4.3 40.6 1.0 O A:ASP103 4.3 37.8 1.0 N A:GLU104 4.5 39.8 1.0 CB A:ASP8 4.5 41.6 1.0 CA A:GLU104 4.6 36.0 1.0 C5' C:DC873 4.6 40.8 1.0 CA A:ASP103 4.8 43.2 1.0 CA A:ASP8 4.8 37.1 1.0 O2 A:DPO903 4.8 46.4 1.0 N A:MET9 4.9 35.9 1.0 O A:MET9 4.9 32.5 1.0 C2' C:DC873 5.0 41.4 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