Magnesium in PDB 5yv2: Dna Polymerase IV - Dna Ternary Complex 14

All present enzymatic activity of Dna Polymerase IV - Dna Ternary Complex 14:
2.7.7.7;

The structure of Dna Polymerase IV - Dna Ternary Complex 14, PDB code: 5yv2 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)	44.86 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.400, 57.250, 110.950, 90.00, 94.75, 90.00
R / Rfree (%)	20.4 / 24.5

The binding sites of Magnesium atom in the Dna Polymerase IV - Dna Ternary Complex 14 (pdb code 5yv2). 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 14, PDB code: 5yv2:
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 14


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 14 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg901 b:29.6 occ:1.00 OP1 H:DT874 2.1 33.6 1.0 O1 F:PO4903 2.3 30.2 0.8 OD2 F:ASP103 2.3 29.7 1.0 O F:MET9 2.4 34.6 1.0 O F:HOH1197 2.5 41.5 1.0 OD1 F:ASP8 2.5 33.1 1.0 MG F:MG902 3.1 30.0 1.0 P F:PO4903 3.3 44.7 0.8 CG F:ASP103 3.4 41.4 1.0 CG F:ASP8 3.4 32.9 1.0 P H:DT874 3.5 33.7 1.0 C F:MET9 3.5 28.1 1.0 O3 F:PO4903 3.5 56.3 0.8 OD1 F:ASP103 3.8 32.6 1.0 O5' H:DT874 3.9 27.0 1.0 OD2 F:ASP8 3.9 36.4 1.0 O4 F:PO4903 3.9 75.8 0.8 N F:MET9 3.9 31.7 1.0 C5' H:DT874 4.0 31.9 1.0 O F:HOH1011 4.1 27.9 1.0 CA F:MET9 4.3 31.6 1.0 O F:HOH1078 4.3 42.4 1.0 C F:ASP8 4.4 32.7 1.0 O F:HOH1077 4.4 27.5 1.0 OP2 H:DT874 4.5 28.1 1.0 O3' H:DC873 4.5 33.4 1.0 CB F:ASP8 4.6 33.8 1.0 O2 F:PO4903 4.6 33.9 0.8 N F:ASP10 4.6 33.2 1.0 CB F:ASP103 4.7 25.8 1.0 N F:CYS11 4.7 29.6 1.0 CB F:MET9 4.7 29.9 1.0 N F:PHE12 4.8 31.0 1.0 CB F:PHE12 4.8 30.7 1.0 CA F:ASP8 4.8 30.8 1.0 CA F:ASP10 4.8 29.7 1.0 O F:ASP8 4.9 31.8 1.0 OE1 F:GLU104 4.9 50.4 1.0 C F:ASP10 5.0 34.2 1.0

Magnesium binding site 2 out of 4 in the Dna Polymerase IV - Dna Ternary Complex 14


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 14 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg902 b:30.0 occ:1.00 OE1 F:GLU104 2.1 50.4 1.0 OD1 F:ASP103 2.1 32.6 1.0 OP1 H:DT874 2.2 33.6 1.0 OD1 F:ASP8 2.4 33.1 1.0 O3' H:DC873 2.8 33.4 1.0 CG F:ASP103 2.8 41.4 1.0 OD2 F:ASP103 2.9 29.7 1.0 P H:DT874 3.0 33.7 1.0 MG F:MG901 3.1 29.6 1.0 CD F:GLU104 3.1 41.2 1.0 CG F:ASP8 3.2 32.9 1.0 OD2 F:ASP8 3.5 36.4 1.0 CB F:GLU104 3.5 32.7 1.0 CG F:GLU104 3.5 31.9 1.0 C5' H:DT874 4.0 31.9 1.0 O5' H:DT874 4.0 27.0 1.0 OG F:SER101 4.0 44.5 1.0 C3' H:DC873 4.1 33.9 1.0 OP2 H:DT874 4.2 28.1 1.0 C F:ASP103 4.2 37.6 1.0 OE2 F:GLU104 4.2 34.4 1.0 CB F:ASP103 4.2 25.8 1.0 O F:ASP103 4.3 34.2 1.0 N F:GLU104 4.4 30.7 1.0 C4' H:DC873 4.4 32.0 1.0 CB F:ASP8 4.5 33.8 1.0 O F:HOH1124 4.5 39.4 1.0 CA F:GLU104 4.5 26.8 1.0 O F:HOH1197 4.7 41.5 1.0 C5' H:DC873 4.7 32.3 1.0 CA F:ASP8 4.7 30.8 1.0 CA F:ASP103 4.7 27.4 1.0 O1 F:PO4903 4.8 30.2 0.8 N F:MET9 4.8 31.7 1.0 O F:MET9 4.9 34.6 1.0 C2' H:DC873 5.0 30.8 1.0

Magnesium binding site 3 out of 4 in the Dna Polymerase IV - Dna Ternary Complex 14


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 14 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:41.2 occ:1.00 OP1 C:DT874 2.2 39.8 1.0 O A:MET9 2.3 29.0 1.0 OD2 A:ASP103 2.3 29.0 1.0 O3 A:PO4903 2.4 39.4 1.0 OD1 A:ASP8 2.5 37.8 1.0 O2 A:PO4904 2.8 64.9 0.6 NZ A:LYS157 3.1 60.3 1.0 MG A:MG902 3.2 46.4 1.0 CG A:ASP103 3.4 39.2 1.0 CG A:ASP8 3.4 41.4 1.0 C A:MET9 3.5 30.9 1.0 P C:DT874 3.6 38.5 1.0 P A:PO4903 3.6 59.5 1.0 OD1 A:ASP103 3.8 35.2 1.0 O2 A:PO4903 3.9 65.4 1.0 OD2 A:ASP8 3.9 49.5 1.0 N A:MET9 3.9 36.8 1.0 O5' C:DT874 4.0 37.4 1.0 P A:PO4904 4.1 60.0 0.6 C5' C:DT874 4.1 37.5 1.0 O4 A:PO4904 4.1 60.0 0.6 CA A:MET9 4.2 37.4 1.0 C A:ASP8 4.3 40.5 1.0 O4 A:PO4903 4.4 77.5 1.0 CE A:LYS157 4.5 48.7 1.0 O3' C:DC873 4.5 38.5 1.0 N A:ASP10 4.6 32.9 1.0 CB A:ASP8 4.6 34.5 1.0 OP2 C:DT874 4.6 38.2 1.0 N A:CYS11 4.7 33.5 1.0 CB A:ASP103 4.7 37.0 1.0 CB A:MET9 4.7 35.3 1.0 N A:PHE12 4.7 33.1 1.0 CB A:PHE12 4.8 30.0 1.0 O1 A:PO4903 4.8 48.5 1.0 CA A:ASP10 4.8 30.3 1.0 CA A:ASP8 4.8 36.2 1.0 O A:ASP8 4.9 36.2 1.0 C A:ASP10 4.9 33.3 1.0 O3 A:PO4904 5.0 66.7 0.6 OE2 A:GLU104 5.0 51.9 1.0

Magnesium binding site 4 out of 4 in the Dna Polymerase IV - Dna Ternary Complex 14


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 14 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:46.4 occ:1.00 OE2 A:GLU104 1.9 51.9 1.0 OD1 A:ASP103 2.2 35.2 1.0 OP1 C:DT874 2.4 39.8 1.0 OD1 A:ASP8 2.4 37.8 1.0 O3' C:DC873 2.8 38.5 1.0 CD A:GLU104 2.9 50.0 1.0 CG A:ASP103 3.0 39.2 1.0 OD2 A:ASP103 3.1 29.0 1.0 P C:DT874 3.1 38.5 1.0 MG A:MG901 3.2 41.2 1.0 CG A:ASP8 3.2 41.4 1.0 CG A:GLU104 3.3 44.6 1.0 OD2 A:ASP8 3.4 49.5 1.0 CB A:GLU104 3.5 39.5 1.0 OG A:SER101 4.0 40.0 1.0 OE1 A:GLU104 4.0 37.7 1.0 C3' C:DC873 4.1 37.7 1.0 C5' C:DT874 4.1 37.5 1.0 O5' C:DT874 4.1 37.4 1.0 O A:ASP103 4.3 32.9 1.0 C A:ASP103 4.3 39.1 1.0 OP2 C:DT874 4.3 38.2 1.0 C4' C:DC873 4.4 38.4 1.0 CB A:ASP103 4.4 37.0 1.0 N A:GLU104 4.4 36.0 1.0 CB A:ASP8 4.5 34.5 1.0 C5' C:DC873 4.6 39.5 1.0 CA A:GLU104 4.6 36.3 1.0 O A:HOH1077 4.6 41.6 1.0 CA A:ASP8 4.8 36.2 1.0 CA A:ASP103 4.8 35.9 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